newly processed, fixed some bugs in code

code/GetQuantitativeValues.py

@@ -13,8 +13,19 @@ def create_output_dir(output_dir):
     if not os.path.exists(output_dir):
         os.makedirs(output_dir)
 
+def save_mask_as_nifti(mask_data, output_file):
+    """Save mask data as NIfTI file."""
+    # Convert boolean mask to integer (0s and 1s)
+    mask_data_int = mask_data.astype(np.uint8)
+    
+    # Create NIfTI image object
+    mask_img = nib.Nifti1Image(mask_data_int, affine=None)
+    
+    # Save NIfTI image
+    nib.save(mask_img, output_file)
+
 
-def process_files(input_path, output_path, create_figures):
+def process_files(input_path, output_path, create_figures, save_nifti_mask):
     """Process DWI files and generate figures."""
     # Define a dictionary to map Experiment values to the desired timepoints
     session_mapping = {
@@ -36,18 +47,14 @@ def process_files(input_path, output_path, create_figures):
         # Extract information from the file path
         subject_id = file_path.split(os.sep)[-5]
         time_point = file_path.split(os.sep)[-4]
-        print(file_path)
         int_time_point = 0 if time_point == "ses-Baseline" else int(time_point.split("-P")[1])
         merged_time_point = session_mapping[int_time_point]
         q_type = os.path.basename(file_path).split("_flipped")[0]
         try:
             searchStroke = os.path.join(os.path.dirname(file_path),"*StrokeMask_scaled.nii")
-            #print(searchStroke)
             stroke_path = glob.glob(searchStroke)[0]
-            print(stroke_path)
         except IndexError:
             stroke_path = False
-
             
         # Create the temp path to search for dwi_masks
         temp_path = os.path.join(os.path.dirname(file_path), "RegisteredTractMasks_adjusted")
@@ -60,7 +67,7 @@ def process_files(input_path, output_path, create_figures):
         # Loop through masks and calculate average values
         max_pixels = -1
         selected_slice = None
-        pix_dialation = [0,1,2]
+        pix_dialation = [0,1,2,3,4]
         for mask_path in tqdm(dwi_masks, desc="Processing masks", leave=False):
             mask_name = os.path.basename(mask_path).replace("registered", "").replace("flipped", "").replace(".nii.gz", "").replace("__dwi_","")
             mask_img = nib.load(mask_path)
@@ -84,13 +91,20 @@ def process_files(input_path, output_path, create_figures):
                     stroke_image = nib.load(stroke_path)
                     stroke_data = stroke_image.get_fdata()    
                     # Subtracting stroke region from mask
-                    mask_data = mask_data & (stroke_data < 1)
+                    if merged_time_point == 3 or merged_time_point == 28:
+                        mask_data = mask_data & (stroke_data < 1)
+                    else:
+                        mask_data = mask_data
+                    
                     masked_data = dwi_data[mask_data > 0]
-                    average_value = np.nanmean(masked_data)  # Handle case when masked_data is empty
+                    non_zero_masked_data = masked_data[masked_data != 0]  # Exclude zero values
+                    average_value = np.nanmean(non_zero_masked_data)  # Calculate mean only on non-zero elements
+
                     strokeFlag = "Stroke"
                 else:
                     masked_data = dwi_data[mask_data > 0]
-                    average_value = np.nanmean(masked_data)  # Handle case when masked_data is empty
+                    non_zero_masked_data = masked_data[masked_data != 0]  # Exclude zero values
+                    average_value = np.nanmean(non_zero_masked_data)  # Calculate mean only on non-zero elements
                     strokeFlag = "Sham"
                 # Create and save the figure if the flag is True
                 if create_figures:
@@ -108,6 +122,12 @@ def process_files(input_path, output_path, create_figures):
     
                     # Close the plot to release memory
                     plt.close(fig)
+
+                if save_nifti_mask and pp > 0 and merged_time_point in [3, 28] and q_type == "fa":
+                    # Save the mask as NIfTI file
+                    output_nifti_file = os.path.join(output_path,
+                                                      f"{subject_id}_tp_{merged_time_point}_{q_type}_{mask_name}_{pp}.nii.gz")
+                    save_mask_as_nifti(mask_data, output_nifti_file)
     
                 # Append the extracted information to the list
                 csvdata.append([file_path, subject_id, time_point, int_time_point, merged_time_point, q_type, mask_name, pp ,average_value,strokeFlag])
@@ -120,13 +140,13 @@ def process_files(input_path, output_path, create_figures):
     # Return DataFrame
     return df
 
-
 def main():
     # Parse command-line arguments
     parser = argparse.ArgumentParser(description="Process DWI files and generate figures.")
     parser.add_argument("-i", "--input", type=str, required=True, help="Input directory containing DWI files. e.g: proc_data (flipped fa, md etc file must be available. registering of masks must happen before this step")
     parser.add_argument("-o", "--output", type=str, required=True, help="Output directory to save output results (csv and figures).")
     parser.add_argument("-f", "--figures", action="store_true", default=False, help="set if you want figures to be saved as pngs")
+    parser.add_argument("-n", "--nifti-mask", action="store_true", default=False, help="set if you want masks to be saved as NIfTI files.")
 
     args = parser.parse_args()
 
@@ -134,7 +154,7 @@ def main():
     create_output_dir(args.output)
 
     # Process files
-    df = process_files(args.input, args.output,args.figures)
+    df = process_files(args.input, args.output, args.figures, args.nifti_mask)
 
     # Save the DataFrame as CSV
     csv_file = os.path.join(args.output, "Quantitative_results_from_dwi_processing.csv")
@@ -144,6 +164,5 @@ def main():
     # Print the DataFrame
     print(df)
 
-
 if __name__ == "__main__":
     main()

code/correlation_between_bahavior_and_DTI.py

@@ -31,18 +31,18 @@ for dd in df["dialation_amount"].unique():
                     # Filter the DataFrame for the current combination of 'Group', 'merged_timepoint', 'Qtype', and 'mask_name'
                     df_f2 = df[(df["Group"] == ss) & (df["merged_timepoint"] == time_point) & (df["Qtype"] == qq) & (df["mask_name"] == mm) &  (df["dialation_amount"] == dd)]
     
-                    # Remove rows with NaN values in 'Value' or 'averageScore' columns
-                    df_f2 = df_f2.dropna(subset=['Value', 'averageScore'])
+                    # Remove rows with NaN values in 'Value' or 'hindlimb_dropZ-score' columns
+                    df_f2 = df_f2.dropna(subset=['Value', 'hindlimb_dropZ-score'])
     
                     if not df_f2.empty:
                         
                         shapiro_statValue, shapiro_pvalueQValue = shapiro(df_f2["Value"])
-                        shapiro_statScore, shapiro_pvalueBehavior = shapiro(df_f2["averageScore"])
+                        shapiro_statScore, shapiro_pvalueBehavior = shapiro(df_f2["hindlimb_dropZ-score"])
                         
                         if shapiro_pvalueQValue < 0.05 or shapiro_pvalueBehavior < 0.05:
-                            correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2["averageScore"])
+                            correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2["hindlimb_dropZ-score"])
                         else:
-                            correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2["averageScore"])
+                            correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2["hindlimb_dropZ-score"])
                        
     
                         # Store the results in a dictionary

code/heat_maps_correlation.py

@@ -6,11 +6,12 @@ import matplotlib.pyplot as plt
 # Set up the directory paths
 code_dir = os.path.dirname(os.path.abspath(__file__))
 parent_dir = os.path.dirname(code_dir)
-csv_file = os.path.join(parent_dir, 'output', "Correlation_with_behavior", 'correlation_dti_with_behavior5.csv')
+csv_file = os.path.join(parent_dir, 'output', "Correlation_with_behavior", 'correlation_dti_with_behavior.csv')
 output_dir = os.path.dirname(csv_file)
 
 # Read the CSV file into a DataFrame
 df = pd.read_csv(csv_file)
+df = df[df["dialation_amount"] == 3]
 
 # Get unique Qtypes
 qtypes = df["Qtype"].unique()
@@ -33,11 +34,11 @@ for qtype in qtypes:
         group_df = filtered_df[filtered_df["Group"] == group]
         
         # Pivot the filtered DataFrame to prepare for heatmap
-        for j, value in enumerate(['R_corr', 'Pval_corr']):
+        for j, value in enumerate(['R', 'Pval']):
             heatmap_df = group_df.pivot(index='mask_name', columns='merged_timepoint', values=value)
             
             # Plot heatmap
-            sns.heatmap(heatmap_df, ax=axes[i, j], cmap='coolwarm', annot=True, fmt=".2f", cbar=True)
+            sns.heatmap(heatmap_df, ax=axes[i, j], cmap='coolwarm_r', annot=True, fmt=".2f", cbar=True)
             axes[i, j].set_title(f'Group: {group}, Qtype: {qtype}, Value: {value}')
             axes[i, j].set_xlabel('Time Point', fontsize=8)
             axes[i, j].set_ylabel('Tract Name', fontsize=8)
@@ -45,5 +46,5 @@ for qtype in qtypes:
     
     plt.tight_layout()
     save_path = os.path.join(output_dir, f'heatmap_{qtype}_2dialation_corrected_spearman.png')
-    plt.savefig(save_path, dpi=300)
+    #plt.savefig(save_path, dpi=300)
     plt.show()

code/plotting_quantitative_dti_values.py

@@ -62,11 +62,11 @@ input_file_path = os.path.join(parent_dir, 'output', "Final_Quantitative_output"
 df = pd.read_csv(input_file_path)
 qc_csv = os.path.join(parent_dir,"input","AIDAqc_ouptut_for_data","Voting_remapped.csv")
 df_qc = pd.read_csv(qc_csv)
-df_qc_5 = df_qc[(df_qc["Voting outliers (from 5)"]>4) & (df_qc["sequence_type"]=="diff")]
+df_qc_5 = df_qc[(df_qc["Voting outliers (from 5)"]>3) & (df_qc["sequence_type"]=="diff")]
 
 
 # Filtering the dataframe based on conditions
-df_f0 = df[(df["dialation_amount"] == 2) & (~df["merged_timepoint"].isin([42, 56]))]
+df_f0 = df[(df["dialation_amount"] == 3) & (~df["merged_timepoint"].isin([42, 56]))]
 # Merge df_f1 and df_qc_5 on "subjectID" and "merged_timepoint"
 merged_df = pd.merge(df_f0, df_qc_5, on=["subjectID", "merged_timepoint"], how="left", indicator=True)
 

output/Final_Quantitative_output/Quantitative_results_from_dwi_processing_merged_with_behavior_data.csv

@@ -1 +1 @@
-/annex/objects/MD5E-s31157874--59c7c6ce8773fbebf1a8c8142948e578.csv
+/annex/objects/MD5E-s50295933--0597d65c759f1df6e8b8aa918c76b5ea.csv

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_cut_log.txt

@@ -1,67 +1,67 @@
 Model Name: ad_CC_MOp-MOp_cut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0109
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.002    0.001 3.017 0.003  0.001  0.003
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0098
+Min. group size:        156          Log-Likelihood:          inf   
+Max. group size:        205          Converged:               Yes   
+Mean group size:        180.5                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 193575.274 0.000 1.000 -379400.566 379400.566
+merged_timepoint 0.001      0.001 2.573 0.010       0.000      0.002
+Group Var        0.000                                              
+====================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0018    0.9 -0.0748 0.0712  False
-     0      7   0.0078    0.9 -0.0693 0.0849  False
-     0     14   0.0407 0.6214 -0.0354 0.1167  False
-     0     21   0.0653 0.1377 -0.0108 0.1413  False
-     0     28   0.0549 0.3463 -0.0241 0.1338  False
-     3      7   0.0096    0.9 -0.0621 0.0813  False
-     3     14   0.0425 0.5107 -0.0281  0.113  False
-     3     21   0.0671 0.0729 -0.0035 0.1377  False
-     3     28   0.0567 0.2363  -0.017 0.1304  False
-     7     14   0.0328 0.7789  -0.042 0.1077  False
-     7     21   0.0575 0.2373 -0.0173 0.1323  False
-     7     28   0.0471 0.5048 -0.0307 0.1249  False
-    14     21   0.0246    0.9 -0.0491 0.0983  False
-    14     28   0.0142    0.9 -0.0625 0.0909  False
-    21     28  -0.0104    0.9 -0.0871 0.0663  False
+     0      3  -0.0013    0.9 -0.0643 0.0617  False
+     0      7  -0.0333 0.6775 -0.0998 0.0332  False
+     0     14   0.0241 0.8967 -0.0415 0.0897  False
+     0     21    0.033 0.6719 -0.0325 0.0986  False
+     0     28    0.043  0.457  -0.025 0.1111  False
+     3      7  -0.0319 0.6441 -0.0932 0.0294  False
+     3     14   0.0255  0.807 -0.0349 0.0858  False
+     3     21   0.0344 0.5626 -0.0259 0.0947  False
+     3     28   0.0444 0.3306 -0.0186 0.1074  False
+     7     14   0.0574 0.1066 -0.0066 0.1213  False
+     7     21   0.0663 0.0372  0.0024 0.1303   True
+     7     28   0.0763 0.0142  0.0098 0.1428   True
+    14     21   0.0089    0.9 -0.0541 0.0719  False
+    14     28   0.0189    0.9 -0.0466 0.0845  False
+    21     28     0.01    0.9 -0.0556 0.0756  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0421 0.6409 -0.0387 0.1228  False
-     0      7   0.0265    0.9   -0.05 0.1031  False
-     0     14   0.0431 0.5332 -0.0304 0.1166  False
-     0     21   0.0243    0.9 -0.0598 0.1084  False
-     0     28   0.0278    0.9  -0.052 0.1076  False
-     3      7  -0.0156    0.9 -0.0976 0.0664  False
-     3     14    0.001    0.9 -0.0781 0.0802  False
-     3     21  -0.0178    0.9 -0.1069 0.0713  False
-     3     28  -0.0143    0.9 -0.0993 0.0707  False
-     7     14   0.0166    0.9 -0.0583 0.0914  False
-     7     21  -0.0022    0.9 -0.0875 0.0831  False
-     7     28   0.0013    0.9 -0.0798 0.0823  False
-    14     21  -0.0188    0.9 -0.1014 0.0638  False
-    14     28  -0.0153    0.9 -0.0935 0.0629  False
-    21     28   0.0035    0.9 -0.0847 0.0917  False
+     0      3    0.056 0.4534 -0.0325 0.1444  False
+     0      7   0.0255    0.9 -0.0562 0.1072  False
+     0     14   0.0385 0.6912 -0.0399 0.1169  False
+     0     21    0.045 0.6734 -0.0447 0.1348  False
+     0     28   0.0246    0.9 -0.0605 0.1098  False
+     3      7  -0.0305    0.9 -0.1202 0.0593  False
+     3     14  -0.0175    0.9 -0.1043 0.0693  False
+     3     21   -0.011    0.9 -0.1081 0.0862  False
+     3     28  -0.0314    0.9 -0.1243 0.0615  False
+     7     14    0.013    0.9 -0.0669 0.0928  False
+     7     21   0.0195    0.9 -0.0715 0.1105  False
+     7     28  -0.0009    0.9 -0.0874 0.0856  False
+    14     21   0.0065    0.9 -0.0816 0.0946  False
+    14     28  -0.0139    0.9 -0.0973 0.0695  False
+    21     28  -0.0204    0.9 -0.1145 0.0737  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.10020029]	No
-Stroke	Sham	14	[0.52614476]	No
-Stroke	Sham	21	[0.28312575]	No
-Stroke	Sham	28	[0.40668988]	No
-Stroke	Sham	7	[0.0491476]	Yes
-Stroke	Sham	0	[0.76293642]	No
+Stroke	Sham	3	[0.0378204]	Yes
+Stroke	Sham	14	[0.66421351]	No
+Stroke	Sham	21	[0.78907715]	No
+Stroke	Sham	28	[0.25846633]	No
+Stroke	Sham	7	[0.00060319]	Yes
+Stroke	Sham	0	[0.94690315]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_cut_log.txt

@@ -1,67 +1,67 @@
 Model Name: ad_CC_MOp-MOp_dilated_cut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0091
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.001 2.328 0.020  0.000  0.002
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0088
+Min. group size:        156          Log-Likelihood:          inf   
+Max. group size:        205          Converged:               Yes   
+Mean group size:        180.5                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 182887.871 0.000 1.000 -358453.640 358453.640
+merged_timepoint 0.001      0.001 2.183 0.029       0.000      0.002
+Group Var        0.000                                              
+====================================================================
 
 Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0293 0.7524 -0.0351 0.0938  False
-     0      7  -0.0015    0.9 -0.0696 0.0666  False
-     0     14   0.0408 0.5002 -0.0263  0.108  False
-     0     21   0.0551  0.175  -0.012 0.1223  False
-     0     28   0.0465 0.3966 -0.0233 0.1162  False
-     3      7  -0.0308 0.6999 -0.0942 0.0325  False
-     3     14   0.0115    0.9 -0.0508 0.0738  False
-     3     21   0.0258  0.821 -0.0366 0.0881  False
-     3     28   0.0171    0.9  -0.048 0.0822  False
-     7     14   0.0423 0.4422 -0.0237 0.1084  False
-     7     21   0.0566 0.1393 -0.0095 0.1227  False
-     7     28    0.048 0.3412 -0.0207 0.1167  False
-    14     21   0.0143    0.9 -0.0508 0.0794  False
-    14     28   0.0056    0.9 -0.0621 0.0734  False
-    21     28  -0.0087    0.9 -0.0764 0.0591  False
----------------------------------------------------
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0353 0.4518 -0.0203   0.091  False
+     0      7   -0.033 0.5774 -0.0917  0.0258  False
+     0     14   0.0336 0.5456 -0.0243  0.0915  False
+     0     21   0.0468 0.1889 -0.0111  0.1047  False
+     0     28   0.0409 0.3717 -0.0192   0.101  False
+     3      7  -0.0683 0.0048 -0.1224 -0.0142   True
+     3     14  -0.0017    0.9  -0.055  0.0515  False
+     3     21   0.0114    0.9 -0.0418  0.0647  False
+     3     28   0.0055    0.9 -0.0501  0.0612  False
+     7     14   0.0666 0.0107  0.0101   0.123   True
+     7     21   0.0797  0.001  0.0233  0.1362   True
+     7     28   0.0738  0.005  0.0151  0.1325   True
+    14     21   0.0132    0.9 -0.0425  0.0688  False
+    14     28   0.0073    0.9 -0.0506  0.0652  False
+    21     28  -0.0059    0.9 -0.0638   0.052  False
+----------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0486 0.4653  -0.029 0.1263  False
-     0      7   0.0268    0.9 -0.0469 0.1004  False
-     0     14   0.0395 0.5792 -0.0312 0.1102  False
-     0     21    0.029    0.9 -0.0519 0.1099  False
-     0     28   0.0307 0.8419 -0.0461 0.1074  False
-     3      7  -0.0219    0.9 -0.1007  0.057  False
-     3     14  -0.0092    0.9 -0.0853  0.067  False
-     3     21  -0.0196    0.9 -0.1053  0.066  False
-     3     28   -0.018    0.9 -0.0998 0.0638  False
-     7     14   0.0127    0.9 -0.0593 0.0847  False
-     7     21   0.0022    0.9 -0.0798 0.0843  False
-     7     28   0.0039    0.9 -0.0741 0.0819  False
-    14     21  -0.0105    0.9 -0.0899 0.0689  False
-    14     28  -0.0088    0.9  -0.084 0.0664  False
-    21     28   0.0017    0.9 -0.0832 0.0865  False
+     0      3   0.0525 0.5058 -0.0346 0.1395  False
+     0      7    0.025    0.9 -0.0554 0.1053  False
+     0     14   0.0327 0.8012 -0.0444 0.1099  False
+     0     21    0.041 0.7347 -0.0473 0.1293  False
+     0     28   0.0265    0.9 -0.0573 0.1103  False
+     3      7  -0.0275    0.9 -0.1158 0.0608  False
+     3     14  -0.0198    0.9 -0.1052 0.0656  False
+     3     21  -0.0115    0.9 -0.1071 0.0841  False
+     3     28   -0.026    0.9 -0.1174 0.0654  False
+     7     14   0.0078    0.9 -0.0708 0.0864  False
+     7     21    0.016    0.9 -0.0735 0.1056  False
+     7     28   0.0015    0.9 -0.0836 0.0866  False
+    14     21   0.0083    0.9 -0.0784  0.095  False
+    14     28  -0.0062    0.9 -0.0883 0.0759  False
+    21     28  -0.0145    0.9 -0.1071 0.0781  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.60457776]	No
-Stroke	Sham	14	[0.7799069]	No
-Stroke	Sham	21	[0.33493172]	No
-Stroke	Sham	28	[0.23426442]	No
-Stroke	Sham	7	[0.14155218]	No
-Stroke	Sham	0	[0.87953438]	No
+Stroke	Sham	3	[0.63702768]	No
+Stroke	Sham	14	[0.82523409]	No
+Stroke	Sham	21	[0.79268718]	No
+Stroke	Sham	28	[0.2189166]	No
+Stroke	Sham	7	[0.0011087]	Yes
+Stroke	Sham	0	[0.76334283]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CReT_MOp-TRN_ipsilesional_CCcut_log.txt

@@ -1,67 +1,67 @@
 Model Name: ad_CReT_MOp-TRN_ipsilesional_CCcut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0143
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.002    0.001 2.420 0.016  0.000  0.003
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0097
+Min. group size:        156          Log-Likelihood:          inf   
+Max. group size:        205          Converged:               Yes   
+Mean group size:        180.5                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 192238.803 0.000 1.000 -376781.130 376781.130
+merged_timepoint 0.002      0.001 4.380 0.000       0.001      0.003
+Group Var        0.000                                              
+====================================================================
 
 Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05 
-====================================================
-group1 group2 meandiff p-adj   lower   upper  reject
-----------------------------------------------------
-     0      3  -0.0874 0.0222  -0.167 -0.0078   True
-     0      7  -0.0236    0.9 -0.1077  0.0604  False
-     0     14  -0.0312  0.882 -0.1141  0.0517  False
-     0     21   0.0093    0.9 -0.0736  0.0923  False
-     0     28    0.038 0.7744 -0.0481  0.1241  False
-     3      7   0.0637 0.1809 -0.0145  0.1419  False
-     3     14   0.0562 0.2911 -0.0208  0.1331  False
-     3     21   0.0967  0.005  0.0198  0.1737   True
-     3     28   0.1254  0.001  0.0451  0.2058   True
-     7     14  -0.0076    0.9 -0.0891   0.074  False
-     7     21    0.033 0.8358 -0.0486  0.1146  False
-     7     28   0.0617 0.2952 -0.0231  0.1465  False
-    14     21   0.0406 0.6705 -0.0398  0.1209  False
-    14     28   0.0692 0.1675 -0.0144  0.1529  False
-    21     28   0.0287    0.9  -0.055  0.1123  False
-----------------------------------------------------
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0325 0.6454 -0.0951   0.03  False
+     0      7  -0.0518 0.2169 -0.1179 0.0142  False
+     0     14    0.005    0.9 -0.0601 0.0702  False
+     0     21   0.0215    0.9 -0.0436 0.0867  False
+     0     28   0.0654 0.0644 -0.0022  0.133  False
+     3      7  -0.0193    0.9 -0.0802 0.0416  False
+     3     14   0.0376 0.4667 -0.0224 0.0975  False
+     3     21   0.0541 0.1028 -0.0058  0.114  False
+     3     28   0.0979  0.001  0.0354 0.1605   True
+     7     14   0.0568 0.1086 -0.0067 0.1204  False
+     7     21   0.0733 0.0134  0.0098 0.1369   True
+     7     28   0.1172  0.001  0.0512 0.1833   True
+    14     21   0.0165    0.9 -0.0461 0.0791  False
+    14     28   0.0604 0.0868 -0.0048 0.1255  False
+    21     28   0.0439 0.3837 -0.0213  0.109  False
+---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0435 0.7342 -0.0501  0.137  False
-     0      7  -0.0415 0.7287 -0.1302 0.0472  False
-     0     14   0.0184    0.9 -0.0668 0.1035  False
-     0     21   0.0158    0.9 -0.0817 0.1132  False
-     0     28  -0.0071    0.9 -0.0995 0.0853  False
-     3      7   -0.085  0.108 -0.1799   0.01  False
-     3     14  -0.0251    0.9 -0.1168 0.0666  False
-     3     21  -0.0277    0.9 -0.1309 0.0755  False
-     3     28  -0.0506 0.6533 -0.1491 0.0479  False
-     7     14   0.0599 0.3514 -0.0268 0.1466  False
-     7     21   0.0573 0.5445 -0.0415 0.1561  False
-     7     28   0.0344 0.8967 -0.0595 0.1283  False
-    14     21  -0.0026    0.9 -0.0982  0.093  False
-    14     28  -0.0255    0.9  -0.116  0.065  False
-    21     28  -0.0229    0.9 -0.1251 0.0793  False
+     0      3   0.0335 0.8597 -0.0527 0.1198  False
+     0      7   0.0057    0.9 -0.0739 0.0854  False
+     0     14   0.0579  0.251 -0.0186 0.1343  False
+     0     21   0.0524 0.5133 -0.0351 0.1399  False
+     0     28   0.0313 0.8794 -0.0517 0.1143  False
+     3      7  -0.0278    0.9 -0.1153 0.0597  False
+     3     14   0.0243    0.9 -0.0603  0.109  False
+     3     21   0.0188    0.9 -0.0759 0.1136  False
+     3     28  -0.0022    0.9 -0.0928 0.0883  False
+     7     14   0.0521 0.3884 -0.0258   0.13  False
+     7     21   0.0466  0.634 -0.0421 0.1354  False
+     7     28   0.0255    0.9 -0.0588 0.1098  False
+    14     21  -0.0055    0.9 -0.0914 0.0804  False
+    14     28  -0.0266    0.9 -0.1079 0.0547  False
+    21     28  -0.0211    0.9 -0.1129 0.0707  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.01146425]	Yes
-Stroke	Sham	14	[0.4730427]	No
-Stroke	Sham	21	[0.48916469]	No
-Stroke	Sham	28	[0.01778081]	Yes
-Stroke	Sham	7	[0.02629392]	Yes
-Stroke	Sham	0	[0.31029197]	No
+Stroke	Sham	3	[0.0743467]	No
+Stroke	Sham	14	[0.22902056]	No
+Stroke	Sham	21	[0.68043288]	No
+Stroke	Sham	28	[0.05946725]	No
+Stroke	Sham	7	[0.01822743]	Yes
+Stroke	Sham	0	[0.34027512]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CRuT_MOp-RN_ipsilesional_log.txt

@@ -1,67 +1,67 @@
 Model Name: ad_CRuT_MOp-RN_ipsilesional
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0122
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.002    0.001 3.250 0.001  0.001  0.003
-Group Var         0.000                                   
-==========================================================
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM  Dependent Variable:  Value   
+No. Observations:    361      Method:              REML    
+No. Groups:          2        Scale:               0.0104  
+Min. group size:     156      Log-Likelihood:      301.8351
+Max. group size:     205      Converged:           Yes     
+Mean group size:     180.5                                 
+-----------------------------------------------------------
+                 Coef. Std.Err.    z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept        1.049    0.009 113.810 0.000  1.031  1.067
+merged_timepoint 0.003    0.001   4.865 0.000  0.002  0.004
+Group Var        0.000    0.001                            
+===========================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0442 0.4732  -0.115 0.0267  False
-     0      7  -0.0303 0.8347 -0.1052 0.0445  False
-     0     14   0.0148    0.9  -0.059 0.0886  False
-     0     21   0.0367 0.6825 -0.0371 0.1105  False
-     0     28    0.055 0.3095 -0.0216 0.1317  False
-     3      7   0.0138    0.9 -0.0558 0.0835  False
-     3     14    0.059 0.1356 -0.0095 0.1275  False
-     3     21   0.0809 0.0105  0.0124 0.1494   True
-     3     28   0.0992 0.0013  0.0277 0.1708   True
-     7     14   0.0451 0.4767 -0.0275 0.1178  False
-     7     21   0.0671 0.0885 -0.0056 0.1397  False
-     7     28   0.0854 0.0166  0.0099 0.1609   True
-    14     21   0.0219    0.9 -0.0496 0.0935  False
-    14     28   0.0402 0.6118 -0.0342 0.1147  False
-    21     28   0.0183    0.9 -0.0562 0.0928  False
+     0      3  -0.0224    0.9 -0.0873 0.0425  False
+     0      7  -0.0531 0.2294 -0.1216 0.0155  False
+     0     14   0.0293 0.7888 -0.0383 0.0968  False
+     0     21   0.0373 0.5928 -0.0303 0.1049  False
+     0     28   0.0771 0.0218   0.007 0.1473   True
+     3      7  -0.0307 0.7025 -0.0938 0.0325  False
+     3     14   0.0517 0.1643 -0.0105 0.1138  False
+     3     21   0.0597  0.068 -0.0025 0.1218  False
+     3     28   0.0995  0.001  0.0346 0.1645   True
+     7     14   0.0823 0.0054  0.0164 0.1482   True
+     7     21   0.0904 0.0015  0.0245 0.1562   True
+     7     28   0.1302  0.001  0.0617 0.1987   True
+    14     21    0.008    0.9 -0.0569  0.073  False
+    14     28   0.0479  0.324 -0.0197 0.1155  False
+    21     28   0.0398 0.5304 -0.0277 0.1074  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0651  0.327 -0.0272 0.1573  False
-     0      7  -0.0088    0.9 -0.0963 0.0786  False
-     0     14   0.0354 0.8063 -0.0486 0.1193  False
-     0     21   0.0469 0.6962 -0.0492 0.1429  False
-     0     28   0.0132    0.9 -0.0779 0.1043  False
-     3      7  -0.0739   0.21 -0.1675 0.0198  False
-     3     14  -0.0297    0.9 -0.1201 0.0607  False
-     3     21  -0.0182    0.9 -0.1199 0.0836  False
-     3     28  -0.0518   0.62  -0.149 0.0453  False
-     7     14   0.0442 0.6486 -0.0413 0.1297  False
-     7     21   0.0557  0.558 -0.0418 0.1531  False
-     7     28    0.022    0.9 -0.0705 0.1146  False
-    14     21   0.0115    0.9 -0.0828 0.1058  False
-    14     28  -0.0221    0.9 -0.1114 0.0671  False
-    21     28  -0.0337    0.9 -0.1344 0.0671  False
+     0      3   0.0405  0.751 -0.0486 0.1296  False
+     0      7   0.0072    0.9 -0.0751 0.0895  False
+     0     14   0.0534 0.3762 -0.0256 0.1325  False
+     0     21   0.0567 0.4642 -0.0338 0.1471  False
+     0     28   0.0417  0.698 -0.0441 0.1275  False
+     3      7  -0.0333 0.8937 -0.1237 0.0572  False
+     3     14   0.0129    0.9 -0.0745 0.1004  False
+     3     21   0.0162    0.9 -0.0817 0.1141  False
+     3     28   0.0012    0.9 -0.0924 0.0948  False
+     7     14   0.0462 0.5535 -0.0343 0.1267  False
+     7     21   0.0495  0.611 -0.0423 0.1412  False
+     7     28   0.0345 0.8473 -0.0526 0.1217  False
+    14     21   0.0033    0.9 -0.0855  0.092  False
+    14     28  -0.0117    0.9 -0.0957 0.0724  False
+    21     28  -0.0149    0.9 -0.1098 0.0799  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.01707707]	Yes
-Stroke	Sham	14	[0.84066081]	No
-Stroke	Sham	21	[0.6471467]	No
-Stroke	Sham	28	[0.01185435]	Yes
-Stroke	Sham	7	[0.74432185]	No
-Stroke	Sham	0	[0.22964982]	No
+Stroke	Sham	3	[0.04189915]	Yes
+Stroke	Sham	14	[0.65850736]	No
+Stroke	Sham	21	[0.77146476]	No
+Stroke	Sham	28	[0.11621589]	No
+Stroke	Sham	7	[0.00559632]	Yes
+Stroke	Sham	0	[0.54504263]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CST_MOp-int-py_contralesional_CCasROA_log.txt

@@ -1,67 +1,67 @@
 Model Name: ad_CST_MOp-int-py_contralesional_CCasROA
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0203
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.002    0.001 2.219 0.026  0.000  0.003
-Group Var         0.000                                   
-==========================================================
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM  Dependent Variable:  Value   
+No. Observations:    361      Method:              REML    
+No. Groups:          2        Scale:               0.0101  
+Min. group size:     156      Log-Likelihood:      307.6556
+Max. group size:     205      Converged:           Yes     
+Mean group size:     180.5                                 
+-----------------------------------------------------------
+                 Coef. Std.Err.    z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept        1.102    0.008 131.488 0.000  1.085  1.118
+merged_timepoint 0.001    0.001   2.362 0.018  0.000  0.002
+Group Var        0.000                                     
+===========================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0395 0.8093 -0.1334 0.0544  False
-     0      7   0.0294    0.9 -0.0698 0.1286  False
-     0     14   0.0161    0.9 -0.0817 0.1139  False
-     0     21   0.0387 0.8506 -0.0591 0.1365  False
-     0     28   0.0755 0.2718 -0.0261  0.177  False
-     3      7   0.0689 0.2665 -0.0233 0.1611  False
-     3     14   0.0556 0.4928 -0.0352 0.1463  False
-     3     21   0.0782 0.1351 -0.0126 0.1689  False
-     3     28    0.115 0.0077  0.0202 0.2097   True
-     7     14  -0.0133    0.9 -0.1095 0.0829  False
-     7     21   0.0093    0.9 -0.0869 0.1055  False
-     7     28   0.0461 0.7433 -0.0539 0.1461  False
-    14     21   0.0226    0.9 -0.0722 0.1174  False
-    14     28   0.0594 0.5098 -0.0392  0.158  False
-    21     28   0.0368 0.8879 -0.0619 0.1354  False
+     0      3  -0.0468 0.2771   -0.11 0.0165  False
+     0      7  -0.0212    0.9 -0.0879 0.0455  False
+     0     14   0.0008    0.9  -0.065 0.0666  False
+     0     21  -0.0038    0.9 -0.0696  0.062  False
+     0     28   0.0324 0.7199 -0.0359 0.1007  False
+     3      7   0.0256 0.8177  -0.036 0.0871  False
+     3     14   0.0475 0.2156  -0.013 0.1081  False
+     3     21   0.0429 0.3223 -0.0176 0.1035  False
+     3     28   0.0792 0.0052   0.016 0.1424   True
+     7     14    0.022    0.9 -0.0422 0.0861  False
+     7     21   0.0174    0.9 -0.0468 0.0816  False
+     7     28   0.0536 0.1937 -0.0131 0.1203  False
+    14     21  -0.0046    0.9 -0.0678 0.0586  False
+    14     28   0.0316 0.7099 -0.0342 0.0974  False
+    21     28   0.0362 0.5949 -0.0296  0.102  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0222    0.9 -0.1401 0.0957  False
-     0      7  -0.0709  0.451 -0.1827 0.0409  False
-     0     14   -0.017    0.9 -0.1243 0.0903  False
-     0     21  -0.0147    0.9 -0.1375 0.1081  False
-     0     28  -0.0283    0.9 -0.1448 0.0882  False
-     3      7  -0.0487 0.8295 -0.1684  0.071  False
-     3     14   0.0052    0.9 -0.1104 0.1208  False
-     3     21   0.0075    0.9 -0.1226 0.1376  False
-     3     28  -0.0062    0.9 -0.1303  0.118  False
-     7     14   0.0539  0.687 -0.0554 0.1632  False
-     7     21   0.0562  0.756 -0.0683 0.1808  False
-     7     28   0.0426    0.9 -0.0758 0.1609  False
-    14     21   0.0023    0.9 -0.1182 0.1229  False
-    14     28  -0.0114    0.9 -0.1255 0.1028  False
-    21     28  -0.0137    0.9 -0.1425 0.1151  False
+     0      3   0.0235    0.9 -0.0675 0.1145  False
+     0      7   0.0066    0.9 -0.0774 0.0907  False
+     0     14   0.0234    0.9 -0.0573  0.104  False
+     0     21   0.0424 0.7424 -0.0499 0.1348  False
+     0     28   0.0094    0.9 -0.0782  0.097  False
+     3      7  -0.0168    0.9 -0.1091 0.0755  False
+     3     14  -0.0001    0.9 -0.0894 0.0892  False
+     3     21    0.019    0.9 -0.0809 0.1189  False
+     3     28   -0.014    0.9 -0.1096 0.0816  False
+     7     14   0.0167    0.9 -0.0655 0.0989  False
+     7     21   0.0358 0.8702 -0.0578 0.1294  False
+     7     28   0.0028    0.9 -0.0862 0.0918  False
+    14     21   0.0191    0.9 -0.0716 0.1097  False
+    14     28  -0.0139    0.9 -0.0997 0.0719  False
+    21     28   -0.033    0.9 -0.1298 0.0638  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.10489051]	No
-Stroke	Sham	14	[0.63232237]	No
-Stroke	Sham	21	[0.9124788]	No
-Stroke	Sham	28	[0.07907637]	No
-Stroke	Sham	7	[0.13149343]	No
-Stroke	Sham	0	[0.2300208]	No
+Stroke	Sham	3	[0.03342765]	Yes
+Stroke	Sham	14	[0.94939546]	No
+Stroke	Sham	21	[0.55448925]	No
+Stroke	Sham	28	[0.0888678]	No
+Stroke	Sham	7	[0.64864246]	No
+Stroke	Sham	0	[0.29861891]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CST_MOp-int-py_contralesional_CCcut_log.txt

@@ -1,67 +1,67 @@
 Model Name: ad_CST_MOp-int-py_contralesional_CCcut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM  Dependent Variable:  Value   
-No. Observations:   364      Method:              REML    
-No. Groups:         2        Scale:               0.0201  
-Min. group size:    158      Log-Likelihood:      185.3050
-Max. group size:    206      Converged:           No      
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        1.024    0.012 87.215 0.000  1.001  1.047
-merged_timepoint 0.002    0.001  2.124 0.034  0.000  0.003
-Group Var        0.000                                    
-==========================================================
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0102
+Min. group size:        156          Log-Likelihood:          inf   
+Max. group size:        205          Converged:               Yes   
+Mean group size:        180.5                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 197199.860 0.000 1.000 -386504.623 386504.623
+merged_timepoint 0.001      0.001 2.367 0.018       0.000      0.002
+Group Var        0.000                                              
+====================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0402 0.7978 -0.1344 0.0539  False
-     0      7   0.0298    0.9 -0.0697 0.1292  False
-     0     14   0.0126    0.9 -0.0855 0.1106  False
-     0     21   0.0379 0.8647 -0.0601  0.136  False
-     0     28   0.0745 0.2892 -0.0273 0.1763  False
-     3      7     0.07 0.2522 -0.0225 0.1625  False
-     3     14   0.0528 0.5454 -0.0382 0.1438  False
-     3     21   0.0782 0.1369 -0.0128 0.1692  False
-     3     28   0.1147 0.0082  0.0197 0.2097   True
-     7     14  -0.0172    0.9 -0.1137 0.0793  False
-     7     21   0.0082    0.9 -0.0883 0.1046  False
-     7     28   0.0447  0.768 -0.0556  0.145  False
-    14     21   0.0254    0.9 -0.0697 0.1204  False
-    14     28   0.0619  0.469  -0.037 0.1608  False
-    21     28   0.0365  0.894 -0.0624 0.1354  False
+     0      3  -0.0493 0.2327 -0.1132 0.0146  False
+     0      7  -0.0233    0.9 -0.0908 0.0441  False
+     0     14  -0.0019    0.9 -0.0684 0.0646  False
+     0     21  -0.0046    0.9 -0.0711 0.0619  False
+     0     28   0.0311 0.7605 -0.0379 0.1001  False
+     3      7    0.026 0.8138 -0.0362 0.0881  False
+     3     14   0.0474 0.2281 -0.0137 0.1086  False
+     3     21   0.0448 0.2887 -0.0164 0.1059  False
+     3     28   0.0804  0.005  0.0165 0.1443   True
+     7     14   0.0215    0.9 -0.0434 0.0863  False
+     7     21   0.0188    0.9 -0.0461 0.0836  False
+     7     28   0.0544   0.19  -0.013 0.1218  False
+    14     21  -0.0027    0.9 -0.0666 0.0612  False
+    14     28   0.0329 0.6858 -0.0336 0.0994  False
+    21     28   0.0356 0.6195 -0.0309 0.1021  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0194    0.9 -0.1357 0.0969  False
-     0      7  -0.0652 0.5254 -0.1754 0.0451  False
-     0     14  -0.0176    0.9 -0.1235 0.0882  False
-     0     21   -0.014    0.9 -0.1351 0.1071  False
-     0     28    -0.03    0.9 -0.1449 0.0849  False
-     3      7  -0.0458 0.8616 -0.1638 0.0723  False
-     3     14   0.0018    0.9 -0.1122 0.1157  False
-     3     21   0.0054    0.9 -0.1229 0.1337  False
-     3     28  -0.0106    0.9  -0.133 0.1118  False
-     7     14   0.0475 0.7733 -0.0603 0.1553  False
-     7     21   0.0512 0.8138 -0.0717  0.174  False
-     7     28   0.0352    0.9 -0.0815 0.1519  False
-    14     21   0.0036    0.9 -0.1153 0.1225  False
-    14     28  -0.0124    0.9 -0.1249 0.1002  False
-    21     28   -0.016    0.9  -0.143  0.111  False
+     0      3   0.0243    0.9 -0.0667 0.1152  False
+     0      7   0.0076    0.9 -0.0764 0.0916  False
+     0     14   0.0225    0.9 -0.0582 0.1031  False
+     0     21   0.0428 0.7366 -0.0496 0.1351  False
+     0     28   0.0103    0.9 -0.0773 0.0979  False
+     3      7  -0.0167    0.9  -0.109 0.0757  False
+     3     14  -0.0018    0.9 -0.0911 0.0875  False
+     3     21   0.0185    0.9 -0.0814 0.1184  False
+     3     28  -0.0139    0.9 -0.1095 0.0816  False
+     7     14   0.0149    0.9 -0.0673  0.097  False
+     7     21   0.0351 0.8814 -0.0585 0.1288  False
+     7     28   0.0027    0.9 -0.0862 0.0917  False
+    14     21   0.0203    0.9 -0.0703 0.1109  False
+    14     28  -0.0121    0.9 -0.0979 0.0736  False
+    21     28  -0.0324    0.9 -0.1293 0.0644  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.09518825]	No
-Stroke	Sham	14	[0.61412691]	No
-Stroke	Sham	21	[0.90032471]	No
-Stroke	Sham	28	[0.06764643]	No
-Stroke	Sham	7	[0.1502544]	No
-Stroke	Sham	0	[0.25138088]	No
+Stroke	Sham	3	[0.02910458]	Yes
+Stroke	Sham	14	[0.96113758]	No
+Stroke	Sham	21	[0.57368887]	No
+Stroke	Sham	28	[0.09216774]	No
+Stroke	Sham	7	[0.61322217]	No
+Stroke	Sham	0	[0.2588129]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CST_MOp-int-py_contralesional_selfdrawnROA+CCcut_log.txt

@@ -1,67 +1,67 @@
 Model Name: ad_CST_MOp-int-py_contralesional_selfdrawnROA+CCcut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0199
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.002    0.001 2.161 0.031  0.000  0.003
-Group Var         0.000                                   
-==========================================================
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM  Dependent Variable:  Value   
+No. Observations:    361      Method:              REML    
+No. Groups:          2        Scale:               0.0102  
+Min. group size:     156      Log-Likelihood:      305.1544
+Max. group size:     205      Converged:           No      
+Mean group size:     180.5                                 
+-----------------------------------------------------------
+                 Coef. Std.Err.    z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept        1.105    0.008 130.775 0.000  1.088  1.122
+merged_timepoint 0.001    0.001   2.416 0.016  0.000  0.002
+Group Var        0.000                                     
+===========================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0405 0.7904 -0.1341 0.0532  False
-     0      7   0.0304    0.9 -0.0685 0.1293  False
-     0     14   0.0103    0.9 -0.0873 0.1078  False
-     0     21   0.0384 0.8536 -0.0591 0.1359  False
-     0     28   0.0741 0.2891 -0.0272 0.1754  False
-     3      7   0.0708 0.2353 -0.0212 0.1628  False
-     3     14   0.0507 0.5786 -0.0398 0.1412  False
-     3     21   0.0789 0.1265 -0.0116 0.1694  False
-     3     28   0.1145 0.0078    0.02 0.2091   True
-     7     14  -0.0201    0.9 -0.1161 0.0759  False
-     7     21    0.008    0.9 -0.0879  0.104  False
-     7     28   0.0437 0.7803 -0.0561 0.1435  False
-    14     21   0.0281    0.9 -0.0664 0.1227  False
-    14     28   0.0638  0.428 -0.0346 0.1622  False
-    21     28   0.0357    0.9 -0.0627 0.1341  False
+     0      3  -0.0517 0.1926  -0.116 0.0126  False
+     0      7  -0.0246    0.9 -0.0925 0.0432  False
+     0     14  -0.0034    0.9 -0.0703 0.0635  False
+     0     21  -0.0052    0.9 -0.0721 0.0617  False
+     0     28   0.0303  0.782 -0.0391 0.0997  False
+     3      7   0.0271 0.7892 -0.0355 0.0896  False
+     3     14   0.0483 0.2153 -0.0132 0.1099  False
+     3     21   0.0465 0.2537  -0.015  0.108  False
+     3     28    0.082 0.0041  0.0178 0.1463   True
+     7     14   0.0213    0.9  -0.044 0.0865  False
+     7     21   0.0195    0.9 -0.0458 0.0847  False
+     7     28    0.055 0.1856 -0.0128 0.1228  False
+    14     21  -0.0018    0.9 -0.0661 0.0624  False
+    14     28   0.0337 0.6717 -0.0332 0.1006  False
+    21     28   0.0355 0.6269 -0.0314 0.1024  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0205    0.9 -0.1361 0.0952  False
-     0      7  -0.0645 0.5299 -0.1742 0.0451  False
-     0     14  -0.0171    0.9 -0.1224 0.0881  False
-     0     21  -0.0127    0.9 -0.1331 0.1078  False
-     0     28  -0.0292    0.9 -0.1435 0.0851  False
-     3      7  -0.0441 0.8818 -0.1615 0.0734  False
-     3     14   0.0033    0.9   -0.11 0.1167  False
-     3     21   0.0078    0.9 -0.1198 0.1354  False
-     3     28  -0.0087    0.9 -0.1305  0.113  False
-     7     14   0.0474 0.7718 -0.0598 0.1546  False
-     7     21   0.0519 0.8005 -0.0703  0.174  False
-     7     28   0.0353    0.9 -0.0807 0.1514  False
-    14     21   0.0045    0.9 -0.1138 0.1227  False
-    14     28   -0.012    0.9  -0.124 0.0999  False
-    21     28  -0.0165    0.9 -0.1429 0.1098  False
+     0      3   0.0229    0.9 -0.0678 0.1136  False
+     0      7   0.0068    0.9 -0.0769 0.0906  False
+     0     14   0.0223    0.9 -0.0581 0.1027  False
+     0     21   0.0439 0.7139 -0.0481 0.1359  False
+     0     28   0.0105    0.9 -0.0768 0.0978  False
+     3      7  -0.0161    0.9 -0.1081 0.0759  False
+     3     14  -0.0006    0.9 -0.0896 0.0883  False
+     3     21    0.021    0.9 -0.0786 0.1205  False
+     3     28  -0.0124    0.9 -0.1077 0.0828  False
+     7     14   0.0154    0.9 -0.0665 0.0973  False
+     7     21    0.037 0.8461 -0.0563 0.1304  False
+     7     28   0.0037    0.9  -0.085 0.0923  False
+    14     21   0.0216    0.9 -0.0687 0.1119  False
+    14     28  -0.0118    0.9 -0.0973 0.0737  False
+    21     28  -0.0334    0.9 -0.1299 0.0631  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.09763973]	No
-Stroke	Sham	14	[0.56578297]	No
-Stroke	Sham	21	[0.90738246]	No
-Stroke	Sham	28	[0.07065484]	No
-Stroke	Sham	7	[0.13831167]	No
-Stroke	Sham	0	[0.25714921]	No
+Stroke	Sham	3	[0.03021924]	Yes
+Stroke	Sham	14	[0.97095388]	No
+Stroke	Sham	21	[0.57191007]	No
+Stroke	Sham	28	[0.09000373]	No
+Stroke	Sham	7	[0.66630831]	No
+Stroke	Sham	0	[0.22831231]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CST_MOp-int-py_ipsilesional_CCasROA_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CST_MOp-int-py_ipsilesional_CCasROA
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM  Dependent Variable:  Value   
+No. Observations:    361      Method:              REML    
+No. Groups:          2        Scale:               0.0088  
+Min. group size:     156      Log-Likelihood:      331.2841
+Max. group size:     205      Converged:           Yes     
+Mean group size:     180.5                                 
+-----------------------------------------------------------
+                 Coef. Std.Err.    z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept        1.084    0.008 137.928 0.000  1.069  1.099
+merged_timepoint 0.001    0.001   2.029 0.042  0.000  0.002
+Group Var        0.000                                     
+===========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0124    0.9 -0.0481 0.0729  False
+     0      7  -0.0355 0.5867 -0.0993 0.0284  False
+     0     14  -0.0073    0.9 -0.0702 0.0557  False
+     0     21  -0.0059    0.9 -0.0688 0.0571  False
+     0     28    0.056 0.1394 -0.0094 0.1213  False
+     3      7  -0.0479 0.1831 -0.1068  0.011  False
+     3     14  -0.0197    0.9 -0.0776 0.0383  False
+     3     21  -0.0183    0.9 -0.0762 0.0397  False
+     3     28   0.0436 0.3058 -0.0169 0.1041  False
+     7     14   0.0282 0.7454 -0.0332 0.0896  False
+     7     21   0.0296  0.708 -0.0318  0.091  False
+     7     28   0.0915  0.001  0.0276 0.1553   True
+    14     21   0.0014    0.9 -0.0591 0.0619  False
+    14     28   0.0632 0.0484  0.0003 0.1262   True
+    21     28   0.0619 0.0575 -0.0011 0.1248  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0473  0.539 -0.0339 0.1286  False
+     0      7   -0.001    0.9  -0.076  0.074  False
+     0     14   0.0377 0.6372 -0.0343 0.1097  False
+     0     21   0.0405 0.6894 -0.0419 0.1229  False
+     0     28   0.0182    0.9   -0.06 0.0964  False
+     3      7  -0.0483 0.5334 -0.1307 0.0341  False
+     3     14  -0.0097    0.9 -0.0893   0.07  False
+     3     21  -0.0068    0.9  -0.096 0.0824  False
+     3     28  -0.0292    0.9 -0.1145 0.0561  False
+     7     14   0.0387 0.6311 -0.0347  0.112  False
+     7     21   0.0415 0.6816 -0.0421 0.1251  False
+     7     28   0.0191    0.9 -0.0603 0.0986  False
+    14     21   0.0028    0.9 -0.0781 0.0837  False
+    14     28  -0.0195    0.9 -0.0961 0.0571  False
+    21     28  -0.0224    0.9 -0.1088 0.0641  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.54293578]	No
+Stroke	Sham	14	[0.38703027]	No
+Stroke	Sham	21	[0.39594953]	No
+Stroke	Sham	28	[0.03663886]	Yes
+Stroke	Sham	7	[0.30758997]	No
+Stroke	Sham	0	[0.22824717]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CST_MOp-int-py_ipsilesional_CCcut_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CST_MOp-int-py_ipsilesional_CCcut
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0089
+Min. group size:        156          Log-Likelihood:          inf   
+Max. group size:        205          Converged:               Yes   
+Mean group size:        180.5                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 184082.577 0.000 1.000 -360795.221 360795.221
+merged_timepoint 0.001      0.001 2.022 0.043       0.000      0.002
+Group Var        0.000                                              
+====================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0114    0.9 -0.0492 0.0721  False
+     0      7  -0.0371 0.5485 -0.1011  0.027  False
+     0     14  -0.0084    0.9 -0.0716 0.0547  False
+     0     21  -0.0069    0.9 -0.0701 0.0562  False
+     0     28    0.055 0.1554 -0.0105 0.1206  False
+     3      7  -0.0485 0.1747 -0.1075 0.0106  False
+     3     14  -0.0199    0.9  -0.078 0.0382  False
+     3     21  -0.0184    0.9 -0.0765 0.0397  False
+     3     28   0.0436 0.3083 -0.0171 0.1043  False
+     7     14   0.0286 0.7369  -0.033 0.0902  False
+     7     21   0.0301 0.6967 -0.0315 0.0917  False
+     7     28   0.0921  0.001  0.0281 0.1561   True
+    14     21   0.0015    0.9 -0.0592 0.0622  False
+    14     28   0.0635  0.048  0.0003 0.1266   True
+    21     28    0.062 0.0578 -0.0012 0.1251  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3    0.048 0.5269 -0.0333 0.1292  False
+     0      7  -0.0004    0.9 -0.0755 0.0747  False
+     0     14   0.0375  0.641 -0.0345 0.1096  False
+     0     21   0.0424 0.6532 -0.0401 0.1248  False
+     0     28   0.0185    0.9 -0.0598 0.0967  False
+     3      7  -0.0484  0.533 -0.1308 0.0341  False
+     3     14  -0.0104    0.9 -0.0902 0.0693  False
+     3     21  -0.0056    0.9 -0.0949 0.0836  False
+     3     28  -0.0295    0.9 -0.1149 0.0558  False
+     7     14   0.0379 0.6478 -0.0355 0.1113  False
+     7     21   0.0428 0.6572 -0.0409 0.1264  False
+     7     28   0.0189    0.9 -0.0606 0.0983  False
+    14     21   0.0048    0.9 -0.0761 0.0858  False
+    14     28  -0.0191    0.9 -0.0957 0.0575  False
+    21     28  -0.0239    0.9 -0.1104 0.0626  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.53581929]	No
+Stroke	Sham	14	[0.39471737]	No
+Stroke	Sham	21	[0.37518936]	No
+Stroke	Sham	28	[0.03512949]	Yes
+Stroke	Sham	7	[0.28611314]	No
+Stroke	Sham	0	[0.20139569]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CST_MOp-int-py_ipsilesional_selfdrawnROA+CCcut_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CST_MOp-int-py_ipsilesional_selfdrawnROA+CCcut
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0088
+Min. group size:        156          Log-Likelihood:          inf   
+Max. group size:        205          Converged:               Yes   
+Mean group size:        180.5                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 183566.794 0.000 1.000 -359784.305 359784.305
+merged_timepoint 0.001      0.001 2.031 0.042       0.000      0.002
+Group Var        0.000                                              
+====================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0113    0.9 -0.0492 0.0718  False
+     0      7  -0.0357 0.5808 -0.0996 0.0282  False
+     0     14  -0.0075    0.9 -0.0705 0.0555  False
+     0     21  -0.0066    0.9 -0.0696 0.0564  False
+     0     28   0.0548 0.1565 -0.0105 0.1202  False
+     3      7   -0.047    0.2 -0.1059 0.0119  False
+     3     14  -0.0188    0.9 -0.0768 0.0391  False
+     3     21   -0.018    0.9 -0.0759   0.04  False
+     3     28   0.0435 0.3076  -0.017  0.104  False
+     7     14   0.0282 0.7462 -0.0332 0.0896  False
+     7     21   0.0291 0.7226 -0.0324 0.0905  False
+     7     28   0.0905  0.001  0.0267 0.1544   True
+    14     21   0.0009    0.9 -0.0596 0.0614  False
+    14     28   0.0624 0.0541 -0.0006 0.1254  False
+    21     28   0.0615 0.0603 -0.0015 0.1245  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0472 0.5419  -0.034 0.1284  False
+     0      7  -0.0004    0.9 -0.0754 0.0745  False
+     0     14   0.0382 0.6259 -0.0338 0.1101  False
+     0     21   0.0404 0.6908 -0.0419 0.1228  False
+     0     28   0.0192    0.9 -0.0589 0.0974  False
+     3      7  -0.0476 0.5469   -0.13 0.0348  False
+     3     14   -0.009    0.9 -0.0887 0.0706  False
+     3     21  -0.0067    0.9 -0.0959 0.0824  False
+     3     28  -0.0279    0.9 -0.1132 0.0573  False
+     7     14   0.0386 0.6319 -0.0347 0.1119  False
+     7     21   0.0409 0.6935 -0.0427 0.1244  False
+     7     28   0.0197    0.9 -0.0597  0.099  False
+    14     21   0.0023    0.9 -0.0786 0.0831  False
+    14     28  -0.0189    0.9 -0.0955 0.0576  False
+    21     28  -0.0212    0.9 -0.1076 0.0652  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.54265674]	No
+Stroke	Sham	14	[0.39267564]	No
+Stroke	Sham	21	[0.40264947]	No
+Stroke	Sham	28	[0.04003806]	Yes
+Stroke	Sham	7	[0.31856047]	No
+Stroke	Sham	0	[0.20664575]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_OT_och-lgn_lgncut_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_OT_och-lgn_lgncut
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0093
+Min. group size:        156          Log-Likelihood:          inf   
+Max. group size:        205          Converged:               Yes   
+Mean group size:        180.5                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 188660.373 0.000 1.000 -369767.537 369767.537
+merged_timepoint 0.001      0.001 2.714 0.007       0.000      0.002
+Group Var        0.000                                              
+====================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0494 0.2193 -0.1125 0.0137  False
+     0      7  -0.0387  0.545 -0.1053 0.0279  False
+     0     14   0.0041    0.9 -0.0617 0.0698  False
+     0     21   0.0125    0.9 -0.0532 0.0782  False
+     0     28   0.0213    0.9 -0.0468 0.0895  False
+     3      7   0.0107    0.9 -0.0507 0.0721  False
+     3     14   0.0535 0.1165  -0.007 0.1139  False
+     3     21   0.0619 0.0413  0.0015 0.1223   True
+     3     28   0.0707 0.0182  0.0076 0.1339   True
+     7     14   0.0428 0.3946 -0.0213 0.1068  False
+     7     21   0.0512 0.1991 -0.0129 0.1153  False
+     7     28     0.06 0.1036 -0.0066 0.1267  False
+    14     21   0.0084    0.9 -0.0547 0.0716  False
+    14     28   0.0173    0.9 -0.0484  0.083  False
+    21     28   0.0088    0.9 -0.0569 0.0746  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0394 0.7209 -0.0439 0.1226  False
+     0      7   0.0264    0.9 -0.0505 0.1034  False
+     0     14   0.0494 0.3878 -0.0244 0.1233  False
+     0     21   0.0414 0.6914  -0.043 0.1259  False
+     0     28   0.0201    0.9   -0.06 0.1003  False
+     3      7  -0.0129    0.9 -0.0974 0.0716  False
+     3     14   0.0101    0.9 -0.0716 0.0918  False
+     3     21   0.0021    0.9 -0.0894 0.0935  False
+     3     28  -0.0192    0.9 -0.1067 0.0682  False
+     7     14    0.023    0.9 -0.0522 0.0982  False
+     7     21    0.015    0.9 -0.0707 0.1007  False
+     7     28  -0.0063    0.9 -0.0877 0.0751  False
+    14     21   -0.008    0.9 -0.0909  0.075  False
+    14     28  -0.0293 0.8856 -0.1078 0.0492  False
+    21     28  -0.0213    0.9 -0.1099 0.0673  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.0701725]	No
+Stroke	Sham	14	[0.89544246]	No
+Stroke	Sham	21	[0.69055583]	No
+Stroke	Sham	28	[0.1590323]	No
+Stroke	Sham	7	[0.10822623]	No
+Stroke	Sham	0	[0.02321084]	Yes

output/Final_Quantitative_output/mixed_model_analysis/ad_TC_DORsm-SSp+SSs_ipsilesional_END+CCcut_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_TC_DORsm-SSp+SSs_ipsilesional_END+CCcut
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM  Dependent Variable:  Value   
+No. Observations:    361      Method:              REML    
+No. Groups:          2        Scale:               0.0120  
+Min. group size:     156      Log-Likelihood:      276.5207
+Max. group size:     205      Converged:           Yes     
+Mean group size:     180.5                                 
+-----------------------------------------------------------
+                 Coef. Std.Err.    z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept        1.004    0.009 109.745 0.000  0.986  1.022
+merged_timepoint 0.001    0.001   2.156 0.031  0.000  0.002
+Group Var        0.000                                     
+===========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0312 0.7298 -0.0354  0.0979  False
+     0      7  -0.0374 0.6253 -0.1078  0.0329  False
+     0     14   0.0444 0.4434  -0.025  0.1138  False
+     0     21   0.0258 0.8898 -0.0436  0.0952  False
+     0     28   0.0409 0.5653 -0.0311  0.1129  False
+     3      7  -0.0687  0.031 -0.1335 -0.0038   True
+     3     14   0.0132    0.9 -0.0507   0.077  False
+     3     21  -0.0055    0.9 -0.0693  0.0584  False
+     3     28   0.0097    0.9  -0.057  0.0763  False
+     7     14   0.0818  0.008  0.0142  0.1495   True
+     7     21   0.0632 0.0822 -0.0044  0.1309  False
+     7     28   0.0783 0.0193   0.008  0.1487   True
+    14     21  -0.0186    0.9 -0.0853   0.048  False
+    14     28  -0.0035    0.9 -0.0728  0.0659  False
+    21     28   0.0151    0.9 -0.0542  0.0845  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0772 0.2321 -0.0229 0.1773  False
+     0      7   0.0321    0.9 -0.0604 0.1245  False
+     0     14   0.0565 0.4467 -0.0323 0.1452  False
+     0     21   0.0672 0.4011 -0.0343 0.1688  False
+     0     28    0.047 0.6963 -0.0494 0.1433  False
+     3      7  -0.0451 0.7676 -0.1467 0.0564  False
+     3     14  -0.0207    0.9 -0.1189 0.0775  False
+     3     21    -0.01    0.9 -0.1199    0.1  False
+     3     28  -0.0302    0.9 -0.1353 0.0749  False
+     7     14   0.0244    0.9  -0.066 0.1148  False
+     7     21   0.0352    0.9 -0.0678 0.1382  False
+     7     28   0.0149    0.9 -0.0829 0.1128  False
+    14     21   0.0107    0.9  -0.089 0.1104  False
+    14     28  -0.0095    0.9 -0.1039 0.0849  False
+    21     28  -0.0203    0.9 -0.1268 0.0863  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.56147043]	No
+Stroke	Sham	14	[0.62777197]	No
+Stroke	Sham	21	[0.75057615]	No
+Stroke	Sham	28	[0.42849949]	No
+Stroke	Sham	7	[0.02295153]	Yes
+Stroke	Sham	0	[0.04512744]	Yes

output/Final_Quantitative_output/mixed_model_analysis/ad_TC_DORsm-SSp_ll+SSp_ul_ipsilesional_END+higherstepsize__log.txt

@@ -1,67 +1,67 @@
 Model Name: ad_TC_DORsm-SSp_ll+SSp_ul_ipsilesional_END+higherstepsize_
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0137
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.001 2.040 0.041  0.000  0.003
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0120
+Min. group size:        156          Log-Likelihood:          inf   
+Max. group size:        205          Converged:               Yes   
+Mean group size:        180.5                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 213827.460 0.000 1.000 -419094.120 419094.120
+merged_timepoint 0.002      0.001 3.042 0.002       0.001      0.003
+Group Var        0.000                                              
+====================================================================
 
 Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0083    0.9 -0.0594 0.0761  False
-     0      7  -0.0488 0.3685 -0.1204 0.0228  False
-     0     14   0.0301 0.8009 -0.0406 0.1007  False
-     0     21   0.0163    0.9 -0.0543 0.0869  False
-     0     28    0.049 0.3917 -0.0243 0.1224  False
-     3      7  -0.0572 0.1376 -0.1238 0.0094  False
-     3     14   0.0217    0.9 -0.0438 0.0872  False
-     3     21    0.008    0.9 -0.0576 0.0735  False
-     3     28   0.0407 0.5221 -0.0277 0.1091  False
-     7     14   0.0789 0.0159  0.0094 0.1484   True
-     7     21   0.0651 0.0803 -0.0043 0.1346  False
-     7     28   0.0979 0.0018  0.0257 0.1701   True
-    14     21  -0.0138    0.9 -0.0822 0.0547  False
-    14     28    0.019    0.9 -0.0522 0.0902  False
-    21     28   0.0327 0.7447 -0.0385  0.104  False
----------------------------------------------------
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0321 0.6963 -0.0336  0.0978  False
+     0      7  -0.0433 0.4707 -0.1126   0.026  False
+     0     14   0.0555 0.1844 -0.0129  0.1239  False
+     0     21   0.0465  0.371 -0.0218  0.1149  False
+     0     28   0.0614 0.1321 -0.0096  0.1323  False
+     3      7  -0.0754 0.0106 -0.1393 -0.0115   True
+     3     14   0.0234 0.8898 -0.0395  0.0863  False
+     3     21   0.0144    0.9 -0.0485  0.0773  False
+     3     28   0.0292  0.769 -0.0365  0.0949  False
+     7     14   0.0988  0.001  0.0321  0.1655   True
+     7     21   0.0898  0.002  0.0232  0.1565   True
+     7     28   0.1047  0.001  0.0353   0.174   True
+    14     21   -0.009    0.9 -0.0747  0.0567  False
+    14     28   0.0059    0.9 -0.0625  0.0742  False
+    21     28   0.0148    0.9 -0.0535  0.0832  False
+----------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3    0.116 0.0233  0.0099  0.222   True
-     0      7   0.0326    0.9 -0.0679 0.1332  False
-     0     14   0.0563 0.5386 -0.0402 0.1528  False
-     0     21   0.0692 0.4656 -0.0413 0.1796  False
-     0     28   0.0431 0.8222 -0.0617 0.1479  False
-     3      7  -0.0833 0.2286  -0.191 0.0243  False
-     3     14  -0.0597 0.5539 -0.1636 0.0443  False
-     3     21  -0.0468 0.8412 -0.1638 0.0702  False
-     3     28  -0.0728 0.4185 -0.1845 0.0388  False
-     7     14   0.0237    0.9 -0.0746  0.122  False
-     7     21   0.0365    0.9 -0.0755 0.1486  False
-     7     28   0.0105    0.9 -0.0959 0.1169  False
-    14     21   0.0129    0.9 -0.0956 0.1213  False
-    14     28  -0.0132    0.9 -0.1158 0.0895  False
-    21     28   -0.026    0.9 -0.1419 0.0898  False
+     0      3   0.0788 0.2118 -0.0213 0.1789  False
+     0      7   0.0354 0.8687  -0.057 0.1278  False
+     0     14   0.0595 0.3862 -0.0292 0.1482  False
+     0     21   0.0665 0.4143 -0.0351  0.168  False
+     0     28   0.0481  0.677 -0.0482 0.1444  False
+     3      7  -0.0434  0.796 -0.1449 0.0582  False
+     3     14  -0.0193    0.9 -0.1175 0.0789  False
+     3     21  -0.0123    0.9 -0.1222 0.0976  False
+     3     28  -0.0307    0.9 -0.1358 0.0744  False
+     7     14   0.0241    0.9 -0.0663 0.1145  False
+     7     21   0.0311    0.9 -0.0719  0.134  False
+     7     28   0.0127    0.9 -0.0852 0.1105  False
+    14     21    0.007    0.9 -0.0927 0.1067  False
+    14     28  -0.0114    0.9 -0.1058  0.083  False
+    21     28  -0.0184    0.9 -0.1249 0.0881  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.14949716]	No
-Stroke	Sham	14	[0.47365163]	No
-Stroke	Sham	21	[0.98353446]	No
-Stroke	Sham	28	[0.03497483]	Yes
-Stroke	Sham	7	[0.06881805]	No
-Stroke	Sham	0	[0.00114091]	Yes
+Stroke	Sham	3	[0.5912463]	No
+Stroke	Sham	14	[0.46274027]	No
+Stroke	Sham	21	[0.76453291]	No
+Stroke	Sham	28	[0.11213688]	No
+Stroke	Sham	7	[0.00722372]	Yes
+Stroke	Sham	0	[0.02802865]	Yes

output/Final_Quantitative_output/mixed_model_analysis/ad_TC_DORsm-SSp_ll+SSp_ul_ipsilesional_ROI+CCcut_log.txt

@@ -1,18 +1,18 @@
 Model Name: ad_TC_DORsm-SSp_ll+SSp_ul_ipsilesional_ROI+CCcut
           Mixed Linear Model Regression Results
 ==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0175
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   361      Method:              REML    
+No. Groups:         2        Scale:               0.0150  
+Min. group size:    156      Log-Likelihood:      236.5775
+Max. group size:    205      Converged:           Yes     
+Mean group size:    180.5                                 
 ----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
 ----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.002    0.001 2.290 0.022  0.000  0.003
-Group Var         0.000                                   
+Intercept        1.023    0.010 99.953 0.000  1.003  1.043
+merged_timepoint 0.002    0.001  2.887 0.004  0.001  0.003
+Group Var        0.000                                    
 ==========================================================
 
 Posthoc Analysis for Stroke:
@@ -20,48 +20,48 @@ Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0006    0.9 -0.0736 0.0723  False
-     0      7  -0.0406 0.6342 -0.1176 0.0365  False
-     0     14   0.0239    0.9 -0.0521 0.0999  False
-     0     21   0.0215    0.9 -0.0544 0.0975  False
-     0     28   0.0513 0.4243 -0.0276 0.1302  False
-     3      7  -0.0399 0.5837 -0.1116 0.0317  False
-     3     14   0.0246    0.9 -0.0459 0.0951  False
-     3     21   0.0222    0.9 -0.0483 0.0927  False
-     3     28    0.052 0.3283 -0.0217 0.1256  False
-     7     14   0.0645 0.1338 -0.0102 0.1392  False
-     7     21   0.0621 0.1641 -0.0126 0.1369  False
-     7     28   0.0919 0.0103  0.0142 0.1696   True
-    14     21  -0.0024    0.9  -0.076 0.0713  False
-    14     28   0.0274    0.9 -0.0492 0.1041  False
-    21     28   0.0298 0.8621 -0.0469 0.1064  False
+     0      3   0.0151    0.9 -0.0557 0.0858  False
+     0      7    -0.04 0.6205 -0.1146 0.0347  False
+     0     14   0.0495 0.3851 -0.0241 0.1232  False
+     0     21   0.0377 0.6585 -0.0359 0.1114  False
+     0     28   0.0569 0.2699 -0.0195 0.1333  False
+     3      7   -0.055 0.1989 -0.1239 0.0138  False
+     3     14   0.0345 0.6641 -0.0333 0.1022  False
+     3     21   0.0226    0.9 -0.0451 0.0904  False
+     3     28   0.0418 0.5279 -0.0289 0.1126  False
+     7     14   0.0895 0.0056  0.0177 0.1613   True
+     7     21   0.0777 0.0256  0.0058 0.1495   True
+     7     28   0.0969 0.0033  0.0222 0.1715   True
+    14     21  -0.0118    0.9 -0.0826 0.0589  False
+    14     28   0.0074    0.9 -0.0663  0.081  False
+    21     28   0.0192    0.9 -0.0545 0.0929  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.1213 0.0632 -0.0038 0.2464  False
-     0      7   0.0359    0.9 -0.0828 0.1545  False
-     0     14   0.0789 0.3475  -0.035 0.1928  False
-     0     21   0.0912 0.3358 -0.0391 0.2215  False
-     0     28   0.0503 0.8304 -0.0734 0.1739  False
-     3      7  -0.0855 0.3823 -0.2125 0.0416  False
-     3     14  -0.0424    0.9  -0.165 0.0802  False
-     3     21  -0.0301    0.9 -0.1681 0.1079  False
-     3     28  -0.0711 0.6108 -0.2028 0.0607  False
-     7     14   0.0431 0.8886 -0.0729  0.159  False
-     7     21   0.0554 0.8099 -0.0768 0.1875  False
-     7     28   0.0144    0.9 -0.1112   0.14  False
-    14     21   0.0123    0.9 -0.1156 0.1402  False
-    14     28  -0.0287    0.9 -0.1498 0.0924  False
-    21     28   -0.041    0.9 -0.1776 0.0957  False
+     0      3   0.0837 0.3098 -0.0331 0.2005  False
+     0      7   0.0395 0.8963 -0.0683 0.1474  False
+     0     14   0.0782 0.2529 -0.0253 0.1818  False
+     0     21   0.0814  0.358 -0.0371 0.1999  False
+     0     28   0.0497 0.7713 -0.0627 0.1621  False
+     3      7  -0.0441 0.8863 -0.1627 0.0744  False
+     3     14  -0.0054    0.9   -0.12 0.1091  False
+     3     21  -0.0023    0.9 -0.1306  0.126  False
+     3     28   -0.034    0.9 -0.1566 0.0887  False
+     7     14   0.0387 0.8956 -0.0668 0.1442  False
+     7     21   0.0418    0.9 -0.0783  0.162  False
+     7     28   0.0102    0.9  -0.104 0.1244  False
+    14     21   0.0031    0.9 -0.1132 0.1195  False
+    14     28  -0.0285    0.9 -0.1386 0.0816  False
+    21     28  -0.0317    0.9  -0.156 0.0926  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.06450604]	No
-Stroke	Sham	14	[0.78805632]	No
-Stroke	Sham	21	[0.54665728]	No
-Stroke	Sham	28	[0.17759624]	No
-Stroke	Sham	7	[0.14228755]	No
-Stroke	Sham	0	[0.0083156]	Yes
+Stroke	Sham	3	[0.22899908]	No
+Stroke	Sham	14	[0.97083565]	No
+Stroke	Sham	21	[0.74142859]	No
+Stroke	Sham	28	[0.24302321]	No
+Stroke	Sham	7	[0.02879952]	Yes
+Stroke	Sham	0	[0.04328997]	Yes

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_MOp-MOp_dilated_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CC_MOp-MOp_dilated_cut
+              Mixed Linear Model Regression Results
+=================================================================
+Model:                 MixedLM     Dependent Variable:     Value 
+No. Observations:      361         Method:                 REML  
+No. Groups:            2           Scale:                  0.0006
+Min. group size:       156         Log-Likelihood:         inf   
+Max. group size:       205         Converged:              Yes   
+Mean group size:       180.5                                     
+-----------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|   [0.025     0.975] 
+-----------------------------------------------------------------
+Intercept        0.000 49169.360 0.000 1.000 -96370.174 96370.174
+merged_timepoint 0.000     0.000 2.062 0.039      0.000     0.001
+Group Var        0.000                                           
+=================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+==================================================
+group1 group2 meandiff p-adj  lower  upper  reject
+--------------------------------------------------
+     0      3   0.0032   0.9 -0.0132 0.0196  False
+     0      7  -0.0009   0.9 -0.0182 0.0164  False
+     0     14   0.0011   0.9 -0.0159 0.0182  False
+     0     21   0.0033   0.9 -0.0138 0.0203  False
+     0     28   0.0033   0.9 -0.0144 0.0209  False
+     3      7  -0.0041   0.9   -0.02 0.0118  False
+     3     14  -0.0021   0.9 -0.0177 0.0136  False
+     3     21   0.0001   0.9 -0.0156 0.0157  False
+     3     28      0.0   0.9 -0.0163 0.0164  False
+     7     14    0.002   0.9 -0.0146 0.0186  False
+     7     21   0.0041   0.9 -0.0125 0.0208  False
+     7     28   0.0041   0.9 -0.0131 0.0214  False
+    14     21   0.0021   0.9 -0.0142 0.0185  False
+    14     28   0.0021   0.9 -0.0149 0.0192  False
+    21     28     -0.0   0.9  -0.017  0.017  False
+--------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0141 0.4482  -0.008 0.0362  False
+     0      7   0.0067    0.9 -0.0137 0.0271  False
+     0     14   0.0122 0.4727 -0.0074 0.0318  False
+     0     21   0.0238 0.0303  0.0014 0.0462   True
+     0     28   0.0149 0.3367 -0.0064 0.0361  False
+     3      7  -0.0074    0.9 -0.0298  0.015  False
+     3     14  -0.0019    0.9 -0.0235 0.0198  False
+     3     21   0.0098 0.8367 -0.0145  0.034  False
+     3     28   0.0008    0.9 -0.0224  0.024  False
+     7     14   0.0055    0.9 -0.0144 0.0255  False
+     7     21   0.0172 0.2541 -0.0056 0.0399  False
+     7     28   0.0082 0.8737 -0.0134 0.0298  False
+    14     21   0.0116 0.6289 -0.0104 0.0336  False
+    14     28   0.0027    0.9 -0.0182 0.0235  False
+    21     28  -0.0089 0.8734 -0.0325 0.0146  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.06469605]	No
+Stroke	Sham	14	[0.03886165]	Yes
+Stroke	Sham	21	[0.00127062]	Yes
+Stroke	Sham	28	[0.02110625]	Yes
+Stroke	Sham	7	[0.10063108]	No
+Stroke	Sham	0	[0.54994228]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_MOp-MOp_dilated_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_CC_MOp-MOp_dilated
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0007
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.000    0.000 3.365 0.001  0.000  0.001
-Group Var         0.000                                   
-==========================================================
+              Mixed Linear Model Regression Results
+=================================================================
+Model:                 MixedLM     Dependent Variable:     Value 
+No. Observations:      361         Method:                 REML  
+No. Groups:            2           Scale:                  0.0006
+Min. group size:       156         Log-Likelihood:         inf   
+Max. group size:       205         Converged:              Yes   
+Mean group size:       180.5                                     
+-----------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|   [0.025     0.975] 
+-----------------------------------------------------------------
+Intercept        0.000 49207.625 0.000 1.000 -96445.172 96445.172
+merged_timepoint 0.001     0.000 3.989 0.000      0.000     0.001
+Group Var        0.000                                           
+=================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0068    0.9 -0.0132 0.0268  False
-     0      7   0.0137 0.4254 -0.0074 0.0348  False
-     0     14   0.0092 0.7734 -0.0116   0.03  False
-     0     21   0.0133 0.4432 -0.0075 0.0341  False
-     0     28   0.0163  0.255 -0.0053 0.0379  False
-     3      7   0.0069    0.9 -0.0127 0.0265  False
-     3     14   0.0024    0.9 -0.0169 0.0217  False
-     3     21   0.0065    0.9 -0.0128 0.0258  False
-     3     28   0.0095 0.7264 -0.0107 0.0297  False
-     7     14  -0.0045    0.9  -0.025  0.016  False
-     7     21  -0.0004    0.9 -0.0209 0.0201  False
-     7     28   0.0026    0.9 -0.0187 0.0239  False
-    14     21   0.0041    0.9 -0.0161 0.0243  False
-    14     28   0.0071    0.9 -0.0139 0.0281  False
-    21     28    0.003    0.9  -0.018  0.024  False
+     0      3   0.0019    0.9 -0.0158 0.0195  False
+     0      7   0.0042    0.9 -0.0145 0.0228  False
+     0     14   0.0101 0.5961 -0.0083 0.0285  False
+     0     21   0.0116 0.4581 -0.0068   0.03  False
+     0     28   0.0127 0.3983 -0.0064 0.0318  False
+     3      7   0.0023    0.9 -0.0149 0.0195  False
+     3     14   0.0082 0.6998 -0.0087 0.0251  False
+     3     21   0.0097 0.5529 -0.0072 0.0267  False
+     3     28   0.0108 0.4927 -0.0068 0.0285  False
+     7     14   0.0059    0.9  -0.012 0.0239  False
+     7     21   0.0075 0.8176 -0.0105 0.0254  False
+     7     28   0.0085 0.7487 -0.0101 0.0272  False
+    14     21   0.0015    0.9 -0.0162 0.0192  False
+    14     28   0.0026    0.9 -0.0158  0.021  False
+    21     28   0.0011    0.9 -0.0173 0.0195  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0063    0.9 -0.0119 0.0245  False
-     0      7   0.0076 0.7717 -0.0096 0.0249  False
-     0     14   0.0116 0.3364  -0.005 0.0282  False
-     0     21   0.0165 0.1297 -0.0025 0.0354  False
-     0     28   0.0158 0.1219 -0.0022 0.0338  False
-     3      7   0.0013    0.9 -0.0172 0.0198  False
-     3     14   0.0053    0.9 -0.0126 0.0231  False
-     3     21   0.0101 0.6691   -0.01 0.0302  False
-     3     28   0.0095 0.6863 -0.0097 0.0287  False
-     7     14    0.004    0.9 -0.0129 0.0209  False
-     7     21   0.0088 0.7453 -0.0104 0.0281  False
-     7     28   0.0082 0.7655 -0.0101 0.0264  False
-    14     21   0.0048    0.9 -0.0138 0.0235  False
-    14     28   0.0042    0.9 -0.0135 0.0218  False
-    21     28  -0.0007    0.9 -0.0206 0.0192  False
+     0      3   0.0129 0.4617 -0.0076 0.0334  False
+     0      7   0.0081 0.7996 -0.0109  0.027  False
+     0     14   0.0128 0.3272 -0.0054  0.031  False
+     0     21   0.0223 0.0283  0.0015 0.0431   True
+     0     28   0.0187 0.0759 -0.0011 0.0384  False
+     3      7  -0.0048    0.9 -0.0257  0.016  False
+     3     14  -0.0001    0.9 -0.0202 0.0201  False
+     3     21   0.0094 0.8133 -0.0131 0.0319  False
+     3     28   0.0058    0.9 -0.0158 0.0273  False
+     7     14   0.0048    0.9 -0.0138 0.0233  False
+     7     21   0.0142 0.3803 -0.0069 0.0353  False
+     7     28   0.0106 0.6281 -0.0095 0.0307  False
+    14     21   0.0095 0.7377  -0.011 0.0299  False
+    14     28   0.0058    0.9 -0.0135 0.0252  False
+    21     28  -0.0036    0.9 -0.0255 0.0182  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.06079431]	No
-Stroke	Sham	14	[0.0154583]	Yes
-Stroke	Sham	21	[0.02590135]	Yes
-Stroke	Sham	28	[0.05578221]	No
-Stroke	Sham	7	[0.26235955]	No
-Stroke	Sham	0	[0.17429923]	No
+Stroke	Sham	3	[0.0220704]	Yes
+Stroke	Sham	14	[0.23305934]	No
+Stroke	Sham	21	[0.02769003]	Yes
+Stroke	Sham	28	[0.05972109]	No
+Stroke	Sham	7	[0.09566846]	No
+Stroke	Sham	0	[0.28370945]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_SSp_ll-SSp_ll_cut_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_CC_SSp_ll-SSp_ll_cut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0038
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 4.114 0.000  0.001  0.002
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      361          Method:                  REML  
+No. Groups:            2            Scale:                   0.0019
+Min. group size:       156          Log-Likelihood:          inf   
+Max. group size:       205          Converged:               Yes   
+Mean group size:       180.5                                       
+-------------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
+-------------------------------------------------------------------
+Intercept        0.000 86272.201 0.000 1.000 -169090.408 169090.408
+merged_timepoint 0.001     0.000 6.104 0.000       0.001      0.002
+Group Var        0.000                                             
+===================================================================
 
 Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05 
-====================================================
-group1 group2 meandiff p-adj   lower   upper  reject
-----------------------------------------------------
-     0      3  -0.0553 0.0037 -0.0983 -0.0123   True
-     0      7   0.0225 0.6855 -0.0229  0.0679  False
-     0     14   0.0217  0.704 -0.0231  0.0665  False
-     0     21   0.0121    0.9 -0.0327  0.0569  False
-     0     28   0.0189 0.8309 -0.0276  0.0654  False
-     3      7   0.0778  0.001  0.0356    0.12   True
-     3     14    0.077  0.001  0.0354  0.1185   True
-     3     21   0.0674  0.001  0.0258  0.1089   True
-     3     28   0.0742  0.001  0.0308  0.1176   True
-     7     14  -0.0008    0.9 -0.0449  0.0432  False
-     7     21  -0.0104    0.9 -0.0545  0.0336  False
-     7     28  -0.0036    0.9 -0.0494  0.0422  False
-    14     21  -0.0096    0.9  -0.053  0.0338  False
-    14     28  -0.0027    0.9 -0.0479  0.0424  False
-    21     28   0.0069    0.9 -0.0383   0.052  False
-----------------------------------------------------
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   -0.034  0.016 -0.0639 -0.004   True
+     0      7   0.0116 0.8963   -0.02 0.0432  False
+     0     14   0.0279 0.1087 -0.0033  0.059  False
+     0     21   0.0263 0.1515 -0.0049 0.0575  False
+     0     28   0.0243 0.2592  -0.008 0.0567  False
+     3      7   0.0456  0.001  0.0165 0.0747   True
+     3     14   0.0618  0.001  0.0332 0.0905   True
+     3     21   0.0603  0.001  0.0316 0.0889   True
+     3     28   0.0583  0.001  0.0284 0.0882   True
+     7     14   0.0163 0.6211 -0.0141 0.0466  False
+     7     21   0.0147 0.7065 -0.0157 0.0451  False
+     7     28   0.0127   0.84 -0.0189 0.0443  False
+    14     21  -0.0016    0.9 -0.0315 0.0284  False
+    14     28  -0.0035    0.9 -0.0347 0.0276  False
+    21     28   -0.002    0.9 -0.0331 0.0292  False
+---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0225 0.6472  -0.021  0.066  False
-     0      7   0.0193 0.7305  -0.022 0.0605  False
-     0     14   0.0177 0.7649 -0.0219 0.0573  False
-     0     21   0.0436 0.0675 -0.0018 0.0889  False
-     0     28   0.0315 0.2865 -0.0115 0.0745  False
-     3      7  -0.0032    0.9 -0.0474 0.0409  False
-     3     14  -0.0048    0.9 -0.0475 0.0378  False
-     3     21    0.021 0.7778  -0.027  0.069  False
-     3     28    0.009    0.9 -0.0369 0.0548  False
-     7     14  -0.0016    0.9 -0.0419 0.0387  False
-     7     21   0.0243 0.6291 -0.0217 0.0702  False
-     7     28   0.0122    0.9 -0.0315 0.0559  False
-    14     21   0.0259 0.5409 -0.0186 0.0704  False
-    14     28   0.0138    0.9 -0.0283 0.0559  False
-    21     28  -0.0121    0.9 -0.0596 0.0354  False
+     0      3   0.0057    0.9 -0.0286 0.0401  False
+     0      7   0.0144 0.7517 -0.0173 0.0462  False
+     0     14   0.0157 0.6522 -0.0148 0.0462  False
+     0     21   0.0368 0.0319   0.002 0.0717   True
+     0     28   0.0284  0.137 -0.0047 0.0615  False
+     3      7   0.0087    0.9 -0.0262 0.0436  False
+     3     14   0.0099    0.9 -0.0238 0.0437  False
+     3     21   0.0311 0.1709 -0.0067 0.0689  False
+     3     28   0.0227 0.4626 -0.0134 0.0588  False
+     7     14   0.0013    0.9 -0.0298 0.0323  False
+     7     21   0.0224 0.4517  -0.013 0.0578  False
+     7     28    0.014 0.8142 -0.0196 0.0476  False
+    14     21   0.0212 0.4798 -0.0131 0.0554  False
+    14     28   0.0127  0.853 -0.0197 0.0452  False
+    21     28  -0.0084    0.9  -0.045 0.0282  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[4.12537157e-05]	Yes
-Stroke	Sham	14	[0.11488127]	No
-Stroke	Sham	21	[0.3770404]	No
-Stroke	Sham	28	[0.85265415]	No
-Stroke	Sham	7	[0.20484003]	No
-Stroke	Sham	0	[0.37406263]	No
+Stroke	Sham	3	[0.00177383]	Yes
+Stroke	Sham	14	[0.08382831]	No
+Stroke	Sham	21	[0.63103876]	No
+Stroke	Sham	28	[0.98504571]	No
+Stroke	Sham	7	[0.87924131]	No
+Stroke	Sham	0	[0.69023119]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_SSp_ll-SSp_ll_log.txt

@@ -1,18 +1,18 @@
 Model Name: fa_CC_SSp_ll-SSp_ll
           Mixed Linear Model Regression Results
 ==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0009
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   361      Method:              REML    
+No. Groups:         2        Scale:               0.0007  
+Min. group size:    156      Log-Likelihood:      792.5402
+Max. group size:    205      Converged:           Yes     
+Mean group size:    180.5                                 
 ----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
 ----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 5.585 0.000  0.001  0.001
-Group Var         0.000                                   
+Intercept        0.289    0.005 63.724 0.000  0.280  0.298
+merged_timepoint 0.001    0.000  6.710 0.000  0.001  0.001
+Group Var        0.000    0.002                           
 ==========================================================
 
 Posthoc Analysis for Stroke:
@@ -20,48 +20,48 @@ Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0179 0.1873   -0.04 0.0042  False
-     0      7   0.0144 0.4856  -0.009 0.0377  False
-     0     14   0.0116 0.6749 -0.0115 0.0346  False
-     0     21   0.0125 0.6052 -0.0105 0.0355  False
-     0     28   0.0222 0.0848 -0.0017 0.0461  False
-     3      7   0.0323  0.001  0.0106  0.054   True
-     3     14   0.0294 0.0014  0.0081 0.0508   True
-     3     21   0.0304  0.001  0.0091 0.0518   True
-     3     28   0.0401  0.001  0.0178 0.0624   True
-     7     14  -0.0028    0.9 -0.0255 0.0198  False
-     7     21  -0.0019    0.9 -0.0245 0.0208  False
-     7     28   0.0078    0.9 -0.0157 0.0314  False
-    14     21    0.001    0.9 -0.0213 0.0233  False
-    14     28   0.0107  0.745 -0.0125 0.0339  False
-    21     28   0.0097 0.8141 -0.0135 0.0329  False
+     0      3  -0.0147 0.1797 -0.0328 0.0033  False
+     0      7   0.0063    0.9 -0.0127 0.0254  False
+     0     14   0.0159  0.151 -0.0029 0.0346  False
+     0     21    0.018 0.0685 -0.0008 0.0368  False
+     0     28   0.0188 0.0648 -0.0007 0.0383  False
+     3      7    0.021 0.0089  0.0035 0.0386   True
+     3     14   0.0306  0.001  0.0133 0.0479   True
+     3     21   0.0327  0.001  0.0155   0.05   True
+     3     28   0.0336  0.001  0.0155 0.0516   True
+     7     14   0.0095 0.6438 -0.0088 0.0279  False
+     7     21   0.0117 0.4456 -0.0066   0.03  False
+     7     28   0.0125 0.4119 -0.0065 0.0316  False
+    14     21   0.0022    0.9 -0.0159 0.0202  False
+    14     28    0.003    0.9 -0.0158 0.0218  False
+    21     28   0.0008    0.9  -0.018 0.0196  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0089   0.74 -0.0104 0.0281  False
-     0      7   0.0046    0.9 -0.0137 0.0228  False
-     0     14   0.0114 0.4234 -0.0061 0.0288  False
-     0     21   0.0264 0.0028  0.0064 0.0464   True
-     0     28   0.0173 0.0949 -0.0016 0.0363  False
-     3      7  -0.0043    0.9 -0.0238 0.0152  False
-     3     14   0.0025    0.9 -0.0163 0.0213  False
-     3     21   0.0175 0.1672 -0.0037 0.0387  False
-     3     28   0.0085 0.8097 -0.0118 0.0287  False
-     7     14   0.0068 0.8703  -0.011 0.0246  False
-     7     21   0.0218 0.0269  0.0015 0.0421   True
-     7     28   0.0128 0.3996 -0.0065 0.0321  False
-    14     21    0.015 0.2396 -0.0046 0.0347  False
-    14     28    0.006    0.9 -0.0126 0.0246  False
-    21     28  -0.0091 0.7889   -0.03 0.0119  False
+     0      3   0.0114 0.5654 -0.0087 0.0314  False
+     0      7   0.0053    0.9 -0.0132 0.0238  False
+     0     14   0.0141  0.206 -0.0037 0.0319  False
+     0     21   0.0276 0.0019  0.0072 0.0479   True
+     0     28     0.02 0.0376  0.0007 0.0393   True
+     3      7  -0.0061    0.9 -0.0264 0.0143  False
+     3     14   0.0027    0.9  -0.017 0.0224  False
+     3     21   0.0162 0.2806 -0.0058 0.0382  False
+     3     28   0.0086  0.825 -0.0124 0.0297  False
+     7     14   0.0088 0.6992 -0.0093 0.0269  False
+     7     21   0.0223 0.0261  0.0017 0.0429   True
+     7     28   0.0147 0.2599 -0.0049 0.0343  False
+    14     21   0.0135 0.3774 -0.0065 0.0335  False
+    14     28   0.0059    0.9  -0.013 0.0248  False
+    21     28  -0.0076    0.9 -0.0289 0.0138  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[5.9133252e-06]	Yes
-Stroke	Sham	14	[0.25567023]	No
-Stroke	Sham	21	[0.01643561]	Yes
-Stroke	Sham	28	[0.63851444]	No
-Stroke	Sham	7	[0.77161845]	No
-Stroke	Sham	0	[0.40988323]	No
+Stroke	Sham	3	[0.00030632]	Yes
+Stroke	Sham	14	[0.89015616]	No
+Stroke	Sham	21	[0.12835535]	No
+Stroke	Sham	28	[0.53484471]	No
+Stroke	Sham	7	[0.77924558]	No
+Stroke	Sham	0	[0.59850575]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_SSp_ul-SSp_ul_cut_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_CC_SSp_ul-SSp_ul_cut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0022
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 4.422 0.000  0.001  0.002
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      361          Method:                  REML  
+No. Groups:            2            Scale:                   0.0011
+Min. group size:       156          Log-Likelihood:          inf   
+Max. group size:       205          Converged:               Yes   
+Mean group size:       180.5                                       
+-------------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
+-------------------------------------------------------------------
+Intercept        0.000 64833.468 0.000 1.000 -127071.263 127071.263
+merged_timepoint 0.001     0.000 6.758 0.000       0.001      0.002
+Group Var        0.000                                             
+===================================================================
 
 Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05 
-====================================================
-group1 group2 meandiff p-adj   lower   upper  reject
-----------------------------------------------------
-     0      3  -0.0341 0.0306 -0.0662 -0.0019   True
-     0      7   0.0229 0.3808  -0.011  0.0568  False
-     0     14   0.0236 0.3308 -0.0099   0.057  False
-     0     21   0.0126 0.8821 -0.0209  0.0461  False
-     0     28   0.0192 0.5902 -0.0155   0.054  False
-     3      7    0.057  0.001  0.0254  0.0885   True
-     3     14   0.0576  0.001  0.0266  0.0887   True
-     3     21   0.0467  0.001  0.0156  0.0777   True
-     3     28   0.0533  0.001  0.0209  0.0857   True
-     7     14   0.0007    0.9 -0.0323  0.0336  False
-     7     21  -0.0103    0.9 -0.0432  0.0226  False
-     7     28  -0.0037    0.9 -0.0379  0.0305  False
-    14     21   -0.011    0.9 -0.0434  0.0215  False
-    14     28  -0.0043    0.9 -0.0381  0.0294  False
-    21     28   0.0066    0.9 -0.0271  0.0404  False
-----------------------------------------------------
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0193 0.1343 -0.0416 0.0031  False
+     0      7   0.0111 0.7289 -0.0125 0.0346  False
+     0     14   0.0273 0.0112   0.004 0.0506   True
+     0     21   0.0255 0.0224  0.0022 0.0488   True
+     0     28   0.0223  0.089 -0.0019 0.0464  False
+     3      7   0.0303 0.0012  0.0086 0.0521   True
+     3     14   0.0466  0.001  0.0252  0.068   True
+     3     21   0.0448  0.001  0.0234 0.0662   True
+     3     28   0.0415  0.001  0.0192 0.0639   True
+     7     14   0.0162 0.3128 -0.0064 0.0389  False
+     7     21   0.0144 0.4494 -0.0082 0.0371  False
+     7     28   0.0112 0.7195 -0.0124 0.0348  False
+    14     21  -0.0018    0.9 -0.0241 0.0205  False
+    14     28   -0.005    0.9 -0.0283 0.0182  False
+    21     28  -0.0032    0.9 -0.0265   0.02  False
+---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0102    0.9 -0.0237 0.0441  False
-     0      7   0.0115    0.9 -0.0206 0.0436  False
-     0     14   0.0157 0.6591 -0.0151 0.0466  False
-     0     21   0.0294 0.1604 -0.0059 0.0647  False
-     0     28   0.0262 0.2177 -0.0073 0.0597  False
-     3      7   0.0013    0.9 -0.0331 0.0357  False
-     3     14   0.0055    0.9 -0.0277 0.0387  False
-     3     21   0.0192 0.6522 -0.0181 0.0566  False
-     3     28    0.016 0.7611 -0.0197 0.0517  False
-     7     14   0.0042    0.9 -0.0272 0.0356  False
-     7     21   0.0179 0.6752 -0.0179 0.0537  False
-     7     28   0.0147 0.7886 -0.0193 0.0487  False
-    14     21   0.0137 0.8487 -0.0209 0.0483  False
-    14     28   0.0105    0.9 -0.0223 0.0433  False
-    21     28  -0.0032    0.9 -0.0402 0.0338  False
+     0      3     -0.0    0.9 -0.0266 0.0265  False
+     0      7   0.0099 0.8326 -0.0146 0.0345  False
+     0     14    0.015 0.4449 -0.0085 0.0385  False
+     0     21   0.0268  0.052 -0.0001 0.0537  False
+     0     28    0.025   0.06 -0.0006 0.0505  False
+     3      7   0.0099 0.8917  -0.017 0.0369  False
+     3     14    0.015 0.5491  -0.011 0.0411  False
+     3     21   0.0268 0.0905 -0.0023  0.056  False
+     3     28    0.025 0.1074 -0.0029 0.0529  False
+     7     14   0.0051    0.9 -0.0189 0.0291  False
+     7     21   0.0169 0.4809 -0.0105 0.0442  False
+     7     28    0.015 0.5458 -0.0109  0.041  False
+    14     21   0.0118 0.7651 -0.0147 0.0382  False
+    14     28   0.0099 0.8453 -0.0151  0.035  False
+    21     28  -0.0018    0.9 -0.0301 0.0264  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.0009496]	Yes
-Stroke	Sham	14	[0.31518053]	No
-Stroke	Sham	21	[0.29987297]	No
-Stroke	Sham	28	[0.64353791]	No
-Stroke	Sham	7	[0.17292649]	No
-Stroke	Sham	0	[0.88228405]	No
+Stroke	Sham	3	[0.0202595]	Yes
+Stroke	Sham	14	[0.21253937]	No
+Stroke	Sham	21	[0.71126288]	No
+Stroke	Sham	28	[0.52889352]	No
+Stroke	Sham	7	[0.85134169]	No
+Stroke	Sham	0	[0.76580554]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_SSp_ul-SSp_ul_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_CC_SSp_ul-SSp_ul
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0015
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 4.394 0.000  0.001  0.001
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      361          Method:                  REML  
+No. Groups:            2            Scale:                   0.0009
+Min. group size:       156          Log-Likelihood:          inf   
+Max. group size:       205          Converged:               Yes   
+Mean group size:       180.5                                       
+-------------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
+-------------------------------------------------------------------
+Intercept        0.000 57615.617 0.000 1.000 -112924.534 112924.534
+merged_timepoint 0.001     0.000 6.809 0.000       0.001      0.001
+Group Var        0.000                                             
+===================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05 
 ====================================================
 group1 group2 meandiff p-adj   lower   upper  reject
 ----------------------------------------------------
-     0      3   -0.033 0.0067 -0.0598 -0.0061   True
-     0      7   0.0168 0.5259 -0.0116  0.0452  False
-     0     14   0.0157 0.5795 -0.0123  0.0436  False
-     0     21   0.0063    0.9 -0.0216  0.0343  False
-     0     28   0.0131 0.7571 -0.0159  0.0422  False
-     3      7   0.0498  0.001  0.0234  0.0762   True
-     3     14   0.0486  0.001  0.0227  0.0746   True
-     3     21   0.0393  0.001  0.0134  0.0653   True
-     3     28   0.0461  0.001   0.019  0.0732   True
-     7     14  -0.0011    0.9 -0.0287  0.0264  False
-     7     21  -0.0105 0.8758  -0.038  0.0171  False
-     7     28  -0.0037    0.9 -0.0323  0.0249  False
-    14     21  -0.0093    0.9 -0.0364  0.0178  False
-    14     28  -0.0025    0.9 -0.0307  0.0257  False
-    21     28   0.0068    0.9 -0.0214   0.035  False
+     0      3  -0.0233 0.0091 -0.0429 -0.0038   True
+     0      7    0.005    0.9 -0.0156  0.0256  False
+     0     14   0.0202 0.0515 -0.0001  0.0406  False
+     0     21   0.0203 0.0511 -0.0001  0.0406  False
+     0     28   0.0151 0.3152  -0.006  0.0361  False
+     3      7   0.0284  0.001  0.0094  0.0473   True
+     3     14   0.0436  0.001  0.0249  0.0623   True
+     3     21   0.0436  0.001  0.0249  0.0623   True
+     3     28   0.0384  0.001  0.0189  0.0579   True
+     7     14   0.0152 0.2367 -0.0046   0.035  False
+     7     21   0.0152 0.2355 -0.0046  0.0351  False
+     7     28     0.01 0.6984 -0.0105  0.0306  False
+    14     21      0.0    0.9 -0.0195  0.0195  False
+    14     28  -0.0052    0.9 -0.0255  0.0151  False
+    21     28  -0.0052    0.9 -0.0255  0.0151  False
 ----------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0062    0.9 -0.0214 0.0338  False
-     0      7   0.0059    0.9 -0.0203 0.0321  False
-     0     14   0.0108 0.7918 -0.0143 0.0359  False
-     0     21    0.027 0.0797 -0.0018 0.0557  False
-     0     28   0.0208 0.2415 -0.0064 0.0481  False
-     3      7  -0.0003    0.9 -0.0283 0.0278  False
-     3     14   0.0046    0.9 -0.0224 0.0317  False
-     3     21   0.0208 0.3648 -0.0097 0.0512  False
-     3     28   0.0146 0.6693 -0.0144 0.0437  False
-     7     14   0.0049    0.9 -0.0207 0.0305  False
-     7     21   0.0211  0.301 -0.0081 0.0502  False
-     7     28   0.0149 0.6126 -0.0128 0.0426  False
-    14     21   0.0162 0.5551  -0.012 0.0444  False
-    14     28     0.01 0.8813 -0.0167 0.0368  False
-    21     28  -0.0061    0.9 -0.0363  0.024  False
+     0      3   0.0012    0.9 -0.0224 0.0248  False
+     0      7   0.0061    0.9 -0.0157 0.0279  False
+     0     14   0.0119 0.5624  -0.009 0.0328  False
+     0     21   0.0272 0.0159  0.0033 0.0512   True
+     0     28    0.022 0.0634 -0.0007 0.0447  False
+     3      7   0.0049    0.9 -0.0191 0.0288  False
+     3     14   0.0107 0.7402 -0.0125 0.0338  False
+     3     21    0.026 0.0488  0.0001 0.0519   True
+     3     28   0.0208 0.1555  -0.004 0.0456  False
+     7     14   0.0058    0.9 -0.0155 0.0271  False
+     7     21   0.0211 0.1275 -0.0032 0.0454  False
+     7     28   0.0159 0.3536 -0.0072  0.039  False
+    14     21   0.0153 0.4191 -0.0082 0.0388  False
+    14     28   0.0101 0.7508 -0.0121 0.0324  False
+    21     28  -0.0052    0.9 -0.0303 0.0199  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.00017546]	Yes
-Stroke	Sham	14	[0.70248548]	No
-Stroke	Sham	21	[0.04725519]	Yes
-Stroke	Sham	28	[0.24881882]	No
-Stroke	Sham	7	[0.25775816]	No
-Stroke	Sham	0	[0.88983913]	No
+Stroke	Sham	3	[0.00402133]	Yes
+Stroke	Sham	14	[0.29021262]	No
+Stroke	Sham	21	[0.38390594]	No
+Stroke	Sham	28	[0.25740969]	No
+Stroke	Sham	7	[0.78618023]	No
+Stroke	Sham	0	[0.92388939]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CReT_MOp-TRN_contralesional_CCcut_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_CReT_MOp-TRN_contralesional_CCcut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0016
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.000    0.000 2.024 0.043  0.000  0.001
-Group Var         0.000                                   
-==========================================================
+              Mixed Linear Model Regression Results
+=================================================================
+Model:                 MixedLM     Dependent Variable:     Value 
+No. Observations:      361         Method:                 REML  
+No. Groups:            2           Scale:                  0.0007
+Min. group size:       156         Log-Likelihood:         inf   
+Max. group size:       205         Converged:              Yes   
+Mean group size:       180.5                                     
+-----------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|   [0.025     0.975] 
+-----------------------------------------------------------------
+Intercept        0.000 50275.672 0.000 1.000 -98538.506 98538.506
+merged_timepoint 0.000     0.000 2.673 0.008      0.000     0.001
+Group Var        0.000                                           
+=================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0157 0.5573 -0.0117  0.043  False
-     0      7   0.0217 0.2596 -0.0072 0.0506  False
-     0     14   0.0013    0.9 -0.0272 0.0297  False
-     0     21   0.0135 0.7189 -0.0149  0.042  False
-     0     28   0.0197 0.3955 -0.0099 0.0493  False
-     3      7    0.006    0.9 -0.0208 0.0329  False
-     3     14  -0.0144 0.6028 -0.0408  0.012  False
-     3     21  -0.0021    0.9 -0.0286 0.0243  False
-     3     28    0.004    0.9 -0.0236 0.0316  False
-     7     14  -0.0205 0.2908 -0.0485 0.0076  False
-     7     21  -0.0082    0.9 -0.0362 0.0198  False
-     7     28   -0.002    0.9 -0.0311 0.0271  False
-    14     21   0.0123 0.7689 -0.0153 0.0399  False
-    14     28   0.0185 0.4387 -0.0103 0.0472  False
-    21     28   0.0062    0.9 -0.0225 0.0349  False
+     0      3   0.0119 0.4884 -0.0075 0.0313  False
+     0      7    0.009 0.7765 -0.0115 0.0295  False
+     0     14   0.0017    0.9 -0.0184 0.0219  False
+     0     21    0.008 0.8489 -0.0122 0.0282  False
+     0     28   0.0137 0.4168 -0.0072 0.0347  False
+     3      7  -0.0029    0.9 -0.0218  0.016  False
+     3     14  -0.0102 0.5983 -0.0287 0.0084  False
+     3     21  -0.0039    0.9 -0.0225 0.0146  False
+     3     28   0.0018    0.9 -0.0176 0.0212  False
+     7     14  -0.0073 0.8933  -0.027 0.0124  False
+     7     21   -0.001    0.9 -0.0207 0.0187  False
+     7     28   0.0047    0.9 -0.0158 0.0252  False
+    14     21   0.0063    0.9 -0.0131 0.0257  False
+    14     28    0.012 0.5242 -0.0082 0.0322  False
+    21     28   0.0057    0.9 -0.0145 0.0259  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0134 0.7903 -0.0445 0.0177  False
-     0      7   0.0005    0.9 -0.0289   0.03  False
-     0     14   0.0046    0.9 -0.0237 0.0329  False
-     0     21   0.0077    0.9 -0.0246 0.0401  False
-     0     28   0.0139  0.753 -0.0168 0.0446  False
-     3      7   0.0139 0.7724 -0.0176 0.0455  False
-     3     14    0.018 0.5276 -0.0125 0.0484  False
-     3     21   0.0211 0.4833 -0.0132 0.0554  False
-     3     28   0.0273 0.1598 -0.0054   0.06  False
-     7     14    0.004    0.9 -0.0248 0.0328  False
-     7     21   0.0072    0.9 -0.0256   0.04  False
-     7     28   0.0134 0.7937 -0.0178 0.0446  False
-    14     21   0.0032    0.9 -0.0286 0.0349  False
-    14     28   0.0093    0.9 -0.0207 0.0394  False
-    21     28   0.0062    0.9 -0.0278 0.0401  False
+     0      3    0.005    0.9 -0.0131 0.0231  False
+     0      7   0.0104 0.4689 -0.0063 0.0271  False
+     0     14   0.0134 0.1559 -0.0026 0.0295  False
+     0     21   0.0173 0.0786 -0.0011 0.0356  False
+     0     28    0.018 0.0379  0.0006 0.0354   True
+     3      7   0.0054    0.9 -0.0129 0.0238  False
+     3     14   0.0085  0.715 -0.0093 0.0262  False
+     3     21   0.0123 0.4811 -0.0076 0.0321  False
+     3     28    0.013 0.3597  -0.006  0.032  False
+     7     14    0.003    0.9 -0.0133 0.0194  False
+     7     21   0.0068 0.8955 -0.0118 0.0254  False
+     7     28   0.0076 0.7925 -0.0101 0.0253  False
+    14     21   0.0038    0.9 -0.0142 0.0218  False
+    14     28   0.0046    0.9 -0.0125 0.0216  False
+    21     28   0.0008    0.9 -0.0185   0.02  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.07687143]	No
-Stroke	Sham	14	[0.2089668]	No
-Stroke	Sham	21	[0.66801243]	No
-Stroke	Sham	28	[0.72922903]	No
-Stroke	Sham	7	[0.12809899]	No
-Stroke	Sham	0	[0.52040578]	No
+Stroke	Sham	3	[0.21087263]	No
+Stroke	Sham	14	[0.17142853]	No
+Stroke	Sham	21	[0.27841899]	No
+Stroke	Sham	28	[0.58394666]	No
+Stroke	Sham	7	[0.91856711]	No
+Stroke	Sham	0	[0.89396042]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CRuT_MOp-RN_contralesional_mirrored_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_CRuT_MOp-RN_contralesional_mirrored
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0012
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.000    0.000 2.427 0.015  0.000  0.001
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      361          Method:                  REML  
+No. Groups:            2            Scale:                   0.0007
+Min. group size:       156          Log-Likelihood:          inf   
+Max. group size:       205          Converged:               Yes   
+Mean group size:       180.5                                       
+-------------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
+-------------------------------------------------------------------
+Intercept        0.000 52047.995 0.000 1.000 -102012.196 102012.196
+merged_timepoint 0.000     0.000 2.751 0.006       0.000      0.001
+Group Var        0.000                                             
+===================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0094    0.9 -0.0164 0.0352  False
-     0      7   0.0184 0.3781 -0.0088 0.0456  False
-     0     14   0.0045    0.9 -0.0224 0.0313  False
-     0     21   0.0169 0.4587 -0.0099 0.0438  False
-     0     28    0.015 0.6156 -0.0129 0.0429  False
-     3      7    0.009    0.9 -0.0163 0.0343  False
-     3     14  -0.0049    0.9 -0.0298   0.02  False
-     3     21   0.0075    0.9 -0.0174 0.0324  False
-     3     28   0.0056    0.9 -0.0204 0.0316  False
-     7     14  -0.0139 0.6329 -0.0403 0.0125  False
-     7     21  -0.0015    0.9 -0.0279 0.0249  False
-     7     28  -0.0034    0.9 -0.0309  0.024  False
-    14     21   0.0125 0.7128 -0.0135 0.0385  False
-    14     28   0.0105 0.8628 -0.0166 0.0376  False
-    21     28   -0.002    0.9  -0.029 0.0251  False
+     0      3   0.0019    0.9 -0.0184 0.0222  False
+     0      7   0.0071    0.9 -0.0143 0.0285  False
+     0     14   0.0027    0.9 -0.0184 0.0239  False
+     0     21   0.0082 0.8657  -0.013 0.0293  False
+     0     28   0.0074    0.9 -0.0146 0.0293  False
+     3      7   0.0052    0.9 -0.0146  0.025  False
+     3     14   0.0009    0.9 -0.0186 0.0203  False
+     3     21   0.0063    0.9 -0.0131 0.0257  False
+     3     28   0.0055    0.9 -0.0148 0.0258  False
+     7     14  -0.0043    0.9  -0.025 0.0163  False
+     7     21   0.0011    0.9 -0.0195 0.0217  False
+     7     28   0.0003    0.9 -0.0211 0.0217  False
+    14     21   0.0054    0.9 -0.0149 0.0257  False
+    14     28   0.0046    0.9 -0.0165 0.0258  False
+    21     28  -0.0008    0.9 -0.0219 0.0203  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0053    0.9 -0.0308 0.0201  False
-     0      7   0.0099  0.827 -0.0143  0.034  False
-     0     14   0.0137  0.528 -0.0095 0.0369  False
-     0     21   0.0148 0.5816 -0.0117 0.0413  False
-     0     28   0.0133 0.6261 -0.0118 0.0385  False
-     3      7   0.0152 0.5302 -0.0106 0.0411  False
-     3     14    0.019 0.2441 -0.0059  0.044  False
-     3     21   0.0201 0.3097  -0.008 0.0482  False
-     3     28   0.0187 0.3405 -0.0081 0.0455  False
-     7     14   0.0038    0.9 -0.0198 0.0274  False
-     7     21   0.0049    0.9  -0.022 0.0318  False
-     7     28   0.0035    0.9 -0.0221  0.029  False
-    14     21   0.0011    0.9 -0.0249 0.0272  False
-    14     28  -0.0003    0.9  -0.025 0.0243  False
-    21     28  -0.0014    0.9 -0.0293 0.0264  False
+     0      3   0.0093  0.676 -0.0093  0.028  False
+     0      7   0.0129 0.2672 -0.0044 0.0301  False
+     0     14   0.0154 0.0844 -0.0012  0.032  False
+     0     21   0.0193 0.0441  0.0003 0.0382   True
+     0     28   0.0188 0.0344  0.0008 0.0368   True
+     3      7   0.0035    0.9 -0.0154 0.0225  False
+     3     14   0.0061    0.9 -0.0123 0.0244  False
+     3     21   0.0099  0.703 -0.0106 0.0304  False
+     3     28   0.0095 0.7031 -0.0101 0.0291  False
+     7     14   0.0026    0.9 -0.0143 0.0194  False
+     7     21   0.0064    0.9 -0.0128 0.0256  False
+     7     28    0.006    0.9 -0.0123 0.0242  False
+    14     21   0.0038    0.9 -0.0148 0.0225  False
+    14     28   0.0034    0.9 -0.0142  0.021  False
+    21     28  -0.0004    0.9 -0.0203 0.0194  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.37253566]	No
-Stroke	Sham	14	[0.07325188]	No
-Stroke	Sham	21	[0.71458073]	No
-Stroke	Sham	28	[0.62133784]	No
-Stroke	Sham	7	[0.64372852]	No
-Stroke	Sham	0	[0.65223641]	No
+Stroke	Sham	3	[0.53424895]	No
+Stroke	Sham	14	[0.25117752]	No
+Stroke	Sham	21	[0.36509277]	No
+Stroke	Sham	28	[0.25021475]	No
+Stroke	Sham	7	[0.68276012]	No
+Stroke	Sham	0	[0.58845064]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CRuT_MOp-RN_ipsilesional_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CRuT_MOp-RN_ipsilesional
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      361          Method:                  REML  
+No. Groups:            2            Scale:                   0.0010
+Min. group size:       156          Log-Likelihood:          inf   
+Max. group size:       205          Converged:               Yes   
+Mean group size:       180.5                                       
+-------------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
+-------------------------------------------------------------------
+Intercept        0.000 63074.601 0.000 1.000 -123623.946 123623.946
+merged_timepoint 0.000     0.000 2.078 0.038       0.000      0.001
+Group Var        0.000                                             
+===================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0154 0.4128 -0.0081 0.0389  False
+     0      7   -0.007    0.9 -0.0318 0.0178  False
+     0     14  -0.0041    0.9 -0.0286 0.0203  False
+     0     21   0.0015    0.9  -0.023 0.0259  False
+     0     28   0.0155 0.4947 -0.0099 0.0409  False
+     3      7  -0.0225 0.0571 -0.0453 0.0004  False
+     3     14  -0.0196 0.1279 -0.0421 0.0029  False
+     3     21   -0.014  0.478 -0.0365 0.0085  False
+     3     28   0.0001    0.9 -0.0234 0.0236  False
+     7     14   0.0029    0.9 -0.0209 0.0268  False
+     7     21   0.0085    0.9 -0.0153 0.0324  False
+     7     28   0.0226 0.0978 -0.0022 0.0473  False
+    14     21   0.0056    0.9 -0.0179 0.0291  False
+    14     28   0.0196 0.1944 -0.0048 0.0441  False
+    21     28    0.014 0.5564 -0.0104 0.0385  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0126 0.6155 -0.0109  0.036  False
+     0      7   0.0096 0.7697  -0.012 0.0312  False
+     0     14   0.0173 0.1588 -0.0034 0.0381  False
+     0     21   0.0188 0.2066  -0.005 0.0426  False
+     0     28     0.02 0.1135 -0.0025 0.0425  False
+     3      7   -0.003    0.9 -0.0267 0.0208  False
+     3     14   0.0048    0.9 -0.0182 0.0277  False
+     3     21   0.0062    0.9 -0.0195 0.0319  False
+     3     28   0.0074    0.9 -0.0172  0.032  False
+     7     14   0.0078 0.8953 -0.0134 0.0289  False
+     7     21   0.0092 0.8694 -0.0149 0.0333  False
+     7     28   0.0104 0.7501 -0.0125 0.0333  False
+    14     21   0.0015    0.9 -0.0219 0.0248  False
+    14     28   0.0027    0.9 -0.0194 0.0247  False
+    21     28   0.0012    0.9 -0.0237 0.0261  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.57553482]	No
+Stroke	Sham	14	[0.02866569]	Yes
+Stroke	Sham	21	[0.12030472]	No
+Stroke	Sham	28	[0.81295326]	No
+Stroke	Sham	7	[0.06883907]	No
+Stroke	Sham	0	[0.69813404]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CST_MOp-int-py_contralesional_CCasROA_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_CST_MOp-int-py_contralesional_CCasROA
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0026
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 2.279 0.023  0.000  0.001
-Group Var         0.000                                   
-==========================================================
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM  Dependent Variable:  Value   
+No. Observations:    361      Method:              REML    
+No. Groups:          2        Scale:               0.0007  
+Min. group size:     156      Log-Likelihood:      784.0121
+Max. group size:     205      Converged:           No      
+Mean group size:     180.5                                 
+-----------------------------------------------------------
+                 Coef. Std.Err.    z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept        0.390    0.002 175.073 0.000  0.385  0.394
+merged_timepoint 0.000    0.000   2.968 0.003  0.000  0.001
+Group Var        0.000                                     
+===========================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0092    0.9 -0.0255  0.044  False
-     0      7   0.0275 0.2633 -0.0092 0.0642  False
-     0     14   0.0085    0.9 -0.0277 0.0447  False
-     0     21   0.0232 0.4414  -0.013 0.0594  False
-     0     28   0.0304 0.1891 -0.0072 0.0679  False
-     3      7   0.0183 0.6208 -0.0159 0.0524  False
-     3     14  -0.0008    0.9 -0.0344 0.0328  False
-     3     21    0.014 0.8173 -0.0196 0.0475  False
-     3     28   0.0211 0.5102  -0.014 0.0562  False
-     7     14   -0.019 0.6215 -0.0546 0.0166  False
-     7     21  -0.0043    0.9 -0.0399 0.0313  False
-     7     28   0.0029    0.9 -0.0342 0.0399  False
-    14     21   0.0147 0.8102 -0.0203 0.0498  False
-    14     28   0.0219 0.5143 -0.0146 0.0584  False
-    21     28   0.0072    0.9 -0.0294 0.0437  False
+     0      3   0.0107 0.6144 -0.0092 0.0307  False
+     0      7   0.0119 0.5695 -0.0091  0.033  False
+     0     14    0.003    0.9 -0.0178 0.0237  False
+     0     21   0.0105 0.6693 -0.0103 0.0313  False
+     0     28   0.0185 0.1377  -0.003   0.04  False
+     3      7   0.0012    0.9 -0.0182 0.0206  False
+     3     14  -0.0078 0.8316 -0.0269 0.0113  False
+     3     21  -0.0003    0.9 -0.0193 0.0188  False
+     3     28   0.0078  0.862 -0.0122 0.0277  False
+     7     14  -0.0089 0.7746 -0.0292 0.0113  False
+     7     21  -0.0014    0.9 -0.0217 0.0188  False
+     7     28   0.0066    0.9 -0.0145 0.0276  False
+    14     21   0.0075  0.881 -0.0124 0.0275  False
+    14     28   0.0155 0.2652 -0.0052 0.0363  False
+    21     28    0.008 0.8672 -0.0128 0.0288  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0233 0.5609 -0.0643 0.0176  False
-     0      7  -0.0155 0.8431 -0.0543 0.0233  False
-     0     14  -0.0028    0.9 -0.0401 0.0345  False
-     0     21  -0.0091    0.9 -0.0518 0.0335  False
-     0     28   0.0042    0.9 -0.0363 0.0446  False
-     3      7   0.0078    0.9 -0.0337 0.0494  False
-     3     14   0.0205 0.6568 -0.0196 0.0607  False
-     3     21   0.0142    0.9  -0.031 0.0594  False
-     3     28   0.0275 0.4447 -0.0156 0.0706  False
-     7     14   0.0127    0.9 -0.0253 0.0506  False
-     7     21   0.0064    0.9 -0.0369 0.0496  False
-     7     28   0.0196 0.7121 -0.0214 0.0607  False
-    14     21  -0.0063    0.9 -0.0482 0.0355  False
-    14     28    0.007    0.9 -0.0327 0.0466  False
-    21     28   0.0133    0.9 -0.0314  0.058  False
+     0      3   0.0071 0.8897  -0.012 0.0262  False
+     0      7   0.0126 0.3131  -0.005 0.0302  False
+     0     14   0.0127 0.2592 -0.0042 0.0297  False
+     0     21   0.0143 0.2799 -0.0051 0.0337  False
+     0     28    0.018 0.0593 -0.0004 0.0364  False
+     3      7   0.0055    0.9 -0.0139 0.0249  False
+     3     14   0.0056    0.9 -0.0131 0.0244  False
+     3     21   0.0072    0.9 -0.0138 0.0282  False
+     3     28   0.0109 0.6039 -0.0092  0.031  False
+     7     14   0.0001    0.9 -0.0171 0.0174  False
+     7     21   0.0017    0.9  -0.018 0.0213  False
+     7     28   0.0054    0.9 -0.0133 0.0241  False
+    14     21   0.0016    0.9 -0.0175 0.0206  False
+    14     28   0.0053    0.9 -0.0127 0.0233  False
+    21     28   0.0037    0.9 -0.0166  0.024  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.50250857]	No
-Stroke	Sham	14	[0.38715447]	No
-Stroke	Sham	21	[0.34627014]	No
-Stroke	Sham	28	[0.73519512]	No
-Stroke	Sham	7	[0.11956435]	No
-Stroke	Sham	0	[0.14252137]	No
+Stroke	Sham	3	[0.50921848]	No
+Stroke	Sham	14	[0.24307494]	No
+Stroke	Sham	21	[0.67233741]	No
+Stroke	Sham	28	[0.88012581]	No
+Stroke	Sham	7	[0.97750292]	No
+Stroke	Sham	0	[0.94114891]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CST_MOp-int-py_contralesional_CCcut_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_CST_MOp-int-py_contralesional_CCcut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0026
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 2.119 0.034  0.000  0.001
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      361          Method:                  REML  
+No. Groups:            2            Scale:                   0.0007
+Min. group size:       156          Log-Likelihood:          inf   
+Max. group size:       205          Converged:               Yes   
+Mean group size:       180.5                                       
+-------------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
+-------------------------------------------------------------------
+Intercept        0.000 52216.842 0.000 1.000 -102343.130 102343.130
+merged_timepoint 0.000     0.000 2.816 0.005       0.000      0.001
+Group Var        0.000                                             
+===================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0099    0.9 -0.0247 0.0445  False
-     0      7   0.0286   0.22  -0.008 0.0652  False
-     0     14   0.0074    0.9 -0.0287 0.0435  False
-     0     21   0.0231 0.4435  -0.013 0.0591  False
-     0     28   0.0298 0.2025 -0.0076 0.0673  False
-     3      7   0.0187 0.5958 -0.0153 0.0527  False
-     3     14  -0.0025    0.9 -0.0359  0.031  False
-     3     21   0.0132 0.8528 -0.0203 0.0467  False
-     3     28   0.0199 0.5626  -0.015 0.0549  False
-     7     14  -0.0212 0.5183 -0.0567 0.0143  False
-     7     21  -0.0055    0.9  -0.041   0.03  False
-     7     28   0.0012    0.9 -0.0357 0.0381  False
-    14     21   0.0157 0.7638 -0.0193 0.0506  False
-    14     28   0.0224 0.4865  -0.014 0.0588  False
-    21     28   0.0067    0.9 -0.0296 0.0431  False
+     0      3   0.0108 0.6092 -0.0092 0.0309  False
+     0      7   0.0117 0.5921 -0.0095 0.0328  False
+     0     14    0.002    0.9 -0.0188 0.0228  False
+     0     21   0.0106  0.661 -0.0102 0.0315  False
+     0     28   0.0177  0.177 -0.0039 0.0393  False
+     3      7   0.0008    0.9 -0.0187 0.0203  False
+     3     14  -0.0088 0.7411  -0.028 0.0103  False
+     3     21  -0.0002    0.9 -0.0194 0.0189  False
+     3     28   0.0068    0.9 -0.0132 0.0269  False
+     7     14  -0.0097 0.7178   -0.03 0.0106  False
+     7     21   -0.001    0.9 -0.0213 0.0193  False
+     7     28    0.006    0.9 -0.0151 0.0271  False
+    14     21   0.0086 0.7909 -0.0114 0.0286  False
+    14     28   0.0157 0.2569 -0.0051 0.0365  False
+    21     28   0.0071    0.9 -0.0138 0.0279  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0223  0.595  -0.063 0.0184  False
-     0      7  -0.0134    0.9  -0.052 0.0252  False
-     0     14  -0.0022    0.9 -0.0392 0.0348  False
-     0     21  -0.0092    0.9 -0.0516 0.0332  False
-     0     28   0.0032    0.9  -0.037 0.0434  False
-     3      7   0.0089    0.9 -0.0324 0.0503  False
-     3     14   0.0201 0.6679 -0.0197   0.06  False
-     3     21   0.0131    0.9 -0.0317  0.058  False
-     3     28   0.0256 0.5166 -0.0173 0.0684  False
-     7     14   0.0112    0.9 -0.0265 0.0489  False
-     7     21   0.0042    0.9 -0.0388 0.0472  False
-     7     28   0.0166 0.8292 -0.0242 0.0575  False
-    14     21   -0.007    0.9 -0.0486 0.0346  False
-    14     28   0.0054    0.9  -0.034 0.0448  False
-    21     28   0.0124    0.9  -0.032 0.0569  False
+     0      3    0.008 0.8099 -0.0111 0.0271  False
+     0      7   0.0126 0.3113  -0.005 0.0303  False
+     0     14   0.0129 0.2451 -0.0041 0.0299  False
+     0     21   0.0139 0.3096 -0.0055 0.0333  False
+     0     28   0.0178 0.0644 -0.0006 0.0362  False
+     3      7   0.0046    0.9 -0.0148  0.024  False
+     3     14   0.0049    0.9 -0.0139 0.0237  False
+     3     21   0.0059    0.9 -0.0151 0.0269  False
+     3     28   0.0098 0.6961 -0.0103 0.0299  False
+     7     14   0.0003    0.9  -0.017 0.0176  False
+     7     21   0.0013    0.9 -0.0184  0.021  False
+     7     28   0.0052    0.9 -0.0135 0.0239  False
+    14     21    0.001    0.9 -0.0181 0.0201  False
+    14     28   0.0049    0.9 -0.0131 0.0229  False
+    21     28   0.0039    0.9 -0.0165 0.0243  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.47885735]	No
-Stroke	Sham	14	[0.35437657]	No
-Stroke	Sham	21	[0.2993808]	No
-Stroke	Sham	28	[0.65329697]	No
-Stroke	Sham	7	[0.11287096]	No
-Stroke	Sham	0	[0.16038521]	No
+Stroke	Sham	3	[0.4994195]	No
+Stroke	Sham	14	[0.23261618]	No
+Stroke	Sham	21	[0.82051893]	No
+Stroke	Sham	28	[0.84004261]	No
+Stroke	Sham	7	[0.93273516]	No
+Stroke	Sham	0	[0.83422462]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CST_MOp-int-py_contralesional_selfdrawnROA+CCcut_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_CST_MOp-int-py_contralesional_selfdrawnROA+CCcut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0026
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 2.134 0.033  0.000  0.001
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      361          Method:                  REML  
+No. Groups:            2            Scale:                   0.0007
+Min. group size:       156          Log-Likelihood:          inf   
+Max. group size:       205          Converged:               Yes   
+Mean group size:       180.5                                       
+-------------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
+-------------------------------------------------------------------
+Intercept        0.000 52590.299 0.000 1.000 -103075.092 103075.092
+merged_timepoint 0.000     0.000 2.888 0.004       0.000      0.001
+Group Var        0.000                                             
+===================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3     0.01    0.9 -0.0246 0.0446  False
-     0      7   0.0289 0.2077 -0.0076 0.0655  False
-     0     14   0.0066    0.9 -0.0294 0.0426  False
-     0     21   0.0234 0.4287 -0.0127 0.0594  False
-     0     28     0.03 0.1955 -0.0074 0.0674  False
-     3      7   0.0189  0.585 -0.0151 0.0529  False
-     3     14  -0.0034    0.9 -0.0368   0.03  False
-     3     21   0.0133 0.8453 -0.0201 0.0468  False
-     3     28     0.02 0.5588 -0.0149 0.0549  False
-     7     14  -0.0223 0.4621 -0.0578 0.0131  False
-     7     21  -0.0056    0.9  -0.041 0.0299  False
-     7     28   0.0011    0.9 -0.0358 0.0379  False
-    14     21   0.0167 0.7125 -0.0182 0.0517  False
-    14     28   0.0234 0.4369  -0.013 0.0597  False
-    21     28   0.0067    0.9 -0.0297  0.043  False
+     0      3     0.01 0.6861 -0.0102 0.0302  False
+     0      7   0.0112 0.6333 -0.0101 0.0325  False
+     0     14   0.0014    0.9 -0.0196 0.0224  False
+     0     21   0.0104 0.6907 -0.0107 0.0314  False
+     0     28   0.0176 0.1878 -0.0042 0.0394  False
+     3      7   0.0012    0.9 -0.0184 0.0209  False
+     3     14  -0.0086 0.7669  -0.028 0.0107  False
+     3     21   0.0003    0.9  -0.019 0.0197  False
+     3     28   0.0076 0.8789 -0.0126 0.0278  False
+     7     14  -0.0099 0.7094 -0.0304 0.0106  False
+     7     21  -0.0009    0.9 -0.0214 0.0196  False
+     7     28   0.0064    0.9 -0.0149 0.0277  False
+    14     21    0.009 0.7697 -0.0112 0.0292  False
+    14     28   0.0163 0.2299 -0.0047 0.0373  False
+    21     28   0.0073    0.9 -0.0137 0.0283  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0225 0.5836 -0.0631  0.018  False
-     0      7  -0.0132    0.9 -0.0516 0.0252  False
-     0     14  -0.0021    0.9  -0.039 0.0348  False
-     0     21  -0.0087    0.9 -0.0509 0.0335  False
-     0     28   0.0032    0.9 -0.0369 0.0432  False
-     3      7   0.0093    0.9 -0.0318 0.0505  False
-     3     14   0.0204 0.6524 -0.0193 0.0601  False
-     3     21   0.0138    0.9 -0.0309 0.0585  False
-     3     28   0.0257 0.5068  -0.017 0.0684  False
-     7     14   0.0111    0.9 -0.0265 0.0486  False
-     7     21   0.0045    0.9 -0.0383 0.0473  False
-     7     28   0.0164 0.8374 -0.0243  0.057  False
-    14     21  -0.0066    0.9  -0.048 0.0348  False
-    14     28   0.0053    0.9 -0.0339 0.0445  False
-    21     28   0.0119    0.9 -0.0324 0.0562  False
+     0      3   0.0078 0.8295 -0.0114  0.027  False
+     0      7   0.0126 0.3223 -0.0052 0.0303  False
+     0     14    0.013 0.2394  -0.004 0.0301  False
+     0     21   0.0147 0.2568 -0.0048 0.0342  False
+     0     28   0.0179  0.064 -0.0006 0.0364  False
+     3      7   0.0048    0.9 -0.0148 0.0243  False
+     3     14   0.0052    0.9 -0.0136 0.0241  False
+     3     21   0.0069    0.9 -0.0143  0.028  False
+     3     28   0.0101 0.6764 -0.0101 0.0303  False
+     7     14   0.0005    0.9 -0.0169 0.0178  False
+     7     21   0.0021    0.9 -0.0177 0.0219  False
+     7     28   0.0053    0.9 -0.0135 0.0241  False
+    14     21   0.0016    0.9 -0.0175 0.0208  False
+    14     28   0.0049    0.9 -0.0133  0.023  False
+    21     28   0.0032    0.9 -0.0172 0.0237  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.46924618]	No
-Stroke	Sham	14	[0.31570383]	No
-Stroke	Sham	21	[0.312058]	No
-Stroke	Sham	28	[0.64888988]	No
-Stroke	Sham	7	[0.10619164]	No
-Stroke	Sham	0	[0.16062947]	No
+Stroke	Sham	3	[0.51041366]	No
+Stroke	Sham	14	[0.2251182]	No
+Stroke	Sham	21	[0.77313202]	No
+Stroke	Sham	28	[0.79440998]	No
+Stroke	Sham	7	[0.90336161]	No
+Stroke	Sham	0	[0.7781168]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CST_MOp-int-py_ipsilesional_CCasROA_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_CST_MOp-int-py_ipsilesional_CCasROA
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0023
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 2.016 0.044  0.000  0.001
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      361          Method:                  REML  
+No. Groups:            2            Scale:                   0.0008
+Min. group size:       156          Log-Likelihood:          inf   
+Max. group size:       205          Converged:               Yes   
+Mean group size:       180.5                                       
+-------------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
+-------------------------------------------------------------------
+Intercept        0.000 55771.636 0.000 1.000 -109310.399 109310.399
+merged_timepoint 0.000     0.000 2.807 0.005       0.000      0.001
+Group Var        0.000                                             
+===================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0206 0.5306 -0.0556 0.0144  False
-     0      7   0.0105    0.9 -0.0265 0.0475  False
-     0     14    -0.01    0.9 -0.0464 0.0265  False
-     0     21   0.0067    0.9 -0.0297 0.0432  False
-     0     28   0.0171 0.7588 -0.0208 0.0549  False
-     3      7   0.0311 0.1007 -0.0033 0.0655  False
-     3     14   0.0107    0.9 -0.0232 0.0445  False
-     3     21   0.0274 0.1878 -0.0065 0.0612  False
-     3     28   0.0377 0.0289  0.0024  0.073   True
-     7     14  -0.0204 0.5625 -0.0563 0.0154  False
-     7     21  -0.0038    0.9 -0.0396 0.0321  False
-     7     28   0.0066    0.9 -0.0307 0.0439  False
-    14     21   0.0167 0.7241 -0.0186  0.052  False
-    14     28    0.027 0.2835 -0.0097 0.0638  False
-    21     28   0.0104    0.9 -0.0264 0.0471  False
+     0      3   0.0067    0.9 -0.0139 0.0273  False
+     0      7  -0.0084 0.8629 -0.0302 0.0133  False
+     0     14  -0.0088 0.8285 -0.0302 0.0127  False
+     0     21  -0.0015    0.9  -0.023 0.0199  False
+     0     28   0.0192 0.1335  -0.003 0.0415  False
+     3      7  -0.0151 0.2579 -0.0352  0.005  False
+     3     14  -0.0154 0.2196 -0.0352 0.0043  False
+     3     21  -0.0082 0.8179 -0.0279 0.0115  False
+     3     28   0.0126 0.4983 -0.0081 0.0332  False
+     7     14  -0.0003    0.9 -0.0212 0.0206  False
+     7     21   0.0069    0.9  -0.014 0.0278  False
+     7     28   0.0277 0.0043  0.0059 0.0494   True
+    14     21   0.0072    0.9 -0.0134 0.0278  False
+    14     28    0.028 0.0031  0.0065 0.0494   True
+    21     28   0.0207 0.0645 -0.0007 0.0422  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0013    0.9 -0.0319 0.0345  False
-     0      7  -0.0165 0.6383  -0.048  0.015  False
-     0     14   0.0005    0.9 -0.0297 0.0307  False
-     0     21  -0.0063    0.9 -0.0409 0.0283  False
-     0     28   0.0036    0.9 -0.0292 0.0364  False
-     3      7  -0.0178 0.6317 -0.0515  0.016  False
-     3     14  -0.0008    0.9 -0.0334 0.0317  False
-     3     21  -0.0076    0.9 -0.0442 0.0291  False
-     3     28   0.0023    0.9 -0.0327 0.0372  False
-     7     14   0.0169 0.5929 -0.0138 0.0477  False
-     7     21   0.0102    0.9 -0.0249 0.0453  False
-     7     28     0.02 0.5094 -0.0133 0.0534  False
-    14     21  -0.0067    0.9 -0.0407 0.0272  False
-    14     28   0.0031    0.9 -0.0291 0.0352  False
-    21     28   0.0098    0.9 -0.0264 0.0461  False
+     0      3   0.0148 0.3172  -0.006 0.0355  False
+     0      7   0.0068    0.9 -0.0123  0.026  False
+     0     14   0.0145 0.2133 -0.0039 0.0329  False
+     0     21   0.0168 0.1988 -0.0042 0.0379  False
+     0     28   0.0177 0.1149 -0.0023 0.0377  False
+     3      7  -0.0079 0.8783  -0.029 0.0131  False
+     3     14  -0.0003    0.9 -0.0207 0.0201  False
+     3     21    0.002    0.9 -0.0208 0.0248  False
+     3     28   0.0029    0.9 -0.0189 0.0247  False
+     7     14   0.0076  0.828 -0.0111 0.0264  False
+     7     21     0.01 0.7293 -0.0114 0.0313  False
+     7     28   0.0109 0.6169 -0.0094 0.0312  False
+    14     21   0.0023    0.9 -0.0183  0.023  False
+    14     28   0.0032    0.9 -0.0163 0.0228  False
+    21     28   0.0009    0.9 -0.0212  0.023  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.08361214]	No
-Stroke	Sham	14	[0.24370631]	No
-Stroke	Sham	21	[0.36427526]	No
-Stroke	Sham	28	[0.37178342]	No
-Stroke	Sham	7	[0.04098195]	Yes
-Stroke	Sham	0	[0.85772539]	No
+Stroke	Sham	3	[0.60090718]	No
+Stroke	Sham	14	[0.01508172]	Yes
+Stroke	Sham	21	[0.09307623]	No
+Stroke	Sham	28	[0.42738542]	No
+Stroke	Sham	7	[0.10929558]	No
+Stroke	Sham	0	[0.53122629]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CST_MOp-int-py_ipsilesional_CCcut_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CST_MOp-int-py_ipsilesional_CCcut
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      361          Method:                  REML  
+No. Groups:            2            Scale:                   0.0008
+Min. group size:       156          Log-Likelihood:          inf   
+Max. group size:       205          Converged:               Yes   
+Mean group size:       180.5                                       
+-------------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
+-------------------------------------------------------------------
+Intercept        0.000 55539.194 0.000 1.000 -108854.819 108854.819
+merged_timepoint 0.000     0.000 2.791 0.005       0.000      0.001
+Group Var        0.000                                             
+===================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0066    0.9  -0.014 0.0272  False
+     0      7  -0.0085 0.8551 -0.0303 0.0132  False
+     0     14  -0.0088 0.8251 -0.0302 0.0126  False
+     0     21  -0.0016    0.9  -0.023 0.0198  False
+     0     28   0.0193 0.1286 -0.0029 0.0415  False
+     3      7  -0.0152 0.2529 -0.0352 0.0049  False
+     3     14  -0.0154 0.2188 -0.0351 0.0043  False
+     3     21  -0.0082 0.8147 -0.0279 0.0115  False
+     3     28   0.0127 0.4849 -0.0079 0.0333  False
+     7     14  -0.0003    0.9 -0.0212 0.0206  False
+     7     21   0.0069    0.9  -0.014 0.0278  False
+     7     28   0.0278 0.0039  0.0061 0.0496   True
+    14     21   0.0072    0.9 -0.0134 0.0278  False
+    14     28   0.0281 0.0028  0.0067 0.0495   True
+    21     28   0.0209 0.0601 -0.0005 0.0423  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0155 0.2501  -0.005  0.036  False
+     0      7   0.0069 0.8979  -0.012 0.0259  False
+     0     14   0.0144 0.2089 -0.0038 0.0325  False
+     0     21   0.0171 0.1707 -0.0037 0.0379  False
+     0     28   0.0174 0.1168 -0.0023 0.0372  False
+     3      7  -0.0086 0.8181 -0.0294 0.0122  False
+     3     14  -0.0012    0.9 -0.0213 0.0189  False
+     3     21   0.0016    0.9 -0.0209 0.0241  False
+     3     28   0.0019    0.9 -0.0196 0.0234  False
+     7     14   0.0074 0.8383 -0.0111 0.0259  False
+     7     21   0.0102 0.7017 -0.0109 0.0313  False
+     7     28   0.0105 0.6357 -0.0095 0.0305  False
+    14     21   0.0028    0.9 -0.0176 0.0232  False
+    14     28   0.0031    0.9 -0.0163 0.0224  False
+    21     28   0.0003    0.9 -0.0215 0.0221  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.56124489]	No
+Stroke	Sham	14	[0.01741046]	Yes
+Stroke	Sham	21	[0.09445709]	No
+Stroke	Sham	28	[0.36814452]	No
+Stroke	Sham	7	[0.11158166]	No
+Stroke	Sham	0	[0.48840569]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CST_MOp-int-py_ipsilesional_selfdrawnROA+CCcut_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_CST_MOp-int-py_ipsilesional_selfdrawnROA+CCcut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0023
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 1.971 0.049  0.000  0.001
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      361          Method:                  REML  
+No. Groups:            2            Scale:                   0.0008
+Min. group size:       156          Log-Likelihood:          inf   
+Max. group size:       205          Converged:               Yes   
+Mean group size:       180.5                                       
+-------------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
+-------------------------------------------------------------------
+Intercept        0.000 55738.087 0.000 1.000 -109244.644 109244.644
+merged_timepoint 0.000     0.000 2.793 0.005       0.000      0.001
+Group Var        0.000                                             
+===================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0203 0.5486 -0.0554 0.0148  False
-     0      7   0.0105    0.9 -0.0266 0.0475  False
-     0     14  -0.0097    0.9 -0.0463 0.0268  False
-     0     21   0.0068    0.9 -0.0297 0.0433  False
-     0     28   0.0169 0.7689 -0.0211 0.0548  False
-     3      7   0.0308 0.1094 -0.0037 0.0652  False
-     3     14   0.0106    0.9 -0.0233 0.0445  False
-     3     21   0.0271 0.1986 -0.0068  0.061  False
-     3     28   0.0372 0.0334  0.0018 0.0726   True
-     7     14  -0.0202 0.5753 -0.0562 0.0157  False
-     7     21  -0.0037    0.9 -0.0396 0.0323  False
-     7     28   0.0064    0.9  -0.031 0.0438  False
-    14     21   0.0165 0.7331 -0.0189 0.0519  False
-    14     28   0.0266 0.3034 -0.0102 0.0635  False
-    21     28   0.0101    0.9 -0.0268 0.0469  False
+     0      3   0.0065    0.9 -0.0141 0.0271  False
+     0      7  -0.0084 0.8671 -0.0302 0.0134  False
+     0     14  -0.0086 0.8438 -0.0301 0.0129  False
+     0     21  -0.0016    0.9 -0.0231 0.0199  False
+     0     28    0.019 0.1423 -0.0033 0.0413  False
+     3      7  -0.0149 0.2739  -0.035 0.0052  False
+     3     14  -0.0151 0.2436 -0.0349 0.0047  False
+     3     21  -0.0081 0.8286 -0.0278 0.0117  False
+     3     28   0.0125 0.5019 -0.0081 0.0332  False
+     7     14  -0.0002    0.9 -0.0211 0.0208  False
+     7     21   0.0068    0.9 -0.0141 0.0278  False
+     7     28   0.0274 0.0049  0.0056 0.0492   True
+    14     21    0.007    0.9 -0.0136 0.0277  False
+    14     28   0.0276 0.0038  0.0061 0.0491   True
+    21     28   0.0206 0.0685 -0.0009 0.0421  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0005    0.9 -0.0328 0.0339  False
-     0      7   -0.017 0.6164 -0.0486 0.0147  False
-     0     14  -0.0002    0.9 -0.0306 0.0302  False
-     0     21  -0.0073    0.9 -0.0421 0.0274  False
-     0     28   0.0032    0.9 -0.0297 0.0362  False
-     3      7  -0.0175 0.6492 -0.0514 0.0164  False
-     3     14  -0.0007    0.9 -0.0335  0.032  False
-     3     21  -0.0079    0.9 -0.0447  0.029  False
-     3     28   0.0027    0.9 -0.0324 0.0378  False
-     7     14   0.0167 0.6078 -0.0142 0.0477  False
-     7     21   0.0096    0.9 -0.0256 0.0449  False
-     7     28   0.0202 0.5058 -0.0133 0.0537  False
-    14     21  -0.0071    0.9 -0.0412  0.027  False
-    14     28   0.0035    0.9 -0.0289 0.0358  False
-    21     28   0.0106    0.9 -0.0259  0.047  False
+     0      3   0.0152 0.2832 -0.0055 0.0359  False
+     0      7    0.007 0.8988 -0.0121 0.0261  False
+     0     14   0.0144 0.2135 -0.0039 0.0327  False
+     0     21   0.0167 0.2011 -0.0043 0.0377  False
+     0     28   0.0179 0.1055  -0.002 0.0378  False
+     3      7  -0.0082 0.8553 -0.0292 0.0128  False
+     3     14  -0.0008    0.9 -0.0211 0.0195  False
+     3     21   0.0015    0.9 -0.0212 0.0242  False
+     3     28   0.0027    0.9  -0.019 0.0244  False
+     7     14   0.0074 0.8436 -0.0112 0.0261  False
+     7     21   0.0097 0.7459 -0.0115  0.031  False
+     7     28   0.0109 0.6109 -0.0093 0.0311  False
+    14     21   0.0023    0.9 -0.0183 0.0229  False
+    14     28   0.0035    0.9  -0.016  0.023  False
+    21     28   0.0012    0.9 -0.0208 0.0232  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.08812776]	No
-Stroke	Sham	14	[0.25234923]	No
-Stroke	Sham	21	[0.34659219]	No
-Stroke	Sham	28	[0.39886825]	No
-Stroke	Sham	7	[0.04498613]	Yes
-Stroke	Sham	0	[0.8152567]	No
+Stroke	Sham	3	[0.56669501]	No
+Stroke	Sham	14	[0.0169285]	Yes
+Stroke	Sham	21	[0.09851929]	No
+Stroke	Sham	28	[0.4441613]	No
+Stroke	Sham	7	[0.11270578]	No
+Stroke	Sham	0	[0.51161222]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_TC_DORsm-SSp+SSs_contralesional_END+CCcut_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_TC_DORsm-SSp+SSs_contralesional_END+CCcut
-           Mixed Linear Model Regression Results
-===========================================================
-Model:               MixedLM  Dependent Variable:  Value   
-No. Observations:    364      Method:              REML    
-No. Groups:          2        Scale:               0.0012  
-Min. group size:     158      Log-Likelihood:      688.0620
-Max. group size:     206      Converged:           Yes     
-Mean group size:     182.0                                 
------------------------------------------------------------
-                 Coef. Std.Err.    z    P>|z| [0.025 0.975]
------------------------------------------------------------
-Intercept        0.361    0.003 122.536 0.000  0.355  0.367
-merged_timepoint 0.001    0.000   4.775 0.000  0.001  0.001
-Group Var        0.000                                     
-===========================================================
+              Mixed Linear Model Regression Results
+=================================================================
+Model:                 MixedLM     Dependent Variable:     Value 
+No. Observations:      361         Method:                 REML  
+No. Groups:            2           Scale:                  0.0006
+Min. group size:       156         Log-Likelihood:         inf   
+Max. group size:       205         Converged:              Yes   
+Mean group size:       180.5                                     
+-----------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|   [0.025     0.975] 
+-----------------------------------------------------------------
+Intercept        0.000 48722.944 0.000 1.000 -95495.215 95495.215
+merged_timepoint 0.001     0.000 4.993 0.000      0.000     0.001
+Group Var        0.000                                           
+=================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3    0.004    0.9 -0.0222 0.0303  False
-     0      7   0.0239 0.1331 -0.0038 0.0516  False
-     0     14   0.0168 0.4901 -0.0106 0.0441  False
-     0     21   0.0226 0.1668 -0.0047   0.05  False
-     0     28   0.0281 0.0536 -0.0003 0.0565  False
-     3      7   0.0199 0.2321 -0.0059 0.0457  False
-     3     14   0.0127  0.674 -0.0126 0.0381  False
-     3     21   0.0186  0.285 -0.0067  0.044  False
-     3     28   0.0241 0.0975 -0.0024 0.0506  False
-     7     14  -0.0072    0.9  -0.034 0.0197  False
-     7     21  -0.0013    0.9 -0.0282 0.0256  False
-     7     28   0.0042    0.9 -0.0238 0.0321  False
-    14     21   0.0059    0.9 -0.0206 0.0324  False
-    14     28   0.0114 0.8238 -0.0162 0.0389  False
-    21     28   0.0055    0.9 -0.0221  0.033  False
+     0      3  -0.0052    0.9 -0.0239 0.0135  False
+     0      7   0.0104 0.6304 -0.0093 0.0301  False
+     0     14   0.0072 0.8955 -0.0123 0.0266  False
+     0     21   0.0123 0.4516 -0.0071 0.0318  False
+     0     28   0.0148 0.2846 -0.0054  0.035  False
+     3      7   0.0156  0.136 -0.0025 0.0338  False
+     3     14   0.0124 0.3517 -0.0055 0.0302  False
+     3     21   0.0176 0.0575 -0.0003 0.0354  False
+     3     28     0.02 0.0277  0.0013 0.0387   True
+     7     14  -0.0033    0.9 -0.0222 0.0157  False
+     7     21   0.0019    0.9  -0.017 0.0209  False
+     7     28   0.0044    0.9 -0.0153 0.0241  False
+    14     21   0.0052    0.9 -0.0135 0.0239  False
+    14     28   0.0077 0.8534 -0.0118 0.0271  False
+    21     28   0.0025    0.9  -0.017 0.0219  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   -0.013 0.6302 -0.0376 0.0116  False
-     0      7   0.0006    0.9 -0.0227 0.0239  False
-     0     14   0.0122 0.6004 -0.0102 0.0346  False
-     0     21   0.0191 0.2671 -0.0065 0.0447  False
-     0     28   0.0177 0.2946 -0.0067  0.042  False
-     3      7   0.0136  0.603 -0.0114 0.0386  False
-     3     14   0.0252 0.0348  0.0011 0.0493   True
-     3     21   0.0321 0.0105  0.0049 0.0592   True
-     3     28   0.0307 0.0104  0.0047 0.0566   True
-     7     14   0.0116 0.6609 -0.0112 0.0344  False
-     7     21   0.0185 0.3176 -0.0075 0.0445  False
-     7     28   0.0171 0.3516 -0.0076 0.0418  False
-    14     21   0.0069    0.9 -0.0183  0.032  False
-    14     28   0.0054    0.9 -0.0184 0.0293  False
-    21     28  -0.0014    0.9 -0.0283 0.0254  False
+     0      3   0.0003    0.9 -0.0176 0.0182  False
+     0      7   0.0017    0.9 -0.0148 0.0183  False
+     0     14   0.0117 0.2835 -0.0042 0.0275  False
+     0     21   0.0219 0.0086  0.0037 0.0401   True
+     0     28   0.0157 0.0976 -0.0016 0.0329  False
+     3      7   0.0014    0.9 -0.0168 0.0196  False
+     3     14   0.0114 0.4288 -0.0062 0.0289  False
+     3     21   0.0216 0.0225  0.0019 0.0413   True
+     3     28   0.0154 0.1769 -0.0034 0.0342  False
+     7     14   0.0099 0.4864 -0.0062 0.0261  False
+     7     21   0.0202 0.0233  0.0017 0.0386   True
+     7     28    0.014 0.2003 -0.0036 0.0315  False
+    14     21   0.0102 0.5558 -0.0076 0.0281  False
+    14     28    0.004    0.9 -0.0129 0.0209  False
+    21     28  -0.0062    0.9 -0.0253 0.0129  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.64655622]	No
-Stroke	Sham	14	[0.27043189]	No
-Stroke	Sham	21	[0.25382805]	No
-Stroke	Sham	28	[0.82376109]	No
-Stroke	Sham	7	[0.0889746]	No
-Stroke	Sham	0	[0.38469028]	No
+Stroke	Sham	3	[0.2366261]	No
+Stroke	Sham	14	[0.31413081]	No
+Stroke	Sham	21	[0.09353268]	No
+Stroke	Sham	28	[0.61530626]	No
+Stroke	Sham	7	[0.30119469]	No
+Stroke	Sham	0	[0.68785176]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_TC_DORsm-SSp+SSs_ipsilesional_END+CCcut_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_TC_DORsm-SSp+SSs_ipsilesional_END+CCcut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0013
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 3.653 0.000  0.000  0.001
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      361          Method:                  REML  
+No. Groups:            2            Scale:                   0.0012
+Min. group size:       156          Log-Likelihood:          inf   
+Max. group size:       205          Converged:               Yes   
+Mean group size:       180.5                                       
+-------------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
+-------------------------------------------------------------------
+Intercept        0.000 66982.138 0.000 1.000 -131282.578 131282.578
+merged_timepoint 0.001     0.000 3.694 0.000       0.000      0.001
+Group Var        0.000                                             
+===================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0001    0.9 -0.0259 0.0258  False
-     0      7   0.0093    0.9  -0.018 0.0366  False
-     0     14   0.0118 0.7814 -0.0152 0.0387  False
-     0     21    0.015 0.5842 -0.0119  0.042  False
-     0     28   0.0163 0.5437 -0.0117 0.0442  False
-     3      7   0.0094 0.8957 -0.0161 0.0348  False
-     3     14   0.0118 0.7217 -0.0132 0.0368  False
-     3     21   0.0151 0.5092 -0.0099 0.0401  False
-     3     28   0.0163 0.4699 -0.0098 0.0424  False
-     7     14   0.0025    0.9  -0.024  0.029  False
-     7     21   0.0057    0.9 -0.0208 0.0322  False
-     7     28    0.007    0.9 -0.0206 0.0345  False
-    14     21   0.0032    0.9 -0.0229 0.0293  False
-    14     28   0.0045    0.9 -0.0227 0.0317  False
-    21     28   0.0013    0.9 -0.0259 0.0284  False
+     0      3   0.0055    0.9  -0.019   0.03  False
+     0      7   0.0056    0.9 -0.0203 0.0314  False
+     0     14   0.0129 0.6694 -0.0126 0.0384  False
+     0     21   0.0149 0.5371 -0.0106 0.0404  False
+     0     28   0.0159 0.5096 -0.0105 0.0424  False
+     3      7   0.0001    0.9 -0.0238 0.0239  False
+     3     14   0.0074    0.9 -0.0161 0.0309  False
+     3     21   0.0094 0.8389  -0.014 0.0329  False
+     3     28   0.0105 0.7996 -0.0141  0.035  False
+     7     14   0.0073    0.9 -0.0175 0.0322  False
+     7     21   0.0094 0.8814 -0.0155 0.0342  False
+     7     28   0.0104  0.841 -0.0155 0.0362  False
+    14     21    0.002    0.9 -0.0225 0.0265  False
+    14     28   0.0031    0.9 -0.0225 0.0286  False
+    21     28    0.001    0.9 -0.0245 0.0265  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0058    0.9 -0.0228 0.0344  False
-     0      7   0.0125 0.7433 -0.0147 0.0396  False
-     0     14   0.0182 0.3366 -0.0078 0.0443  False
-     0     21   0.0273 0.0923 -0.0025 0.0572  False
-     0     28   0.0215 0.2487 -0.0068 0.0497  False
-     3      7   0.0066    0.9 -0.0224 0.0357  False
-     3     14   0.0124 0.7717 -0.0157 0.0405  False
-     3     21   0.0215  0.367 -0.0101 0.0531  False
-     3     28   0.0156 0.6452 -0.0145 0.0458  False
-     7     14   0.0058    0.9 -0.0208 0.0323  False
-     7     21   0.0149  0.689 -0.0154 0.0451  False
-     7     28    0.009    0.9 -0.0197 0.0377  False
-    14     21   0.0091    0.9 -0.0201 0.0384  False
-    14     28   0.0032    0.9 -0.0245 0.0309  False
-    21     28  -0.0059    0.9 -0.0372 0.0254  False
+     0      3   0.0123 0.7514 -0.0148 0.0395  False
+     0      7   0.0145 0.5483 -0.0106 0.0396  False
+     0     14   0.0226 0.0791 -0.0015 0.0467  False
+     0     21   0.0297 0.0266  0.0021 0.0573   True
+     0     28    0.024 0.0921 -0.0022 0.0501  False
+     3      7   0.0021    0.9 -0.0254 0.0297  False
+     3     14   0.0103 0.8642 -0.0164 0.0369  False
+     3     21   0.0174   0.54 -0.0125 0.0472  False
+     3     28   0.0116 0.8274 -0.0169 0.0402  False
+     7     14   0.0081    0.9 -0.0164 0.0327  False
+     7     21   0.0152  0.602 -0.0127 0.0432  False
+     7     28   0.0095    0.9 -0.0171  0.036  False
+    14     21   0.0071    0.9   -0.02 0.0341  False
+    14     28   0.0014    0.9 -0.0242  0.027  False
+    21     28  -0.0057    0.9 -0.0346 0.0232  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.76412464]	No
-Stroke	Sham	14	[0.69963524]	No
-Stroke	Sham	21	[0.3055409]	No
-Stroke	Sham	28	[0.79159547]	No
-Stroke	Sham	7	[0.96725594]	No
-Stroke	Sham	0	[0.79395919]	No
+Stroke	Sham	3	[0.66743136]	No
+Stroke	Sham	14	[0.44582648]	No
+Stroke	Sham	21	[0.17324058]	No
+Stroke	Sham	28	[0.53947449]	No
+Stroke	Sham	7	[0.46564271]	No
+Stroke	Sham	0	[0.77036324]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_TC_DORsm-SSp_ll+SSp_ul_contralesional_END+higherstepsize_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_TC_DORsm-SSp_ll+SSp_ul_contralesional_END+higherstepsize
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0016
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 4.307 0.000  0.001  0.001
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      361          Method:                  REML  
+No. Groups:            2            Scale:                   0.0010
+Min. group size:       156          Log-Likelihood:          inf   
+Max. group size:       205          Converged:               Yes   
+Mean group size:       180.5                                       
+-------------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
+-------------------------------------------------------------------
+Intercept        0.000 61916.896 0.000 1.000 -121354.886 121354.886
+merged_timepoint 0.001     0.000 4.218 0.000       0.000      0.001
+Group Var        0.000                                             
+===================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0036    0.9  -0.027 0.0342  False
-     0      7   0.0238 0.2819 -0.0085 0.0561  False
-     0     14   0.0199 0.4688 -0.0119 0.0518  False
-     0     21   0.0216 0.3742 -0.0102 0.0535  False
-     0     28   0.0283 0.1414 -0.0048 0.0614  False
-     3      7   0.0202 0.3881 -0.0099 0.0502  False
-     3     14   0.0163 0.5933 -0.0133 0.0459  False
-     3     21    0.018 0.4992 -0.0116 0.0476  False
-     3     28   0.0246 0.2005 -0.0062 0.0555  False
-     7     14  -0.0039    0.9 -0.0352 0.0275  False
-     7     21  -0.0022    0.9 -0.0335 0.0292  False
-     7     28   0.0045    0.9 -0.0281 0.0371  False
-    14     21   0.0017    0.9 -0.0292 0.0326  False
-    14     28   0.0083    0.9 -0.0238 0.0405  False
-    21     28   0.0066    0.9 -0.0255 0.0388  False
+     0      3  -0.0056    0.9 -0.0293 0.0181  False
+     0      7   0.0125 0.6816 -0.0126 0.0375  False
+     0     14   0.0103  0.817 -0.0144 0.0349  False
+     0     21   0.0121 0.6921 -0.0125 0.0368  False
+     0     28   0.0171 0.3932 -0.0085 0.0427  False
+     3      7    0.018 0.2201  -0.005 0.0411  False
+     3     14   0.0158 0.3416 -0.0069 0.0385  False
+     3     21   0.0177 0.2222  -0.005 0.0404  False
+     3     28   0.0227 0.0698  -0.001 0.0464  False
+     7     14  -0.0022    0.9 -0.0263 0.0219  False
+     7     21  -0.0003    0.9 -0.0244 0.0237  False
+     7     28   0.0046    0.9 -0.0204 0.0297  False
+    14     21   0.0019    0.9 -0.0218 0.0256  False
+    14     28   0.0068    0.9 -0.0178 0.0315  False
+    21     28    0.005    0.9 -0.0197 0.0296  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0167 0.4317 -0.0426 0.0092  False
-     0      7   0.0063    0.9 -0.0183 0.0308  False
-     0     14   0.0123 0.6389 -0.0113 0.0359  False
-     0     21   0.0232 0.1344 -0.0037 0.0502  False
-     0     28   0.0167 0.4174 -0.0089 0.0423  False
-     3      7    0.023 0.1244 -0.0033 0.0493  False
-     3     14    0.029  0.015  0.0036 0.0544   True
-     3     21   0.0399 0.0012  0.0114 0.0685   True
-     3     28   0.0334  0.007  0.0061 0.0607   True
-     7     14    0.006    0.9  -0.018 0.0301  False
-     7     21    0.017 0.4766 -0.0104 0.0443  False
-     7     28   0.0104 0.8386 -0.0156 0.0364  False
-    14     21   0.0109 0.8206 -0.0156 0.0374  False
-    14     28   0.0044    0.9 -0.0207 0.0295  False
-    21     28  -0.0065    0.9 -0.0348 0.0218  False
+     0      3   -0.006    0.9 -0.0289 0.0169  False
+     0      7   0.0077    0.9 -0.0135 0.0288  False
+     0     14   0.0121 0.5143 -0.0082 0.0324  False
+     0     21   0.0223 0.0674 -0.0009 0.0455  False
+     0     28   0.0159 0.2987 -0.0061 0.0379  False
+     3      7   0.0136 0.5306 -0.0096 0.0368  False
+     3     14   0.0181 0.1887 -0.0043 0.0405  False
+     3     21   0.0283 0.0175  0.0032 0.0534   True
+     3     28   0.0219 0.0954 -0.0021 0.0459  False
+     7     14   0.0045    0.9 -0.0162 0.0251  False
+     7     21   0.0146 0.4726 -0.0089 0.0382  False
+     7     28   0.0083 0.8906 -0.0141 0.0306  False
+    14     21   0.0102 0.7637 -0.0126  0.033  False
+    14     28   0.0038    0.9 -0.0178 0.0254  False
+    21     28  -0.0064    0.9 -0.0307  0.018  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.44512693]	No
-Stroke	Sham	14	[0.50414866]	No
-Stroke	Sham	21	[0.14702113]	No
-Stroke	Sham	28	[0.84606881]	No
-Stroke	Sham	7	[0.59836112]	No
-Stroke	Sham	0	[0.38009622]	No
+Stroke	Sham	3	[0.72175235]	No
+Stroke	Sham	14	[0.55407757]	No
+Stroke	Sham	21	[0.14897269]	No
+Stroke	Sham	28	[0.82759446]	No
+Stroke	Sham	7	[0.81498819]	No
+Stroke	Sham	0	[0.7166752]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_TC_DORsm-SSp_ll+SSp_ul_contralesional_ROI+CCcut_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_TC_DORsm-SSp_ll+SSp_ul_contralesional_ROI+CCcut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0023
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 3.399 0.001  0.000  0.001
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      361          Method:                  REML  
+No. Groups:            2            Scale:                   0.0016
+Min. group size:       156          Log-Likelihood:          inf   
+Max. group size:       205          Converged:               Yes   
+Mean group size:       180.5                                       
+-------------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
+-------------------------------------------------------------------
+Intercept        0.000 77668.745 0.000 1.000 -152227.943 152227.943
+merged_timepoint 0.001     0.000 3.347 0.001       0.000      0.001
+Group Var        0.000                                             
+===================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0141 0.8488 -0.0214 0.0496  False
-     0      7   0.0353 0.0793 -0.0023 0.0728  False
-     0     14   0.0303 0.1761 -0.0067 0.0674  False
-     0     21   0.0262 0.3237 -0.0108 0.0633  False
-     0     28   0.0329 0.1403 -0.0055 0.0713  False
-     3      7   0.0212 0.5029 -0.0137 0.0561  False
-     3     14   0.0162 0.7233 -0.0181 0.0506  False
-     3     21   0.0121    0.9 -0.0222 0.0465  False
-     3     28   0.0188  0.639 -0.0171 0.0547  False
-     7     14  -0.0049    0.9 -0.0414 0.0315  False
-     7     21   -0.009    0.9 -0.0455 0.0274  False
-     7     28  -0.0024    0.9 -0.0402 0.0355  False
-    14     21  -0.0041    0.9   -0.04 0.0318  False
-    14     28   0.0026    0.9 -0.0348 0.0399  False
-    21     28   0.0067    0.9 -0.0307  0.044  False
+     0      3   0.0042    0.9 -0.0253 0.0336  False
+     0      7   0.0233  0.263 -0.0078 0.0543  False
+     0     14   0.0218 0.3191 -0.0088 0.0524  False
+     0     21   0.0184 0.5105 -0.0122  0.049  False
+     0     28   0.0233 0.2878 -0.0085  0.055  False
+     3      7   0.0191 0.3945 -0.0095 0.0477  False
+     3     14   0.0176 0.4688 -0.0105 0.0458  False
+     3     21   0.0143 0.6679 -0.0139 0.0424  False
+     3     28   0.0191 0.4265 -0.0103 0.0485  False
+     7     14  -0.0015    0.9 -0.0313 0.0284  False
+     7     21  -0.0048    0.9 -0.0347  0.025  False
+     7     28      0.0    0.9  -0.031  0.031  False
+    14     21  -0.0034    0.9 -0.0328 0.0261  False
+    14     28   0.0015    0.9 -0.0291 0.0321  False
+    21     28   0.0048    0.9 -0.0258 0.0355  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0209 0.4329 -0.0532 0.0115  False
-     0      7   0.0059    0.9 -0.0248 0.0366  False
-     0     14   0.0139 0.7202 -0.0155 0.0434  False
-     0     21   0.0259 0.2365 -0.0078 0.0596  False
-     0     28   0.0111    0.9 -0.0209  0.043  False
-     3      7   0.0267 0.1817 -0.0061 0.0596  False
-     3     14   0.0348 0.0226  0.0031 0.0665   True
-     3     21   0.0467  0.003   0.011 0.0825   True
-     3     28   0.0319 0.0808 -0.0022  0.066  False
-     7     14   0.0081    0.9 -0.0219 0.0381  False
-     7     21     0.02 0.5351 -0.0142 0.0542  False
-     7     28   0.0052    0.9 -0.0273 0.0377  False
-    14     21   0.0119    0.9 -0.0212  0.045  False
-    14     28  -0.0029    0.9 -0.0342 0.0284  False
-    21     28  -0.0148  0.809 -0.0502 0.0205  False
+     0      3   -0.012 0.8208 -0.0411 0.0171  False
+     0      7   0.0054    0.9 -0.0215 0.0323  False
+     0     14    0.012 0.7316 -0.0138 0.0378  False
+     0     21   0.0212 0.3081 -0.0083 0.0507  False
+     0     28   0.0112 0.8412 -0.0168 0.0392  False
+     3      7   0.0174 0.5299 -0.0122 0.0469  False
+     3     14    0.024 0.1529 -0.0045 0.0526  False
+     3     21   0.0332 0.0369  0.0012 0.0652   True
+     3     28   0.0232 0.2481 -0.0074 0.0538  False
+     7     14   0.0067    0.9 -0.0196 0.0329  False
+     7     21   0.0158   0.63 -0.0141 0.0458  False
+     7     28   0.0058    0.9 -0.0226 0.0343  False
+    14     21   0.0092    0.9 -0.0198 0.0381  False
+    14     28  -0.0008    0.9 -0.0283 0.0266  False
+    21     28    -0.01    0.9  -0.041  0.021  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.16087028]	No
-Stroke	Sham	14	[0.76825281]	No
-Stroke	Sham	21	[0.1219538]	No
-Stroke	Sham	28	[0.87227025]	No
-Stroke	Sham	7	[0.38027585]	No
-Stroke	Sham	0	[0.2055141]	No
+Stroke	Sham	3	[0.52801285]	No
+Stroke	Sham	14	[0.93990284]	No
+Stroke	Sham	21	[0.21672841]	No
+Stroke	Sham	28	[0.8980838]	No
+Stroke	Sham	7	[0.48090022]	No
+Stroke	Sham	0	[0.3274905]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_TC_DORsm-SSp_ll+SSp_ul_ipsilesional_END+higherstepsize__log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_TC_DORsm-SSp_ll+SSp_ul_ipsilesional_END+higherstepsize_
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0015
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 3.106 0.002  0.000  0.001
-Group Var         0.000                                   
-==========================================================
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM  Dependent Variable:  Value   
+No. Observations:    361      Method:              REML    
+No. Groups:          2        Scale:               0.0013  
+Min. group size:     156      Log-Likelihood:      676.8823
+Max. group size:     205      Converged:           Yes     
+Mean group size:     180.5                                 
+-----------------------------------------------------------
+                 Coef. Std.Err.    z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept        0.363    0.003 121.052 0.000  0.357  0.369
+merged_timepoint 0.001    0.000   4.217 0.000  0.000  0.001
+Group Var        0.000                                     
+===========================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3    0.006    0.9 -0.0234 0.0353  False
-     0      7   0.0106    0.9 -0.0204 0.0416  False
-     0     14   0.0136 0.7718  -0.017 0.0441  False
-     0     21   0.0138 0.7586 -0.0168 0.0444  False
-     0     28   0.0174 0.6006 -0.0144 0.0491  False
-     3      7   0.0046    0.9 -0.0242 0.0335  False
-     3     14   0.0076    0.9 -0.0208 0.0359  False
-     3     21   0.0078    0.9 -0.0205 0.0362  False
-     3     28   0.0114 0.8687 -0.0182  0.041  False
-     7     14   0.0029    0.9 -0.0271  0.033  False
-     7     21   0.0032    0.9 -0.0269 0.0333  False
-     7     28   0.0068    0.9 -0.0245  0.038  False
-    14     21   0.0002    0.9 -0.0294 0.0299  False
-    14     28   0.0038    0.9  -0.027 0.0347  False
-    21     28   0.0036    0.9 -0.0273 0.0344  False
+     0      3   0.0187 0.3221 -0.0077 0.0451  False
+     0      7   0.0067    0.9 -0.0211 0.0346  False
+     0     14   0.0189 0.3599 -0.0086 0.0464  False
+     0     21   0.0221 0.1947 -0.0054 0.0495  False
+     0     28   0.0298 0.0344  0.0013 0.0584   True
+     3      7   -0.012 0.7311 -0.0377 0.0137  False
+     3     14   0.0001    0.9 -0.0251 0.0254  False
+     3     21   0.0033    0.9  -0.022 0.0286  False
+     3     28   0.0111 0.8096 -0.0153 0.0375  False
+     7     14   0.0122 0.7544 -0.0146  0.039  False
+     7     21   0.0153 0.5585 -0.0115 0.0421  False
+     7     28   0.0231 0.1655 -0.0047  0.051  False
+    14     21   0.0032    0.9 -0.0232 0.0296  False
+    14     28    0.011 0.8452 -0.0165 0.0384  False
+    21     28   0.0078    0.9 -0.0197 0.0353  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   -0.005    0.9 -0.0328 0.0228  False
-     0      7   0.0029    0.9 -0.0235 0.0292  False
-     0     14   0.0157 0.4758 -0.0096  0.041  False
-     0     21   0.0202 0.3381 -0.0087 0.0492  False
-     0     28   0.0169 0.4877 -0.0106 0.0443  False
-     3      7   0.0079    0.9 -0.0203 0.0361  False
-     3     14   0.0207 0.2466 -0.0065 0.0479  False
-     3     21   0.0252 0.1718 -0.0054 0.0559  False
-     3     28   0.0219 0.2645 -0.0074 0.0511  False
-     7     14   0.0128 0.6803  -0.013 0.0386  False
-     7     21   0.0173 0.5262  -0.012 0.0467  False
-     7     28    0.014 0.6744 -0.0139 0.0419  False
-    14     21   0.0045    0.9 -0.0239 0.0329  False
-    14     28   0.0012    0.9 -0.0257 0.0281  False
-    21     28  -0.0034    0.9 -0.0337  0.027  False
+     0      3   0.0064    0.9 -0.0205 0.0332  False
+     0      7   0.0079    0.9 -0.0169 0.0327  False
+     0     14   0.0217  0.095 -0.0021 0.0455  False
+     0     21   0.0244 0.1083 -0.0029 0.0516  False
+     0     28   0.0221 0.1401 -0.0037 0.0479  False
+     3      7   0.0015    0.9 -0.0257 0.0288  False
+     3     14   0.0154 0.5371  -0.011 0.0417  False
+     3     21    0.018 0.4924 -0.0115 0.0475  False
+     3     28   0.0157 0.5794 -0.0125 0.0439  False
+     7     14   0.0139 0.5573 -0.0104 0.0381  False
+     7     21   0.0165  0.516 -0.0111 0.0441  False
+     7     28   0.0142 0.6068  -0.012 0.0405  False
+    14     21   0.0026    0.9 -0.0241 0.0294  False
+    14     28   0.0004    0.9  -0.025 0.0257  False
+    21     28  -0.0023    0.9 -0.0308 0.0263  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.21966597]	No
-Stroke	Sham	14	[0.85182345]	No
-Stroke	Sham	21	[0.81707511]	No
-Stroke	Sham	28	[0.65633157]	No
-Stroke	Sham	7	[0.14750624]	No
-Stroke	Sham	0	[0.70899005]	No
+Stroke	Sham	3	[0.38418309]	No
+Stroke	Sham	14	[0.58575711]	No
+Stroke	Sham	21	[0.63597541]	No
+Stroke	Sham	28	[0.5608486]	No
+Stroke	Sham	7	[0.66035682]	No
+Stroke	Sham	0	[0.80351802]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_TC_DORsm-SSp_ll+SSp_ul_ipsilesional_ROI+CCcut_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_TC_DORsm-SSp_ll+SSp_ul_ipsilesional_ROI+CCcut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0018
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 3.027 0.002  0.000  0.001
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      361          Method:                  REML  
+No. Groups:            2            Scale:                   0.0016
+Min. group size:       156          Log-Likelihood:          inf   
+Max. group size:       205          Converged:               Yes   
+Mean group size:       180.5                                       
+-------------------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
+-------------------------------------------------------------------
+Intercept        0.000 77113.337 0.000 1.000 -151139.364 151139.364
+merged_timepoint 0.001     0.000 3.819 0.000       0.000      0.001
+Group Var        0.000                                             
+===================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0061    0.9 -0.0248 0.0371  False
-     0      7   0.0134 0.8276 -0.0193 0.0461  False
-     0     14    0.014 0.7848 -0.0182 0.0463  False
-     0     21    0.018 0.5841 -0.0143 0.0502  False
-     0     28   0.0218 0.4242 -0.0117 0.0553  False
-     3      7   0.0073    0.9 -0.0231 0.0377  False
-     3     14   0.0079    0.9  -0.022 0.0378  False
-     3     21   0.0118 0.8504 -0.0181 0.0418  False
-     3     28   0.0157 0.6764 -0.0156 0.0469  False
-     7     14   0.0006    0.9 -0.0311 0.0324  False
-     7     21   0.0046    0.9 -0.0272 0.0363  False
-     7     28   0.0084    0.9 -0.0246 0.0414  False
-    14     21   0.0039    0.9 -0.0273 0.0352  False
-    14     28   0.0077    0.9 -0.0248 0.0403  False
-    21     28   0.0038    0.9 -0.0287 0.0364  False
+     0      3   0.0142 0.6931 -0.0147  0.043  False
+     0      7     0.01    0.9 -0.0205 0.0404  False
+     0     14   0.0227 0.2544 -0.0073 0.0527  False
+     0     21    0.022 0.2854  -0.008 0.0521  False
+     0     28   0.0308  0.055 -0.0004 0.0619  False
+     3      7  -0.0042    0.9 -0.0323 0.0239  False
+     3     14   0.0085    0.9 -0.0191 0.0361  False
+     3     21   0.0079    0.9 -0.0197 0.0355  False
+     3     28   0.0166 0.5529 -0.0122 0.0455  False
+     7     14   0.0127 0.7865 -0.0166  0.042  False
+     7     21   0.0121 0.8231 -0.0172 0.0414  False
+     7     28   0.0208 0.3655 -0.0096 0.0513  False
+    14     21  -0.0006    0.9 -0.0295 0.0282  False
+    14     28   0.0081    0.9 -0.0219 0.0381  False
+    21     28   0.0087    0.9 -0.0213 0.0388  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0101    0.9 -0.0401 0.0199  False
-     0      7   0.0063    0.9 -0.0221 0.0348  False
-     0     14   0.0192 0.3295 -0.0081 0.0465  False
-     0     21   0.0174 0.5834 -0.0139 0.0486  False
-     0     28   0.0106    0.9 -0.0191 0.0402  False
-     3      7   0.0165 0.6093  -0.014 0.0469  False
-     3     14   0.0294 0.0506    -0.0 0.0588  False
-     3     21   0.0275 0.1629 -0.0056 0.0606  False
-     3     28   0.0207 0.4113 -0.0109 0.0523  False
-     7     14   0.0129 0.7359 -0.0149 0.0407  False
-     7     21   0.0111    0.9 -0.0206 0.0428  False
-     7     28   0.0043    0.9 -0.0258 0.0344  False
-    14     21  -0.0018    0.9 -0.0325 0.0288  False
-    14     28  -0.0086    0.9 -0.0377 0.0204  False
-    21     28  -0.0068    0.9 -0.0396  0.026  False
+     0      3   0.0042    0.9 -0.0258 0.0342  False
+     0      7   0.0102 0.8914 -0.0175 0.0379  False
+     0     14   0.0244 0.0909 -0.0022  0.051  False
+     0     21   0.0217 0.3141 -0.0087 0.0522  False
+     0     28   0.0174 0.5037 -0.0114 0.0463  False
+     3      7    0.006    0.9 -0.0244 0.0364  False
+     3     14   0.0202  0.358 -0.0092 0.0496  False
+     3     21   0.0175 0.6253 -0.0155 0.0504  False
+     3     28   0.0132  0.809 -0.0183 0.0447  False
+     7     14   0.0142 0.6352 -0.0129 0.0413  False
+     7     21   0.0115 0.8872 -0.0194 0.0423  False
+     7     28   0.0072    0.9 -0.0221 0.0365  False
+    14     21  -0.0027    0.9 -0.0326 0.0271  False
+    14     28   -0.007    0.9 -0.0353 0.0213  False
+    21     28  -0.0043    0.9 -0.0362 0.0277  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.29052541]	No
-Stroke	Sham	14	[0.4498976]	No
-Stroke	Sham	21	[0.79990313]	No
-Stroke	Sham	28	[0.51001913]	No
-Stroke	Sham	7	[0.69606152]	No
-Stroke	Sham	0	[0.73809472]	No
+Stroke	Sham	3	[0.7282952]	No
+Stroke	Sham	14	[0.49886832]	No
+Stroke	Sham	21	[0.58651728]	No
+Stroke	Sham	28	[0.4938302]	No
+Stroke	Sham	7	[0.49952438]	No
+Stroke	Sham	0	[0.51959295]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CC_MOp-MOp_cut_log.txt

@@ -1,67 +1,67 @@
 Model Name: md_CC_MOp-MOp_cut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0069
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.002    0.000 3.406 0.001  0.001  0.002
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0053
+Min. group size:        156          Log-Likelihood:          inf   
+Max. group size:        205          Converged:               Yes   
+Mean group size:        180.5                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 142811.254 0.000 1.000 -279904.914 279904.914
+merged_timepoint 0.001      0.000 3.100 0.002       0.000      0.002
+Group Var        0.000                                              
+====================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0066    0.9 -0.0647 0.0516  False
-     0      7   0.0088    0.9 -0.0527 0.0702  False
-     0     14   0.0432 0.3175 -0.0174 0.1038  False
-     0     21   0.0631 0.0359  0.0025 0.1237   True
-     0     28    0.051 0.1862 -0.0119 0.1139  False
-     3      7   0.0153    0.9 -0.0418 0.0725  False
-     3     14   0.0497 0.1163 -0.0065  0.106  False
-     3     21   0.0697  0.006  0.0134 0.1259   True
-     3     28   0.0575 0.0586 -0.0012 0.1163  False
-     7     14   0.0344 0.5503 -0.0252 0.0941  False
-     7     21   0.0544 0.0963 -0.0053  0.114  False
-     7     28   0.0422 0.3696 -0.0197 0.1042  False
-    14     21   0.0199    0.9 -0.0388 0.0786  False
-    14     28   0.0078    0.9 -0.0533 0.0689  False
-    21     28  -0.0121    0.9 -0.0732  0.049  False
+     0      3  -0.0076    0.9 -0.0555 0.0403  False
+     0      7  -0.0202 0.8424 -0.0708 0.0303  False
+     0     14   0.0265 0.6248 -0.0233 0.0764  False
+     0     21   0.0348 0.3419 -0.0151 0.0846  False
+     0     28   0.0409 0.2098 -0.0109 0.0926  False
+     3      7  -0.0126    0.9 -0.0592  0.034  False
+     3     14   0.0341 0.2693 -0.0117   0.08  False
+     3     21   0.0424 0.0878 -0.0035 0.0882  False
+     3     28   0.0485 0.0453  0.0006 0.0963   True
+     7     14   0.0468 0.0669 -0.0018 0.0954  False
+     7     21    0.055 0.0165  0.0064 0.1036   True
+     7     28   0.0611  0.008  0.0106 0.1116   True
+    14     21   0.0082    0.9 -0.0396 0.0561  False
+    14     28   0.0143    0.9 -0.0355 0.0642  False
+    21     28   0.0061    0.9 -0.0437 0.0559  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0221    0.9 -0.0409  0.085  False
-     0      7    0.019    0.9 -0.0407 0.0787  False
-     0     14   0.0294 0.6542 -0.0279 0.0867  False
-     0     21   0.0035    0.9 -0.0621 0.0691  False
-     0     28   0.0154    0.9 -0.0468 0.0776  False
-     3      7  -0.0031    0.9  -0.067 0.0609  False
-     3     14   0.0074    0.9 -0.0544 0.0691  False
-     3     21  -0.0185    0.9  -0.088  0.051  False
-     3     28  -0.0066    0.9  -0.073 0.0597  False
-     7     14   0.0105    0.9 -0.0479 0.0688  False
-     7     21  -0.0154    0.9  -0.082 0.0511  False
-     7     28  -0.0036    0.9 -0.0668 0.0597  False
-    14     21  -0.0259 0.8377 -0.0903 0.0385  False
-    14     28   -0.014    0.9  -0.075  0.047  False
-    21     28   0.0119    0.9 -0.0569 0.0807  False
+     0      3   0.0307 0.6981 -0.0324 0.0937  False
+     0      7   0.0175    0.9 -0.0407 0.0758  False
+     0     14   0.0243 0.7824 -0.0316 0.0803  False
+     0     21   0.0184    0.9 -0.0455 0.0824  False
+     0     28   0.0127    0.9  -0.048 0.0734  False
+     3      7  -0.0132    0.9 -0.0772 0.0508  False
+     3     14  -0.0063    0.9 -0.0682 0.0555  False
+     3     21  -0.0122    0.9 -0.0815  0.057  False
+     3     28  -0.0179    0.9 -0.0842 0.0483  False
+     7     14   0.0068    0.9 -0.0501 0.0638  False
+     7     21   0.0009    0.9  -0.064 0.0658  False
+     7     28  -0.0048    0.9 -0.0664 0.0569  False
+    14     21  -0.0059    0.9 -0.0687 0.0569  False
+    14     28  -0.0116    0.9 -0.0711 0.0479  False
+    21     28  -0.0057    0.9 -0.0728 0.0614  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.10739049]	No
-Stroke	Sham	14	[0.92448591]	No
-Stroke	Sham	21	[0.03377416]	Yes
-Stroke	Sham	28	[0.19452939]	No
-Stroke	Sham	7	[0.09278964]	No
-Stroke	Sham	0	[0.68348494]	No
+Stroke	Sham	3	[0.03090795]	Yes
+Stroke	Sham	14	[0.99807817]	No
+Stroke	Sham	21	[0.62712935]	No
+Stroke	Sham	28	[0.10681444]	No
+Stroke	Sham	7	[0.00280311]	Yes
+Stroke	Sham	0	[0.87641959]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CC_MOp-MOp_dilated_cut_log.txt

@@ -1,67 +1,67 @@
 Model Name: md_CC_MOp-MOp_dilated_cut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0058
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 2.846 0.004  0.000  0.002
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0047
+Min. group size:        156          Log-Likelihood:          inf   
+Max. group size:        205          Converged:               Yes   
+Mean group size:        180.5                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 134305.875 0.000 1.000 -263234.678 263234.678
+merged_timepoint 0.001      0.000 2.355 0.019       0.000      0.002
+Group Var        0.000                                              
+====================================================================
 
 Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0177    0.9 -0.0353 0.0707  False
-     0      7  -0.0004    0.9 -0.0564 0.0557  False
-     0     14    0.038 0.3577 -0.0172 0.0933  False
-     0     21   0.0531 0.0679 -0.0022 0.1083  False
-     0     28   0.0434 0.2538  -0.014 0.1007  False
-     3      7  -0.0181    0.9 -0.0702  0.034  False
-     3     14   0.0203 0.8492 -0.0309 0.0716  False
-     3     21   0.0353 0.3555 -0.0159 0.0866  False
-     3     28   0.0257 0.7124 -0.0279 0.0792  False
-     7     14   0.0384 0.3277  -0.016 0.0927  False
-     7     21   0.0534 0.0572 -0.0009 0.1078  False
-     7     28   0.0437 0.2301 -0.0128 0.1002  False
-    14     21    0.015    0.9 -0.0385 0.0686  False
-    14     28   0.0053    0.9 -0.0504 0.0611  False
-    21     28  -0.0097    0.9 -0.0654  0.046  False
----------------------------------------------------
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0224 0.6513 -0.0209  0.0657  False
+     0      7  -0.0234 0.6597  -0.069  0.0223  False
+     0     14   0.0271 0.5107  -0.018  0.0722  False
+     0     21   0.0409 0.0997 -0.0042  0.0859  False
+     0     28   0.0346 0.2772 -0.0122  0.0813  False
+     3      7  -0.0457 0.0248 -0.0878 -0.0036   True
+     3     14   0.0048    0.9 -0.0367  0.0462  False
+     3     21   0.0185 0.7667 -0.0229    0.06  False
+     3     28   0.0122    0.9 -0.0311  0.0555  False
+     7     14   0.0505 0.0141  0.0065  0.0944   True
+     7     21   0.0642  0.001  0.0203  0.1082   True
+     7     28   0.0579 0.0045  0.0123  0.1036   True
+    14     21   0.0137    0.9 -0.0295   0.057  False
+    14     28   0.0075    0.9 -0.0376  0.0525  False
+    21     28  -0.0063    0.9 -0.0513  0.0388  False
+----------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3    0.023 0.8567 -0.0359 0.0818  False
-     0      7   0.0189    0.9 -0.0369 0.0746  False
-     0     14   0.0282 0.6324 -0.0254 0.0817  False
-     0     21   0.0083    0.9 -0.0529 0.0696  False
-     0     28   0.0204    0.9 -0.0377 0.0785  False
-     3      7  -0.0041    0.9 -0.0638 0.0556  False
-     3     14   0.0052    0.9 -0.0524 0.0629  False
-     3     21  -0.0147    0.9 -0.0795 0.0502  False
-     3     28  -0.0026    0.9 -0.0645 0.0594  False
-     7     14   0.0093    0.9 -0.0452 0.0638  False
-     7     21  -0.0106    0.9 -0.0727 0.0516  False
-     7     28   0.0015    0.9 -0.0575 0.0605  False
-    14     21  -0.0199    0.9   -0.08 0.0403  False
-    14     28  -0.0078    0.9 -0.0647 0.0491  False
-    21     28   0.0121    0.9 -0.0522 0.0763  False
+     0      3   0.0289 0.7185  -0.032 0.0898  False
+     0      7   0.0169    0.9 -0.0393 0.0732  False
+     0     14   0.0202 0.8826 -0.0338 0.0742  False
+     0     21   0.0149    0.9 -0.0469 0.0767  False
+     0     28   0.0136    0.9  -0.045 0.0722  False
+     3      7  -0.0119    0.9 -0.0737 0.0499  False
+     3     14  -0.0086    0.9 -0.0684 0.0511  False
+     3     21   -0.014    0.9 -0.0809 0.0529  False
+     3     28  -0.0153    0.9 -0.0793 0.0487  False
+     7     14   0.0033    0.9 -0.0517 0.0583  False
+     7     21   -0.002    0.9 -0.0647 0.0607  False
+     7     28  -0.0033    0.9 -0.0629 0.0562  False
+    14     21  -0.0053    0.9  -0.066 0.0554  False
+    14     28  -0.0066    0.9 -0.0641 0.0508  False
+    21     28  -0.0013    0.9 -0.0661 0.0635  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.95807378]	No
-Stroke	Sham	14	[0.39449075]	No
-Stroke	Sham	21	[0.04786402]	Yes
-Stroke	Sham	28	[0.09991819]	No
-Stroke	Sham	7	[0.2858972]	No
-Stroke	Sham	0	[0.87030108]	No
+Stroke	Sham	3	[0.87666217]	No
+Stroke	Sham	14	[0.54930837]	No
+Stroke	Sham	21	[0.30220089]	No
+Stroke	Sham	28	[0.07844929]	No
+Stroke	Sham	7	[0.00677388]	Yes
+Stroke	Sham	0	[0.78461815]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CC_MOs-MOs_cut_log.txt

@@ -1,67 +1,67 @@
 Model Name: md_CC_MOs-MOs_cut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM  Dependent Variable:  Value   
-No. Observations:   364      Method:              REML    
-No. Groups:         2        Scale:               0.0078  
-Min. group size:    158      Log-Likelihood:      356.1808
-Max. group size:    206      Converged:           Yes     
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        0.743    0.008 89.946 0.000  0.727  0.759
-merged_timepoint 0.001    0.000  2.272 0.023  0.000  0.002
-Group Var        0.000    0.001                           
-==========================================================
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0064
+Min. group size:        156          Log-Likelihood:          inf   
+Max. group size:        205          Converged:               Yes   
+Mean group size:        180.5                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 156699.713 0.000 1.000 -307125.795 307125.795
+merged_timepoint 0.001      0.000 2.101 0.036       0.000      0.002
+Group Var        0.000                                              
+====================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0147    0.9 -0.0422 0.0716  False
-     0      7     0.02    0.9 -0.0401 0.0801  False
-     0     14   0.0409 0.3543 -0.0184 0.1002  False
-     0     21   0.0599  0.046  0.0006 0.1192   True
-     0     28    0.047 0.2443 -0.0146 0.1085  False
-     3      7   0.0053    0.9 -0.0506 0.0612  False
-     3     14   0.0262 0.7173 -0.0288 0.0812  False
-     3     21   0.0452 0.1742 -0.0098 0.1002  False
-     3     28   0.0322 0.5772 -0.0252 0.0897  False
-     7     14   0.0209    0.9 -0.0374 0.0792  False
-     7     21   0.0399 0.3642 -0.0184 0.0982  False
-     7     28    0.027 0.7692 -0.0336 0.0876  False
-    14     21    0.019    0.9 -0.0385 0.0764  False
-    14     28    0.006    0.9 -0.0537 0.0658  False
-    21     28  -0.0129    0.9 -0.0727 0.0468  False
+     0      3  -0.0008    0.9 -0.0545  0.053  False
+     0      7  -0.0099    0.9 -0.0667 0.0468  False
+     0     14   0.0349 0.4727 -0.0211 0.0908  False
+     0     21   0.0321 0.5567 -0.0238  0.088  False
+     0     28    0.035 0.5093 -0.0231  0.093  False
+     3      7  -0.0091    0.9 -0.0614 0.0432  False
+     3     14   0.0357 0.3491 -0.0158 0.0871  False
+     3     21   0.0329 0.4448 -0.0186 0.0844  False
+     3     28   0.0358 0.3975  -0.018 0.0895  False
+     7     14   0.0448 0.1743 -0.0097 0.0994  False
+     7     21    0.042 0.2346 -0.0125 0.0966  False
+     7     28   0.0449 0.2078 -0.0118 0.1016  False
+    14     21  -0.0028    0.9 -0.0565  0.051  False
+    14     28   0.0001    0.9 -0.0559  0.056  False
+    21     28   0.0029    0.9 -0.0531 0.0588  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0379 0.6752 -0.0378 0.1136  False
-     0      7   0.0137    0.9 -0.0581 0.0855  False
-     0     14   0.0178    0.9 -0.0511 0.0867  False
-     0     21   0.0152    0.9 -0.0637 0.0941  False
-     0     28   0.0129    0.9 -0.0619 0.0877  False
-     3      7  -0.0242    0.9 -0.1011 0.0527  False
-     3     14  -0.0201    0.9 -0.0943 0.0541  False
-     3     21  -0.0227    0.9 -0.1062 0.0608  False
-     3     28   -0.025    0.9 -0.1047 0.0548  False
-     7     14   0.0041    0.9 -0.0661 0.0743  False
-     7     21   0.0015    0.9 -0.0785 0.0815  False
-     7     28  -0.0008    0.9 -0.0768 0.0752  False
-    14     21  -0.0026    0.9   -0.08 0.0748  False
-    14     28  -0.0049    0.9 -0.0781 0.0684  False
-    21     28  -0.0023    0.9  -0.085 0.0804  False
+     0      3    0.049  0.296 -0.0185 0.1165  False
+     0      7   0.0146    0.9 -0.0478  0.077  False
+     0     14    0.017    0.9 -0.0429 0.0768  False
+     0     21   0.0254 0.8895 -0.0431 0.0939  False
+     0     28   0.0096    0.9 -0.0554 0.0746  False
+     3      7  -0.0344 0.6723 -0.1029 0.0341  False
+     3     14   -0.032  0.703 -0.0983 0.0342  False
+     3     21  -0.0236    0.9 -0.0978 0.0506  False
+     3     28  -0.0394 0.5846 -0.1103 0.0315  False
+     7     14   0.0024    0.9 -0.0586 0.0634  False
+     7     21   0.0108    0.9 -0.0587 0.0803  False
+     7     28   -0.005    0.9  -0.071 0.0611  False
+    14     21   0.0084    0.9 -0.0588 0.0757  False
+    14     28  -0.0073    0.9  -0.071 0.0563  False
+    21     28  -0.0158    0.9 -0.0877 0.0561  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.11665273]	No
-Stroke	Sham	14	[0.82991033]	No
-Stroke	Sham	21	[0.41614924]	No
-Stroke	Sham	28	[0.69183004]	No
-Stroke	Sham	7	[0.16127883]	No
-Stroke	Sham	0	[0.37905712]	No
+Stroke	Sham	3	[0.00467299]	Yes
+Stroke	Sham	14	[0.74222301]	No
+Stroke	Sham	21	[0.92297078]	No
+Stroke	Sham	28	[0.36442848]	No
+Stroke	Sham	7	[0.01277025]	Yes
+Stroke	Sham	0	[0.55677453]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CC_SSp_ll-SSp_ll_cut_log.txt

@@ -1,67 +1,67 @@
 Model Name: md_CC_SSp_ll-SSp_ll_cut
-           Mixed Linear Model Regression Results
-===========================================================
-Model:               MixedLM   Dependent Variable:   Value 
-No. Observations:    364       Method:               REML  
-No. Groups:          2         Scale:                0.0139
-Min. group size:     158       Log-Likelihood:       inf   
-Max. group size:     206       Converged:            Yes   
-Mean group size:     182.0                                 
------------------------------------------------------------
-                 Coef.  Std.Err.   z    P>|z| [0.025 0.975]
------------------------------------------------------------
-Intercept         0.000                                    
-merged_timepoint -0.002    0.001 -3.863 0.000 -0.004 -0.001
-Group Var         0.000                                    
-===========================================================
+                Mixed Linear Model Regression Results
+======================================================================
+Model:                  MixedLM       Dependent Variable:       Value 
+No. Observations:       361           Method:                   REML  
+No. Groups:             2             Scale:                    0.0107
+Min. group size:        156           Log-Likelihood:           inf   
+Max. group size:        205           Converged:                Yes   
+Mean group size:        180.5                                         
+----------------------------------------------------------------------
+                 Coef.   Std.Err.    z    P>|z|    [0.025     0.975]  
+----------------------------------------------------------------------
+Intercept        -0.000 202164.871 -0.000 1.000 -396235.865 396235.865
+merged_timepoint -0.002      0.001 -2.800 0.005      -0.003     -0.000
+Group Var         0.000                                               
+======================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05 
 ====================================================
 group1 group2 meandiff p-adj   lower   upper  reject
 ----------------------------------------------------
-     0      3   0.2256  0.001  0.1488  0.3024   True
-     0      7  -0.0024    0.9 -0.0835  0.0787  False
-     0     14   0.0505 0.4601 -0.0295  0.1305  False
-     0     21    0.017    0.9  -0.063   0.097  False
-     0     28   0.0104    0.9 -0.0727  0.0935  False
-     3      7   -0.228  0.001 -0.3035 -0.1526   True
-     3     14  -0.1752  0.001 -0.2494 -0.1009   True
-     3     21  -0.2086  0.001 -0.2829 -0.1344   True
-     3     28  -0.2152  0.001 -0.2927 -0.1376   True
-     7     14   0.0529 0.3866 -0.0258  0.1316  False
-     7     21   0.0194    0.9 -0.0593  0.0981  False
-     7     28   0.0128    0.9  -0.069  0.0947  False
-    14     21  -0.0335 0.7905  -0.111   0.044  False
-    14     28    -0.04 0.6848 -0.1207  0.0407  False
-    21     28  -0.0065    0.9 -0.0872  0.0742  False
+     0      3   0.1796  0.001  0.1129  0.2464   True
+     0      7  -0.0228    0.9 -0.0933  0.0476  False
+     0     14    0.054 0.2256 -0.0155  0.1235  False
+     0     21   0.0549 0.2091 -0.0145  0.1244  False
+     0     28  -0.0063    0.9 -0.0784  0.0658  False
+     3      7  -0.2025  0.001 -0.2674 -0.1375   True
+     3     14  -0.1256  0.001 -0.1895 -0.0617   True
+     3     21  -0.1247  0.001 -0.1886 -0.0608   True
+     3     28  -0.1859  0.001 -0.2526 -0.1191   True
+     7     14   0.0769 0.0161  0.0091  0.1446   True
+     7     21   0.0778 0.0142    0.01  0.1455   True
+     7     28   0.0166    0.9 -0.0539   0.087  False
+    14     21   0.0009    0.9 -0.0658  0.0677  False
+    14     28  -0.0603 0.1298 -0.1298  0.0092  False
+    21     28  -0.0612 0.1194 -0.1307  0.0083  False
 ----------------------------------------------------
 Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05 
-====================================================
-group1 group2 meandiff p-adj   lower   upper  reject
-----------------------------------------------------
-     0      3   0.0728 0.0244  0.0059  0.1397   True
-     0      7   0.0108    0.9 -0.0527  0.0742  False
-     0     14  -0.0032    0.9 -0.0641  0.0577  False
-     0     21   0.0093    0.9 -0.0604   0.079  False
-     0     28  -0.0048    0.9 -0.0709  0.0613  False
-     3      7   -0.062 0.0951   -0.13  0.0059  False
-     3     14   -0.076  0.013 -0.1416 -0.0104   True
-     3     21  -0.0635 0.1354 -0.1374  0.0103  False
-     3     28  -0.0776 0.0217 -0.1481 -0.0071   True
-     7     14   -0.014    0.9  -0.076  0.0481  False
-     7     21  -0.0015    0.9 -0.0722  0.0692  False
-     7     28  -0.0156    0.9 -0.0827  0.0516  False
-    14     21   0.0125    0.9 -0.0559  0.0809  False
-    14     28  -0.0016    0.9 -0.0664  0.0632  False
-    21     28  -0.0141    0.9 -0.0872   0.059  False
-----------------------------------------------------
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0472 0.3047 -0.0184 0.1128  False
+     0      7   0.0106    0.9 -0.0499 0.0712  False
+     0     14   -0.004    0.9 -0.0621 0.0542  False
+     0     21   0.0122    0.9 -0.0544 0.0788  False
+     0     28   -0.003    0.9 -0.0661 0.0601  False
+     3      7  -0.0366 0.5944 -0.1031   0.03  False
+     3     14  -0.0512 0.2022 -0.1155 0.0132  False
+     3     21   -0.035 0.6988 -0.1071  0.037  False
+     3     28  -0.0502 0.2911 -0.1191 0.0187  False
+     7     14  -0.0146    0.9 -0.0739 0.0446  False
+     7     21   0.0015    0.9  -0.066  0.069  False
+     7     28  -0.0136    0.9 -0.0778 0.0505  False
+    14     21   0.0162    0.9 -0.0492 0.0815  False
+    14     28    0.001    0.9 -0.0609 0.0628  False
+    21     28  -0.0152    0.9  -0.085 0.0546  False
+---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.00243782]	Yes
-Stroke	Sham	14	[0.05485291]	No
-Stroke	Sham	21	[0.79370546]	No
-Stroke	Sham	28	[0.93348063]	No
-Stroke	Sham	7	[0.00715317]	Yes
-Stroke	Sham	0	[0.4498344]	No
+Stroke	Sham	3	[0.00067405]	Yes
+Stroke	Sham	14	[0.00384556]	Yes
+Stroke	Sham	21	[0.19006409]	No
+Stroke	Sham	28	[0.96883991]	No
+Stroke	Sham	7	[0.00888935]	Yes
+Stroke	Sham	0	[0.79385561]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CC_SSp_ul-SSp_ul_cut_log.txt

@@ -1,67 +1,67 @@
 Model Name: md_CC_SSp_ul-SSp_ul_cut
-           Mixed Linear Model Regression Results
-===========================================================
-Model:               MixedLM   Dependent Variable:   Value 
-No. Observations:    364       Method:               REML  
-No. Groups:          2         Scale:                0.0124
-Min. group size:     158       Log-Likelihood:       inf   
-Max. group size:     206       Converged:            Yes   
-Mean group size:     182.0                                 
------------------------------------------------------------
-                 Coef.  Std.Err.   z    P>|z| [0.025 0.975]
------------------------------------------------------------
-Intercept         0.000                                    
-merged_timepoint -0.002    0.001 -3.076 0.002 -0.003 -0.001
-Group Var         0.000                                    
-===========================================================
+                Mixed Linear Model Regression Results
+======================================================================
+Model:                  MixedLM       Dependent Variable:       Value 
+No. Observations:       361           Method:                   REML  
+No. Groups:             2             Scale:                    0.0092
+Min. group size:        156           Log-Likelihood:           inf   
+Max. group size:        205           Converged:                Yes   
+Mean group size:        180.5                                         
+----------------------------------------------------------------------
+                 Coef.   Std.Err.    z    P>|z|    [0.025     0.975]  
+----------------------------------------------------------------------
+Intercept        -0.000 187597.856 -0.000 1.000 -367685.041 367685.041
+merged_timepoint -0.001      0.001 -2.160 0.031      -0.002     -0.000
+Group Var         0.000                                               
+======================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05 
 ====================================================
 group1 group2 meandiff p-adj   lower   upper  reject
 ----------------------------------------------------
-     0      3   0.2005  0.001  0.1267  0.2742   True
-     0      7   0.0005    0.9 -0.0774  0.0784  False
-     0     14   0.0515 0.3899 -0.0254  0.1283  False
-     0     21   0.0221    0.9 -0.0547   0.099  False
-     0     28   0.0213    0.9 -0.0585  0.1011  False
-     3      7     -0.2  0.001 -0.2725 -0.1275   True
-     3     14   -0.149  0.001 -0.2203 -0.0777   True
-     3     21  -0.1783  0.001 -0.2496  -0.107   True
-     3     28  -0.1792  0.001 -0.2537 -0.1047   True
-     7     14    0.051 0.3817 -0.0246  0.1266  False
-     7     21   0.0216    0.9  -0.054  0.0972  False
-     7     28   0.0208    0.9 -0.0578  0.0994  False
-    14     21  -0.0294  0.853 -0.1038  0.0451  False
-    14     28  -0.0302 0.8606 -0.1077  0.0473  False
-    21     28  -0.0008    0.9 -0.0784  0.0767  False
+     0      3   0.1593  0.001   0.098  0.2206   True
+     0      7  -0.0183    0.9  -0.083  0.0464  False
+     0     14   0.0511 0.1973 -0.0127  0.1149  False
+     0     21   0.0532 0.1613 -0.0106   0.117  False
+     0     28   0.0057    0.9 -0.0605  0.0719  False
+     3      7  -0.1776  0.001 -0.2373  -0.118   True
+     3     14  -0.1083  0.001  -0.167 -0.0496   True
+     3     21  -0.1061  0.001 -0.1648 -0.0474   True
+     3     28  -0.1537  0.001  -0.215 -0.0924   True
+     7     14   0.0694 0.0191  0.0072  0.1316   True
+     7     21   0.0715  0.014  0.0093  0.1337   True
+     7     28    0.024 0.8914 -0.0407  0.0887  False
+    14     21   0.0021    0.9 -0.0592  0.0634  False
+    14     28  -0.0454 0.3194 -0.1092  0.0184  False
+    21     28  -0.0475 0.2693 -0.1113  0.0163  False
 ----------------------------------------------------
 Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05 
-====================================================
-group1 group2 meandiff p-adj   lower   upper  reject
-----------------------------------------------------
-     0      3   0.0646 0.0561  -0.001  0.1302  False
-     0      7   0.0159    0.9 -0.0463  0.0781  False
-     0     14  -0.0026    0.9 -0.0623  0.0571  False
-     0     21   0.0158    0.9 -0.0525  0.0841  False
-     0     28   0.0024    0.9 -0.0624  0.0672  False
-     3      7  -0.0487 0.2867 -0.1153  0.0179  False
-     3     14  -0.0672 0.0347 -0.1315 -0.0029   True
-     3     21  -0.0488 0.3783 -0.1212  0.0235  False
-     3     28  -0.0622 0.1036 -0.1313  0.0069  False
-     7     14  -0.0185    0.9 -0.0793  0.0423  False
-     7     21  -0.0001    0.9 -0.0694  0.0692  False
-     7     28  -0.0135    0.9 -0.0793  0.0524  False
-    14     21   0.0184    0.9 -0.0487  0.0855  False
-    14     28    0.005    0.9 -0.0585  0.0685  False
-    21     28  -0.0134    0.9  -0.085  0.0583  False
-----------------------------------------------------
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0438 0.3839 -0.0214  0.109  False
+     0      7   0.0135    0.9 -0.0468 0.0737  False
+     0     14  -0.0022    0.9   -0.06 0.0556  False
+     0     21   0.0172    0.9  -0.049 0.0834  False
+     0     28   0.0021    0.9 -0.0607 0.0648  False
+     3      7  -0.0303 0.7441 -0.0965 0.0358  False
+     3     14   -0.046 0.3058   -0.11  0.018  False
+     3     21  -0.0266 0.8879 -0.0982  0.045  False
+     3     28  -0.0417 0.4949 -0.1102 0.0268  False
+     7     14  -0.0157    0.9 -0.0746 0.0432  False
+     7     21   0.0037    0.9 -0.0634 0.0709  False
+     7     28  -0.0114    0.9 -0.0752 0.0524  False
+    14     21   0.0194    0.9 -0.0456 0.0844  False
+    14     28   0.0043    0.9 -0.0572 0.0658  False
+    21     28  -0.0151    0.9 -0.0845 0.0543  False
+---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.00129595]	Yes
-Stroke	Sham	14	[0.0112815]	Yes
-Stroke	Sham	21	[0.98830089]	No
-Stroke	Sham	28	[0.4237445]	No
-Stroke	Sham	7	[0.08532639]	No
-Stroke	Sham	0	[0.79223814]	No
+Stroke	Sham	3	[0.00063118]	Yes
+Stroke	Sham	14	[0.00227219]	Yes
+Stroke	Sham	21	[0.21132111]	No
+Stroke	Sham	28	[0.47916939]	No
+Stroke	Sham	7	[0.03174414]	Yes
+Stroke	Sham	0	[0.52542698]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CReT_MOp-TRN_ipsilesional_CCcut_log.txt

@@ -1,67 +1,67 @@
 Model Name: md_CReT_MOp-TRN_ipsilesional_CCcut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0075
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 2.424 0.015  0.000  0.002
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0049
+Min. group size:        156          Log-Likelihood:          inf   
+Max. group size:        205          Converged:               Yes   
+Mean group size:        180.5                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 136303.840 0.000 1.000 -267150.618 267150.618
+merged_timepoint 0.002      0.000 4.458 0.000       0.001      0.002
+Group Var        0.000                                              
+====================================================================
 
 Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05 
-====================================================
-group1 group2 meandiff p-adj   lower   upper  reject
-----------------------------------------------------
-     0      3  -0.0578 0.0455  -0.115 -0.0007   True
-     0      7  -0.0085    0.9 -0.0689  0.0518  False
-     0     14  -0.0132    0.9 -0.0727  0.0463  False
-     0     21   0.0178    0.9 -0.0417  0.0773  False
-     0     28   0.0302 0.6975 -0.0316   0.092  False
-     3      7   0.0493 0.1218 -0.0069  0.1054  False
-     3     14   0.0446 0.1882 -0.0106  0.0999  False
-     3     21   0.0756 0.0016  0.0204  0.1308   True
-     3     28    0.088  0.001  0.0303  0.1457   True
-     7     14  -0.0046    0.9 -0.0632  0.0539  False
-     7     21   0.0263 0.7611 -0.0322  0.0849  False
-     7     28   0.0387 0.4503 -0.0221  0.0996  False
-    14     21    0.031 0.6177 -0.0267  0.0886  False
-    14     28   0.0434 0.3032 -0.0167  0.1034  False
-    21     28   0.0124    0.9 -0.0476  0.0724  False
-----------------------------------------------------
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0312 0.3137 -0.0748 0.0124  False
+     0      7  -0.0284 0.4855 -0.0744 0.0176  False
+     0     14   0.0128    0.9 -0.0326 0.0581  False
+     0     21   0.0288 0.4526 -0.0166 0.0742  False
+     0     28     0.04 0.1462 -0.0071 0.0871  False
+     3      7   0.0028    0.9 -0.0396 0.0452  False
+     3     14    0.044 0.0325  0.0022 0.0857   True
+     3     21     0.06  0.001  0.0182 0.1017   True
+     3     28   0.0712  0.001  0.0276 0.1148   True
+     7     14   0.0411  0.085 -0.0031 0.0854  False
+     7     21   0.0572 0.0035  0.0129 0.1014   True
+     7     28   0.0683  0.001  0.0223 0.1143   True
+    14     21    0.016 0.8968 -0.0276 0.0596  False
+    14     28   0.0272 0.5139 -0.0182 0.0726  False
+    21     28   0.0112    0.9 -0.0342 0.0566  False
+---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0321 0.7262 -0.0363 0.1005  False
-     0      7  -0.0283 0.7813 -0.0931 0.0365  False
-     0     14   0.0115    0.9 -0.0507 0.0737  False
-     0     21   0.0065    0.9 -0.0647 0.0777  False
-     0     28  -0.0072    0.9 -0.0748 0.0603  False
-     3      7  -0.0604 0.1272 -0.1298  0.009  False
-     3     14  -0.0206    0.9 -0.0876 0.0464  False
-     3     21  -0.0256    0.9  -0.101 0.0498  False
-     3     28  -0.0393 0.5991 -0.1113 0.0326  False
-     7     14   0.0398 0.4635 -0.0236 0.1031  False
-     7     21   0.0348 0.7066 -0.0374  0.107  False
-     7     28    0.021    0.9 -0.0476 0.0896  False
-    14     21   -0.005    0.9 -0.0749 0.0649  False
-    14     28  -0.0187    0.9 -0.0849 0.0474  False
-    21     28  -0.0137    0.9 -0.0884 0.0609  False
+     0      3   0.0211    0.9 -0.0413 0.0834  False
+     0      7   0.0034    0.9 -0.0542  0.061  False
+     0     14   0.0367 0.3991 -0.0186 0.0919  False
+     0     21   0.0303 0.7112  -0.033 0.0935  False
+     0     28   0.0182    0.9 -0.0418 0.0782  False
+     3      7  -0.0177    0.9 -0.0809 0.0456  False
+     3     14   0.0156    0.9 -0.0456 0.0768  False
+     3     21   0.0092    0.9 -0.0592 0.0777  False
+     3     28  -0.0029    0.9 -0.0684 0.0626  False
+     7     14   0.0333  0.526  -0.023 0.0896  False
+     7     21   0.0269 0.8096 -0.0373  0.091  False
+     7     28   0.0148    0.9 -0.0462 0.0757  False
+    14     21  -0.0064    0.9 -0.0685 0.0557  False
+    14     28  -0.0185    0.9 -0.0773 0.0403  False
+    21     28  -0.0121    0.9 -0.0784 0.0542  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.00613323]	Yes
-Stroke	Sham	14	[0.46404731]	No
-Stroke	Sham	21	[0.38436043]	No
-Stroke	Sham	28	[0.03722408]	Yes
-Stroke	Sham	7	[0.06255234]	No
-Stroke	Sham	0	[0.6302699]	No
+Stroke	Sham	3	[0.0292003]	Yes
+Stroke	Sham	14	[0.46570766]	No
+Stroke	Sham	21	[0.7248476]	No
+Stroke	Sham	28	[0.12159922]	No
+Stroke	Sham	7	[0.08496249]	No
+Stroke	Sham	0	[0.43708227]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CRuT_MOp-RN_ipsilesional_log.txt

@@ -1,67 +1,67 @@
 Model Name: md_CRuT_MOp-RN_ipsilesional
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0065
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.002    0.000 3.454 0.001  0.001  0.002
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0052
+Min. group size:        156          Log-Likelihood:          inf   
+Max. group size:        205          Converged:               Yes   
+Mean group size:        180.5                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 141365.369 0.000 1.000 -277071.031 277071.031
+merged_timepoint 0.002      0.000 4.950 0.000       0.001      0.003
+Group Var        0.000                                              
+====================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0393 0.2401 -0.0906  0.012  False
-     0      7   -0.023 0.8017 -0.0773 0.0312  False
-     0     14   0.0125    0.9  -0.041 0.0659  False
-     0     21   0.0286   0.62 -0.0248 0.0821  False
-     0     28   0.0419 0.2546 -0.0136 0.0974  False
-     3      7   0.0163    0.9 -0.0341 0.0667  False
-     3     14   0.0518  0.035  0.0022 0.1014   True
-     3     21   0.0679 0.0016  0.0183 0.1175   True
-     3     28   0.0812  0.001  0.0294  0.133   True
-     7     14   0.0355 0.3792  -0.017 0.0881  False
-     7     21   0.0517 0.0573 -0.0009 0.1042  False
-     7     28    0.065 0.0097  0.0103 0.1196   True
-    14     21   0.0161    0.9 -0.0357 0.0679  False
-    14     28   0.0294 0.6026 -0.0245 0.0834  False
-    21     28   0.0133    0.9 -0.0406 0.0672  False
+     0      3  -0.0244 0.6099 -0.0695 0.0207  False
+     0      7  -0.0331 0.3466 -0.0807 0.0145  False
+     0     14    0.027 0.5526 -0.0199  0.074  False
+     0     21   0.0349 0.2725 -0.0121 0.0818  False
+     0     28   0.0515 0.0317  0.0027 0.1002   True
+     3      7  -0.0086    0.9 -0.0525 0.0352  False
+     3     14   0.0515 0.0094  0.0083 0.0947   True
+     3     21   0.0593 0.0015  0.0161 0.1025   True
+     3     28   0.0759  0.001  0.0308  0.121   True
+     7     14   0.0601 0.0028  0.0143 0.1059   True
+     7     21   0.0679  0.001  0.0222 0.1137   True
+     7     28   0.0845  0.001  0.0369 0.1321   True
+    14     21   0.0078    0.9 -0.0373 0.0529  False
+    14     28   0.0244 0.6454 -0.0225 0.0714  False
+    21     28   0.0166    0.9 -0.0303 0.0635  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3    0.042 0.4683 -0.0253 0.1093  False
-     0      7  -0.0101    0.9 -0.0739 0.0538  False
-     0     14   0.0237 0.8628 -0.0376  0.085  False
-     0     21   0.0282 0.8365 -0.0419 0.0983  False
-     0     28   0.0058    0.9 -0.0607 0.0723  False
-     3      7  -0.0521 0.2435 -0.1204 0.0162  False
-     3     14  -0.0183    0.9 -0.0843 0.0476  False
-     3     21  -0.0138    0.9 -0.0881 0.0604  False
-     3     28  -0.0362 0.6571 -0.1071 0.0346  False
-     7     14   0.0338 0.6083 -0.0286 0.0961  False
-     7     21   0.0383 0.6123 -0.0328 0.1094  False
-     7     28   0.0159    0.9 -0.0517 0.0834  False
-    14     21   0.0045    0.9 -0.0643 0.0734  False
-    14     28  -0.0179    0.9  -0.083 0.0473  False
-    21     28  -0.0224    0.9  -0.096 0.0511  False
+     0      3    0.022    0.9 -0.0425 0.0865  False
+     0      7   0.0007    0.9 -0.0589 0.0603  False
+     0     14   0.0317 0.5871 -0.0255 0.0889  False
+     0     21   0.0334 0.6589  -0.032 0.0988  False
+     0     28   0.0218    0.9 -0.0403 0.0839  False
+     3      7  -0.0213    0.9 -0.0868 0.0441  False
+     3     14   0.0097    0.9 -0.0536 0.0729  False
+     3     21   0.0114    0.9 -0.0594 0.0822  False
+     3     28  -0.0002    0.9 -0.0679 0.0676  False
+     7     14    0.031 0.6232 -0.0273 0.0892  False
+     7     21   0.0327 0.6878 -0.0337 0.0991  False
+     7     28   0.0211    0.9 -0.0419 0.0842  False
+    14     21   0.0017    0.9 -0.0625  0.066  False
+    14     28  -0.0098    0.9 -0.0707  0.051  False
+    21     28  -0.0116    0.9 -0.0802 0.0571  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.00834269]	Yes
-Stroke	Sham	14	[0.85802399]	No
-Stroke	Sham	21	[0.55258977]	No
-Stroke	Sham	28	[0.01460692]	Yes
-Stroke	Sham	7	[0.8687555]	No
-Stroke	Sham	0	[0.34620705]	No
+Stroke	Sham	3	[0.01938846]	Yes
+Stroke	Sham	14	[0.95488821]	No
+Stroke	Sham	21	[0.84544292]	No
+Stroke	Sham	28	[0.12875115]	No
+Stroke	Sham	7	[0.02382926]	Yes
+Stroke	Sham	0	[0.76752385]	No

output/Final_Quantitative_output/mixed_model_analysis/md_OT_och-lgn_lgncut_log.txt

@@ -0,0 +1,67 @@
+Model Name: md_OT_och-lgn_lgncut
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0052
+Min. group size:        156          Log-Likelihood:          inf   
+Max. group size:        205          Converged:               Yes   
+Mean group size:        180.5                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 141310.376 0.000 1.000 -276963.248 276963.248
+merged_timepoint 0.001      0.000 2.133 0.033       0.000      0.002
+Group Var        0.000                                              
+====================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   -0.038 0.1272 -0.0816 0.0056  False
+     0      7  -0.0277 0.5108 -0.0737 0.0183  False
+     0     14    0.003    0.9 -0.0424 0.0484  False
+     0     21   0.0059    0.9 -0.0394 0.0513  False
+     0     28   0.0105    0.9 -0.0366 0.0576  False
+     3      7   0.0103    0.9 -0.0322 0.0527  False
+     3     14   0.0409 0.0581 -0.0008 0.0827  False
+     3     21   0.0439 0.0329  0.0022 0.0857   True
+     3     28   0.0485 0.0197  0.0049 0.0921   True
+     7     14   0.0307   0.35 -0.0136 0.0749  False
+     7     21   0.0336 0.2486 -0.0106 0.0779  False
+     7     28   0.0382 0.1655 -0.0078 0.0842  False
+    14     21    0.003    0.9 -0.0406 0.0466  False
+    14     28   0.0075    0.9 -0.0379 0.0529  False
+    21     28   0.0046    0.9 -0.0408   0.05  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0254  0.878  -0.042 0.0928  False
+     0      7   0.0101    0.9 -0.0521 0.0723  False
+     0     14   0.0273 0.7484 -0.0325  0.087  False
+     0     21   0.0218    0.9 -0.0466 0.0902  False
+     0     28    0.006    0.9 -0.0589 0.0708  False
+     3      7  -0.0153    0.9 -0.0837  0.053  False
+     3     14   0.0018    0.9 -0.0643 0.0679  False
+     3     21  -0.0036    0.9 -0.0776 0.0704  False
+     3     28  -0.0195    0.9 -0.0903 0.0513  False
+     7     14   0.0172    0.9 -0.0437  0.078  False
+     7     21   0.0117    0.9 -0.0576 0.0811  False
+     7     28  -0.0041    0.9   -0.07 0.0617  False
+    14     21  -0.0054    0.9 -0.0726 0.0617  False
+    14     28  -0.0213    0.9 -0.0848 0.0422  False
+    21     28  -0.0158    0.9 -0.0876 0.0559  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.04062227]	Yes
+Stroke	Sham	14	[0.78475587]	No
+Stroke	Sham	21	[0.90088949]	No
+Stroke	Sham	28	[0.29591172]	No
+Stroke	Sham	7	[0.10042619]	No
+Stroke	Sham	0	[0.11398907]	No

output/Final_Quantitative_output/mixed_model_analysis/mixed_model_results.csv

@@ -1,109 +0,0 @@
-Qtype,mask_name,p_value
-fa,CC_MOp-MOp_dilated,0.000764702252832505
-fa,CC_MOp-MOp_dilated_cut,0.14969369072806923
-fa,CC_MOp-MOp_cut,0.4336083759740297
-fa,CC_MOs-MOs,0.03357907070806808
-fa,CC_MOs-MOs_cut,0.41104168674397146
-fa,CC_SSp_ll-SSp_ll,2.3420247004382942e-08
-fa,CC_SSp_ll-SSp_ll_cut,3.895450833514923e-05
-fa,CC_SSp_ul-SSp_ul,1.1102891499223901e-05
-fa,CC_SSp_ul-SSp_ul_cut,9.761926363678802e-06
-fa,OT_och-lgn_lgncut,0.32299773824006406
-fa,CRuT_MOp-RN_contralesional_mirrored,0.015242610315710368
-fa,TC_DORsm-SSp+SSs_contralesional_END+CCcut,1.7967997728026854e-06
-fa,TC_DORsm-SSp_ll+SSp_ul_contralesional_ROI+CCcut,0.0006769648218821898
-fa,TC_DORsm-SSp_ll+SSp_ul_contralesional_END+higherstepsize,1.6521308752117927e-05
-fa,CC_MOp-MOp,0.14732530817837736
-fa,CST_MOp-int-py_contralesional_CCcut,0.03413018669138702
-fa,CST_MOp-int-py_contralesional_CCasROA,0.022691709249644233
-fa,CST_MOp-int-py_contralesional_selfdrawnROA+CCcut,0.03285039097527763
-fa,CST_MOp-int-py_ipsilesional_CCcut,0.06342789980942962
-fa,CST_MOp-int-py_ipsilesional_CCasROA,0.04377441710035278
-fa,CST_MOp-int-py_ipsilesional_selfdrawnROA+CCcut,0.04872279567350309
-fa,CReT_MOp-TRN_contralesional_CCcut,0.042931669227480936
-fa,CReT_MOp-TRN_ipsilesional_CCcut,0.297380410368281
-fa,CRuT_MOp-RN_ipsilesional,0.3064402138562371
-fa,TC_DORsm-SSp_ll+SSp_ul_ipsilesional_ROI+CCcut,0.0024704722893466044
-fa,TC_DORsm-SSp+SSs_ipsilesional_END+CCcut,0.00025944698894002865
-fa,TC_DORsm-SSp_ll+SSp_ul_ipsilesional_END+higherstepsize_,0.0018961082226590703
-md,CC_MOp-MOp_dilated,0.9636283250141883
-md,CC_MOp-MOp_dilated_cut,0.0044321287502354974
-md,CC_MOp-MOp_cut,0.0006589557404981678
-md,CC_MOs-MOs,0.8726529527641804
-md,CC_MOs-MOs_cut,0.02307546169326933
-md,CC_SSp_ll-SSp_ll,0.11466015431153961
-md,CC_SSp_ll-SSp_ll_cut,0.00011216297091787598
-md,CC_SSp_ul-SSp_ul,0.05673484910622114
-md,CC_SSp_ul-SSp_ul_cut,0.00209897547029832
-md,OT_och-lgn_lgncut,0.4859229434344938
-md,CRuT_MOp-RN_contralesional_mirrored,0.2681831018414498
-md,TC_DORsm-SSp+SSs_contralesional_END+CCcut,0.9479194144552905
-md,TC_DORsm-SSp_ll+SSp_ul_contralesional_ROI+CCcut,0.807716916416026
-md,TC_DORsm-SSp_ll+SSp_ul_contralesional_END+higherstepsize,0.8049864597483745
-md,CC_MOp-MOp,0.7881203649980624
-md,CST_MOp-int-py_contralesional_CCcut,0.10903670338348209
-md,CST_MOp-int-py_contralesional_CCasROA,0.09463613493924175
-md,CST_MOp-int-py_contralesional_selfdrawnROA+CCcut,0.10523683914291054
-md,CST_MOp-int-py_ipsilesional_CCcut,0.572869411571136
-md,CST_MOp-int-py_ipsilesional_CCasROA,0.4863863121121865
-md,CST_MOp-int-py_ipsilesional_selfdrawnROA+CCcut,0.5187886425559998
-md,CReT_MOp-TRN_contralesional_CCcut,0.40014152185687957
-md,CReT_MOp-TRN_ipsilesional_CCcut,0.015352203209589714
-md,CRuT_MOp-RN_ipsilesional,0.0005513725158134129
-md,TC_DORsm-SSp_ll+SSp_ul_ipsilesional_ROI+CCcut,0.11703965363731128
-md,TC_DORsm-SSp+SSs_ipsilesional_END+CCcut,0.5511713168651224
-md,TC_DORsm-SSp_ll+SSp_ul_ipsilesional_END+higherstepsize_,0.2252152553826955
-ad,CC_MOp-MOp_dilated,0.5035527768069832
-ad,CC_MOp-MOp_dilated_cut,0.019888203311090865
-ad,CC_MOp-MOp_cut,0.002553935165370371
-ad,CC_MOs-MOs,0.7035185164066022
-ad,CC_MOs-MOs_cut,0.035262822009781446
-ad,CC_SSp_ll-SSp_ll,0.657501745170847
-ad,CC_SSp_ll-SSp_ll_cut,0.014681991500147753
-ad,CC_SSp_ul-SSp_ul,0.25803131213525643
-ad,CC_SSp_ul-SSp_ul_cut,0.04229772359990703
-ad,OT_och-lgn_lgncut,0.6032633924247919
-ad,CRuT_MOp-RN_contralesional_mirrored,0.11847929581436505
-ad,TC_DORsm-SSp+SSs_contralesional_END+CCcut,0.3208906519674166
-ad,TC_DORsm-SSp_ll+SSp_ul_contralesional_ROI+CCcut,0.4278186382610758
-ad,TC_DORsm-SSp_ll+SSp_ul_contralesional_END+higherstepsize,0.21365790599697898
-ad,CC_MOp-MOp,0.9235770992366283
-ad,CST_MOp-int-py_contralesional_CCcut,0.033637626364474316
-ad,CST_MOp-int-py_contralesional_CCasROA,0.026452817251350815
-ad,CST_MOp-int-py_contralesional_selfdrawnROA+CCcut,0.03072549006592736
-ad,CST_MOp-int-py_ipsilesional_CCcut,0.26926514457723194
-ad,CST_MOp-int-py_ipsilesional_CCasROA,0.21082349737538264
-ad,CST_MOp-int-py_ipsilesional_selfdrawnROA+CCcut,0.22856005510184274
-ad,CReT_MOp-TRN_contralesional_CCcut,0.16231373936396853
-ad,CReT_MOp-TRN_ipsilesional_CCcut,0.015538197244647596
-ad,CRuT_MOp-RN_ipsilesional,0.0011529266923220479
-ad,TC_DORsm-SSp_ll+SSp_ul_ipsilesional_ROI+CCcut,0.021993840222511597
-ad,TC_DORsm-SSp+SSs_ipsilesional_END+CCcut,0.12050220796207556
-ad,TC_DORsm-SSp_ll+SSp_ul_ipsilesional_END+higherstepsize_,0.04133446884277687
-rd,CC_MOp-MOp_dilated,0.7009037502266402
-rd,CC_MOp-MOp_dilated_cut,0.0020427344062894535
-rd,CC_MOp-MOp_cut,0.00040884837633998615
-rd,CC_MOs-MOs,0.5993823749023859
-rd,CC_MOs-MOs_cut,0.02060438223570422
-rd,CC_SSp_ll-SSp_ll,0.018898060961979588
-rd,CC_SSp_ll-SSp_ll_cut,6.024320970285604e-06
-rd,CC_SSp_ul-SSp_ul,0.01798663531654731
-rd,CC_SSp_ul-SSp_ul_cut,0.0002694326989084794
-rd,OT_och-lgn_lgncut,0.4023624934085368
-rd,CRuT_MOp-RN_contralesional_mirrored,0.4859182032711996
-rd,TC_DORsm-SSp+SSs_contralesional_END+CCcut,0.3821111109896743
-rd,TC_DORsm-SSp_ll+SSp_ul_contralesional_ROI+CCcut,0.3188948221252429
-rd,TC_DORsm-SSp_ll+SSp_ul_contralesional_END+higherstepsize,0.5949448564197659
-rd,CC_MOp-MOp,0.6230549228787323
-rd,CST_MOp-int-py_contralesional_CCcut,0.2803920439276959
-rd,CST_MOp-int-py_contralesional_CCasROA,0.2590061274423675
-rd,CST_MOp-int-py_contralesional_selfdrawnROA+CCcut,0.2783870436418653
-rd,CST_MOp-int-py_ipsilesional_CCcut,0.939526107056537
-rd,CST_MOp-int-py_ipsilesional_CCasROA,0.8519037826851101
-rd,CST_MOp-int-py_ipsilesional_selfdrawnROA+CCcut,0.8891824914166516
-rd,CReT_MOp-TRN_contralesional_CCcut,0.726175158988331
-rd,CReT_MOp-TRN_ipsilesional_CCcut,0.0201313806135242
-rd,CRuT_MOp-RN_ipsilesional,0.0006269646036643398
-rd,TC_DORsm-SSp_ll+SSp_ul_ipsilesional_ROI+CCcut,0.36634358836557956
-rd,TC_DORsm-SSp+SSs_ipsilesional_END+CCcut,0.8413260348562701
-rd,TC_DORsm-SSp_ll+SSp_ul_ipsilesional_END+higherstepsize_,0.6239315382281756

output/Final_Quantitative_output/mixed_model_analysis/rd_CC_MOp-MOp_cut_log.txt

@@ -1,67 +1,67 @@
 Model Name: rd_CC_MOp-MOp_cut
-          Mixed Linear Model Regression Results
-==========================================================
-Model:              MixedLM   Dependent Variable:   Value 
-No. Observations:   364       Method:               REML  
-No. Groups:         2         Scale:                0.0057
-Min. group size:    158       Log-Likelihood:       inf   
-Max. group size:    206       Converged:            Yes   
-Mean group size:    182.0                                 
-----------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
-----------------------------------------------------------
-Intercept        -0.000                                   
-merged_timepoint  0.001    0.000 3.534 0.000  0.001  0.002
-Group Var         0.000                                   
-==========================================================
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0040
+Min. group size:        156          Log-Likelihood:          inf   
+Max. group size:        205          Converged:               Yes   
+Mean group size:        180.5                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 124111.786 0.000 1.000 -243254.630 243254.630
+merged_timepoint 0.001      0.000 3.344 0.001       0.000      0.002
+Group Var        0.000                                              
+====================================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0089    0.9 -0.0613 0.0434  False
-     0      7   0.0092    0.9  -0.046 0.0645  False
-     0     14   0.0445   0.18   -0.01  0.099  False
-     0     21    0.062 0.0156  0.0075 0.1165   True
-     0     28    0.049 0.1305 -0.0075 0.1056  False
-     3      7   0.0182    0.9 -0.0332 0.0696  False
-     3     14   0.0534 0.0318  0.0028  0.104   True
-     3     21   0.0709 0.0011  0.0204 0.1215   True
-     3     28    0.058 0.0223  0.0052 0.1108   True
-     7     14   0.0352 0.4125 -0.0184 0.0889  False
-     7     21   0.0528 0.0565 -0.0008 0.1064  False
-     7     28   0.0398 0.3151 -0.0159 0.0956  False
-    14     21   0.0175    0.9 -0.0353 0.0704  False
-    14     28   0.0046    0.9 -0.0504 0.0596  False
-    21     28   -0.013    0.9 -0.0679  0.042  False
+     0      3  -0.0107    0.9 -0.0529 0.0314  False
+     0      7  -0.0137    0.9 -0.0582 0.0308  False
+     0     14   0.0277 0.4574 -0.0161 0.0716  False
+     0     21   0.0356 0.1846 -0.0083 0.0795  False
+     0     28   0.0398  0.125 -0.0058 0.0853  False
+     3      7   -0.003    0.9  -0.044 0.0381  False
+     3     14   0.0385 0.0714 -0.0019 0.0789  False
+     3     21   0.0464 0.0141   0.006 0.0867   True
+     3     28   0.0505 0.0089  0.0084 0.0927   True
+     7     14   0.0415 0.0637 -0.0013 0.0843  False
+     7     21   0.0493 0.0136  0.0065 0.0921   True
+     7     28   0.0535 0.0086   0.009  0.098   True
+    14     21   0.0079    0.9 -0.0343   0.05  False
+    14     28    0.012    0.9 -0.0319 0.0559  False
+    21     28   0.0041    0.9 -0.0397  0.048  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3    0.012    0.9 -0.0453 0.0694  False
-     0      7   0.0152    0.9 -0.0392 0.0696  False
-     0     14   0.0226 0.7878 -0.0297 0.0748  False
-     0     21  -0.0069    0.9 -0.0666 0.0529  False
-     0     28   0.0092    0.9 -0.0475 0.0659  False
-     3      7   0.0031    0.9 -0.0551 0.0614  False
-     3     14   0.0105    0.9 -0.0457 0.0668  False
-     3     21  -0.0189    0.9 -0.0822 0.0444  False
-     3     28  -0.0028    0.9 -0.0632 0.0576  False
-     7     14   0.0074    0.9 -0.0458 0.0606  False
-     7     21   -0.022    0.9 -0.0826 0.0386  False
-     7     28   -0.006    0.9 -0.0636 0.0516  False
-    14     21  -0.0294 0.6733 -0.0881 0.0292  False
-    14     28  -0.0134    0.9 -0.0689 0.0422  False
-    21     28   0.0161    0.9 -0.0466 0.0787  False
----------------------------------------------------
+==================================================
+group1 group2 meandiff p-adj  lower  upper  reject
+--------------------------------------------------
+     0      3    0.018   0.9 -0.0356 0.0716  False
+     0      7   0.0135   0.9  -0.036  0.063  False
+     0     14   0.0173   0.9 -0.0302 0.0648  False
+     0     21   0.0052   0.9 -0.0492 0.0596  False
+     0     28   0.0068   0.9 -0.0448 0.0584  False
+     3      7  -0.0045   0.9 -0.0589 0.0499  False
+     3     14  -0.0008   0.9 -0.0533 0.0518  False
+     3     21  -0.0129   0.9 -0.0717  0.046  False
+     3     28  -0.0112   0.9 -0.0675 0.0451  False
+     7     14   0.0038   0.9 -0.0446 0.0522  False
+     7     21  -0.0083   0.9 -0.0635 0.0468  False
+     7     28  -0.0067   0.9 -0.0591 0.0457  False
+    14     21  -0.0121   0.9 -0.0655 0.0413  False
+    14     28  -0.0105   0.9  -0.061 0.0401  False
+    21     28   0.0016   0.9 -0.0554 0.0587  False
+--------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.12941951]	No
-Stroke	Sham	14	[0.55234752]	No
-Stroke	Sham	21	[0.0062876]	Yes
-Stroke	Sham	28	[0.13925467]	No
-Stroke	Sham	7	[0.16464719]	No
-Stroke	Sham	0	[0.62976298]	No
+Stroke	Sham	3	[0.04077441]	Yes
+Stroke	Sham	14	[0.70778361]	No
+Stroke	Sham	21	[0.26919943]	No
+Stroke	Sham	28	[0.07449597]	No
+Stroke	Sham	7	[0.0124491]	Yes
+Stroke	Sham	0	[0.76736685]	No