adjusted code and ran it again

code/correlation_between_bahavior_and_DTI.py

@@ -18,43 +18,44 @@ df = pd.read_csv(input_file_path)
 
 df = df[(df["merged_timepoint"]<40)]
 
-
+tests = ['paw_dragZ-score', 'hindlimb_dropZ-score', 'foot_faultsZ-score','paw_drag', 'hindlimb_drop', 'foot_faults',"averageScore"]
 #%%
 # Empty list to store the results
 results = []
-for dd in df["dialation_amount"].unique():
-    # Iterate over unique values of 'Group', 'merged_timepoint', 'Qtype', and 'mask_name'
-    for ss in df["Group"].unique():
-        for time_point in df["merged_timepoint"].unique():
-            for qq in df["Qtype"].unique():
-                for mm in df["mask_name"].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'])
-    
-                    if not df_f2.empty:
-                        
-                        shapiro_statValue, shapiro_pvalueQValue = shapiro(df_f2["Value"])
-                        shapiro_statScore, shapiro_pvalueBehavior = shapiro(df_f2["averageScore"])
-                        
-                        if shapiro_pvalueQValue < 0.05 or shapiro_pvalueBehavior < 0.05:
-                            correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2["averageScore"])
+for tt in tests:
+    for dd in df["dialation_amount"].unique():
+        # Iterate over unique values of 'Group', 'merged_timepoint', 'Qtype', and 'mask_name'
+        for ss in df["Group"].unique():
+            for time_point in df["merged_timepoint"].unique():
+                for qq in df["Qtype"].unique():
+                    for mm in df["mask_name"].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', tt])
+        
+                        if not df_f2.empty:
+                            
+                            shapiro_statValue, shapiro_pvalueQValue = shapiro(df_f2["Value"])
+                            shapiro_statScore, shapiro_pvalueBehavior = shapiro(df_f2[tt])
+                            
+                            if shapiro_pvalueQValue < 0.05 or shapiro_pvalueBehavior < 0.05:
+                                correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2[tt])
+                            else:
+                                correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2[tt])
+                           
+        
+                            # Store the results in a dictionary
+                            result = {'Group': ss, 'merged_timepoint': time_point, 'Qtype': qq, 'mask_name': mm, 
+                                      'Pval': p_value, 'R': correlation_coefficient,
+                                      "Behavior_test":tt,"dialation_amount":dd}
+        
+                            # Append the dictionary to the results list
+                            results.append(result)
                         else:
-                            correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2["averageScore"])
-                       
-    
-                        # Store the results in a dictionary
-                        result = {'Group': ss, 'merged_timepoint': time_point, 'Qtype': qq, 'mask_name': mm, 
-                                  'Pval': p_value, 'R': correlation_coefficient,
-                                  'shapiro-wilk_pvalue_qtype': shapiro_pvalueQValue,'shapiro-wilk_pvalue_behavior': shapiro_pvalueBehavior,"dialation_amount":dd}
-    
-                        # Append the dictionary to the results list
-                        results.append(result)
-                    else:
-                        print(
-                            f"No valid data found for Group: {ss}, merged_timepoint: {time_point}, Qtype: {qq}, and mask_name: {mm}. Skipping.")
+                            print(
+                                f"No valid data found for Group: {ss}, merged_timepoint: {time_point}, Qtype: {qq}, and mask_name: {mm}. Skipping.")
 
 # Create a DataFrame from the results list
 correlation_results_df = pd.DataFrame(results)
@@ -62,21 +63,23 @@ unique_groups = df["Group"].unique()
 unique_masks = df["mask_name"].unique()
 unique_tp = df["merged_timepoint"].unique()
 unique_dd=df["dialation_amount"].unique()
-for dd in unique_dd:
-    for tt in unique_tp:
-        for mask in unique_masks:
-            for group in unique_groups:
-                time_mask = correlation_results_df['merged_timepoint'] == tt
-                mask_mask = correlation_results_df['mask_name'] == mask
-                group_mask = correlation_results_df['Group'] == group
-                dd_mask =  correlation_results_df["dialation_amount"] == dd
-                combined_mask = time_mask & mask_mask & group_mask & dd_mask
-                
-                p_values = correlation_results_df[combined_mask]['Pval']
-                rejected, p_values_corrected, _, _ = multipletests(p_values, method='fdr_bh')
-    
-                # Assign the corrected p-values to the DataFrame
-                correlation_results_df.loc[combined_mask, 'Pval_corrected'] = p_values_corrected
+# =============================================================================
+# for dd in unique_dd:
+#     for tt in unique_tp:
+#         for mask in unique_masks:
+#             for group in unique_groups:
+#                 time_mask = correlation_results_df['merged_timepoint'] == tt
+#                 mask_mask = correlation_results_df['mask_name'] == mask
+#                 group_mask = correlation_results_df['Group'] == group
+#                 dd_mask =  correlation_results_df["dialation_amount"] == dd
+#                 combined_mask = time_mask & mask_mask & group_mask & dd_mask
+#                 
+#                 p_values = correlation_results_df[combined_mask]['Pval']
+#                 rejected, p_values_corrected, _, _ = multipletests(p_values, method='fdr_bh')
+#     
+#                 # Assign the corrected p-values to the DataFrame
+#                 correlation_results_df.loc[combined_mask, 'Pval_corrected'] = p_values_corrected
+# =============================================================================
 # Define the output file path
 output_file_path = os.path.join(parent_dir, 'output', "Correlation_with_behavior", 'correlation_dti_with_behavior.csv')
 

code/heat_maps_correlation.py

@@ -11,10 +11,11 @@ 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]
+df = df[df["dialation_amount"] == 1]
 
 # Get unique Qtypes
 qtypes = df["Qtype"].unique()
+qtypes = ["fa"]
 
 # Iterate over unique values of 'Qtype'
 for qtype in qtypes:
@@ -38,7 +39,11 @@ for qtype in qtypes:
             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_r', annot=True, fmt=".2f", cbar=True)
+            if value == "R":
+                sns.heatmap(heatmap_df, ax=axes[i, j], cmap='coolwarm', annot=True, fmt=".2f", cbar=True)
+            else:
+                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)

code/incooparate_behavior_data.py

@@ -23,7 +23,8 @@ input_file_behav = os.path.join(parent_dir, 'output',"behavior_analysis" ,'behav
 df_b = pd.read_csv(input_file_behav)
 
 # Merge the columns from df_b into df_q based on subjectID and merged_timepoint columns
-merged_df = pd.merge(df_q, df_b[['subjectID', 'merged_timepoint', 'paw_dragZ-score', 'hindlimb_dropZ-score', 'foot_faultsZ-score', 'averageScore', '2 Cluster', '3 Cluster', '4 Cluster', '5 Cluster', '6 Cluster']], 
+merged_df = pd.merge(df_q, df_b[['subjectID', 'merged_timepoint', 'paw_drag', 'hindlimb_drop', 'foot_faults','paw_dragZ-score', 'hindlimb_dropZ-score', 'foot_faultsZ-score',
+                                 'averageScore', '2 Cluster', '3 Cluster', '4 Cluster', '5 Cluster', '6 Cluster']], 
                      on=['subjectID', 'merged_timepoint'], how='left')
 
 

code/plotting_quantitative_dti_values.py

@@ -13,7 +13,7 @@ import warnings
 warnings.simplefilter(action='ignore')
 
 # Define the PlotBoxplot function
-def PlotBoxplot(filtered_df, qq, mm,dd, output_folder):
+def PlotBoxplot(filtered_df, qq, mm,dd, output_folder,sig):
     """
     Plot boxplots for filtered dataframe and save as images.
 
@@ -24,24 +24,28 @@ def PlotBoxplot(filtered_df, qq, mm,dd, output_folder):
     output_folder (str): Path to the output folder to save images.
     """
     # Set the color palette to Set2
-    sns.set_palette("Set2")
+    sns.set_palette("grey")
     
     # Set the figure size to 18 cm in width
     plt.figure(figsize=(18/2.54, 4))  # Convert 18 cm to inches
     
     # Create a boxplot
-    sns.boxplot(data=filtered_df, x="merged_timepoint", y="Value", hue="Group", fliersize=3 ,flierprops={"marker": "o"})
+    sns.boxplot(data=filtered_df, x="Group", y="Value", hue="merged_timepoint",
+                fliersize=3 ,flierprops={"marker": "o"})
     
     # Set title and labels
-    plt.title(f'{mm}')
+    plt.title(f'{qq}_{mm}_{dd}')
     plt.xlabel('Timepoint')
-    plt.ylabel(qq)
+    plt.ylabel(qq+"(n.a)")
     
     # Show legend without title and frame
-    plt.legend(title=None, frameon=False)
-    
+    plt.legend(title=None, frameon=False,bbox_to_anchor=(1.05, 1), loc='best')
+    plt.tight_layout()
     # Save the plot as an image
-    output_path = os.path.join(output_folder, f'{qq}_{mm}_{dd}_mixedlm_significant.png')
+    if sig:
+        output_path = os.path.join(output_folder, f'{qq}_{mm}_{dd}_mixedlm_significant.png')
+    else:
+        output_path = os.path.join(output_folder, f'{qq}_{mm}_{dd}_mixedlm.png')
     plt.savefig(output_path, dpi=100)
     
     # Close the plot to avoid displaying it
@@ -66,7 +70,7 @@ df_qc_5 = df_qc[(df_qc["Voting outliers (from 5)"]>3) & (df_qc["sequence_type"]=
 
 
 # Filtering the dataframe based on conditions
-df_f0 = df[(~df["merged_timepoint"].isin([42, 56]))]
+df_f0 = df[~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)
 
@@ -84,7 +88,7 @@ for dd in df["dialation_amount"].unique():
     for qq in df["Qtype"].unique():
         for mm in df["mask_name"].unique():
             # Filter the dataframe based on current "Qtype" and "mask_name"
-            filtered_df = df_f1[(df_f1["Qtype"] == qq) & (df_f1["mask_name"] == mm)]
+            filtered_df = df_f1[(df_f1["Qtype"] == qq) & (df_f1["mask_name"] == mm) & (df_f1["dialation_amount"] == dd)]
             
             # Fit the mixed-effects model
             model_name = f"{qq}_{mm}_{dd}"
@@ -92,45 +96,50 @@ for dd in df["dialation_amount"].unique():
             mdf = md.fit(method=["lbfgs"])
             
             # Log file for each combination of qq and mm
-            log_file = os.path.join(mixed_model_dir, f"{model_name}_log.txt")
-           
+            
             
             # Check if the p-value is significant
             if mdf.pvalues['merged_timepoint'] < 0.05:
-                with open(log_file, 'w') as log:
-                    # Print model name to log file
-                    log.write(f"Model Name: {model_name}\n")
-                    
-                    # Print the model summary to log file
-                    log.write(str(mdf.summary()) + '\n')
-                    # Plot and save boxplots for significant models
-                    PlotBoxplot(filtered_df, qq, mm,dd ,mixed_model_dir)
+                log_file = os.path.join(mixed_model_dir, f"{model_name}_log_significant.txt")
+                sig = True
+            else:
+                log_file = os.path.join(mixed_model_dir, f"{model_name}_log.txt")  
+                sig = False
+                
+            with open(log_file, 'w') as log:
+                # Print model name to log file
+                log.write(f"Model Name: {model_name}\n")
+                
+                # Print the model summary to log file
+                log.write(str(mdf.summary()) + '\n')
+                # Plot and save boxplots for significant models
+                PlotBoxplot(filtered_df, qq, mm,dd ,mixed_model_dir,sig)
+                
+                # Perform Tukey's HSD test for post hoc analysis
+                for gg in filtered_df["Group"].unique():
+
+                    filtered_df2 = filtered_df[filtered_df["Group"]==gg]
+                    mc = MultiComparison(filtered_df2["Value"], filtered_df2["merged_timepoint"])
+                    tukey_result = mc.tukeyhsd()
                     
-                    # Perform Tukey's HSD test for post hoc analysis
-                    for gg in filtered_df["Group"].unique():
-
-                        filtered_df2 = filtered_df[filtered_df["Group"]==gg]
-                        mc = MultiComparison(filtered_df2["Value"], filtered_df2["merged_timepoint"])
-                        tukey_result = mc.tukeyhsd()
-                        
-                        # Print the summary of the test to log file
-                        log.write(f"Posthoc Analysis for {gg}:\n")
-                        log.write(str(tukey_result.summary()) + '\n')
-                    
-                    # Perform the Sidak multiple comparisons for the group effect
-                    group_combinations = combinations(filtered_df["Group"].unique(), 2)
-                    log.write("Sidak Multiple Comparisons:\n")
-                    log.write("Group1\tGroup2\tTimePoint\tPValue\tSignificantDifference\n")
-                    for group1, group2 in group_combinations:
-                        for time_point in filtered_df["merged_timepoint"].unique():
-                            group1_data = filtered_df[(filtered_df["Group"] == group1) & (filtered_df["merged_timepoint"] == time_point)]["Value"]
-                            group2_data = filtered_df[(filtered_df["Group"] == group2) & (filtered_df["merged_timepoint"] == time_point)]["Value"]
-                            sidak_result = statsmodels.stats.multitest.multipletests(scipy.stats.ttest_ind(group1_data, group2_data)[1], method='sidak')
-                            if sidak_result[0]:
-                                log.write(f"{group1}\t{group2}\t{time_point}\t{sidak_result[1]}\tYes\n")
-                            else:
-                                log.write(f"{group1}\t{group2}\t{time_point}\t{sidak_result[1]}\tNo\n")
-            
+                    # Print the summary of the test to log file
+                    log.write(f"Posthoc Analysis for {gg}:\n")
+                    log.write(str(tukey_result.summary()) + '\n')
+                
+                # Perform the Sidak multiple comparisons for the group effect
+                group_combinations = combinations(filtered_df["Group"].unique(), 2)
+                log.write("Sidak Multiple Comparisons:\n")
+                log.write("Group1\tGroup2\tTimePoint\tPValue\tSignificantDifference\n")
+                for group1, group2 in group_combinations:
+                    for time_point in filtered_df["merged_timepoint"].unique():
+                        group1_data = filtered_df[(filtered_df["Group"] == group1) & (filtered_df["merged_timepoint"] == time_point)]["Value"]
+                        group2_data = filtered_df[(filtered_df["Group"] == group2) & (filtered_df["merged_timepoint"] == time_point)]["Value"]
+                        sidak_result = statsmodels.stats.multitest.multipletests(scipy.stats.ttest_ind(group1_data, group2_data)[1], method='sidak')
+                        if sidak_result[0]:
+                            log.write(f"{group1}\t{group2}\t{time_point}\t{sidak_result[1]}\tYes\n")
+                        else:
+                            log.write(f"{group1}\t{group2}\t{time_point}\t{sidak_result[1]}\tNo\n")
+        
             # Append the results to the list
             results.append({'Qtype': qq, 'mask_name': mm,'dialation': dd,'p_value': mdf.pvalues['merged_timepoint']})
 

output/Final_Quantitative_output/Quantitative_results_from_dwi_processing_merged_with_behavior_data.csv

@@ -1 +0,0 @@
-/annex/objects/MD5E-s55846190--48323fd86e44c9e00c346b7e20a3b9d6.csv

output/Final_Quantitative_output/Quantitative_results_from_dwi_processing_merged_with_behavior_data.csv

@@ -0,0 +1 @@
+../../.git/annex/objects/fz/j3/MD5E-s57578618--eb11730167f8aabebf48329df06ff726.csv/MD5E-s57578618--eb11730167f8aabebf48329df06ff726.csv

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_0_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_0
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0145
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 89142.059 0.000 1.000 -174715.225 174715.225
-merged_timepoint 0.002     0.000 7.132 0.000       0.002      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  -0.0524  0.001 -0.0878 -0.0169   True
-     0      7  -0.0402 0.0265 -0.0777 -0.0028   True
-     0     14   0.0211 0.5679 -0.0158   0.058  False
-     0     21   0.0383 0.0364  0.0014  0.0752   True
-     0     28   0.0335 0.1254 -0.0048  0.0718  False
-     3      7   0.0121    0.9 -0.0224  0.0466  False
-     3     14   0.0734  0.001  0.0395  0.1074   True
-     3     21   0.0907  0.001  0.0567  0.1246   True
-     3     28   0.0858  0.001  0.0504  0.1213   True
-     7     14   0.0613  0.001  0.0253  0.0973   True
-     7     21   0.0786  0.001  0.0426  0.1146   True
-     7     28   0.0737  0.001  0.0363  0.1111   True
-    14     21   0.0173 0.7056 -0.0182  0.0527  False
-    14     28   0.0124    0.9 -0.0245  0.0493  False
-    21     28  -0.0048    0.9 -0.0417  0.0321  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0272 0.5001 -0.0172 0.0716  False
-     0      7   0.0283 0.3607 -0.0127 0.0693  False
-     0     14   0.0589  0.001  0.0195 0.0983   True
-     0     21   0.0436 0.0643 -0.0014 0.0887  False
-     0     28   0.0266 0.4798 -0.0161 0.0694  False
-     3      7   0.0011    0.9 -0.0439 0.0462  False
-     3     14   0.0317 0.2983 -0.0118 0.0753  False
-     3     21   0.0165    0.9 -0.0323 0.0652  False
-     3     28  -0.0005    0.9 -0.0472 0.0461  False
-     7     14   0.0306 0.2479 -0.0095 0.0707  False
-     7     21   0.0153    0.9 -0.0304  0.061  False
-     7     28  -0.0017    0.9 -0.0451 0.0418  False
-    14     21  -0.0153    0.9 -0.0595  0.029  False
-    14     28  -0.0323  0.238 -0.0741 0.0096  False
-    21     28   -0.017    0.9 -0.0642 0.0303  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[1.01505933e-08]	Yes
-Stroke	Sham	14	[0.02467788]	Yes
-Stroke	Sham	21	[0.77454459]	No
-Stroke	Sham	28	[0.52926269]	No
-Stroke	Sham	7	[3.91214838e-11]	Yes
-Stroke	Sham	0	[0.97963994]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_0_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_0
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0217
+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 287943.914 0.000 1.000 -564359.700 564359.700
+merged_timepoint 0.003      0.001 3.541 0.000       0.001      0.004
+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  -0.1168 0.0099 -0.2152 -0.0184   True
+     0      7  -0.0445 0.8208 -0.1483  0.0594  False
+     0     14   0.0224 0.9888 -0.0801  0.1248  False
+     0     21   0.0377 0.8968 -0.0647  0.1402  False
+     0     28   0.0261  0.981 -0.0802  0.1324  False
+     3      7   0.0723 0.2551 -0.0235  0.1681  False
+     3     14   0.1392 0.0005  0.0449  0.2334   True
+     3     21   0.1545 0.0001  0.0603  0.2487   True
+     3     28   0.1429 0.0006  0.0445  0.2413   True
+     7     14   0.0668 0.3901 -0.0331  0.1667  False
+     7     21   0.0822 0.1732 -0.0177  0.1821  False
+     7     28   0.0706 0.3722 -0.0333  0.1744  False
+    14     21   0.0153 0.9977 -0.0831  0.1138  False
+    14     28   0.0037    1.0 -0.0987  0.1062  False
+    21     28  -0.0116 0.9995 -0.1141  0.0908  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3    0.009 0.9999  -0.111  0.129  False
+     0      7   0.0325 0.9579 -0.0783 0.1434  False
+     0     14    0.076 0.3129 -0.0304 0.1824  False
+     0     21   0.0576 0.7478 -0.0642 0.1793  False
+     0     28   0.0207 0.9954 -0.0948 0.1363  False
+     3      7   0.0236 0.9934 -0.0982 0.1453  False
+     3     14    0.067 0.5711 -0.0507 0.1848  False
+     3     21   0.0486 0.8946 -0.0832 0.1804  False
+     3     28   0.0118 0.9998 -0.1143 0.1378  False
+     7     14   0.0435  0.856 -0.0649 0.1518  False
+     7     21    0.025 0.9919 -0.0985 0.1485  False
+     7     28  -0.0118 0.9997 -0.1291 0.1055  False
+    14     21  -0.0184 0.9978  -0.138 0.1011  False
+    14     28  -0.0553 0.7211 -0.1684 0.0579  False
+    21     28  -0.0368  0.961 -0.1645 0.0909  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00062066]	Yes
+Stroke	Sham	14	[0.25477953]	No
+Stroke	Sham	21	[0.65950977]	No
+Stroke	Sham	28	[0.91006599]	No
+Stroke	Sham	7	[0.00533932]	Yes
+Stroke	Sham	0	[0.94655799]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_1_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_1
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0145
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 89142.059 0.000 1.000 -174715.225 174715.225
-merged_timepoint 0.002     0.000 7.132 0.000       0.002      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  -0.0524  0.001 -0.0878 -0.0169   True
-     0      7  -0.0402 0.0265 -0.0777 -0.0028   True
-     0     14   0.0211 0.5679 -0.0158   0.058  False
-     0     21   0.0383 0.0364  0.0014  0.0752   True
-     0     28   0.0335 0.1254 -0.0048  0.0718  False
-     3      7   0.0121    0.9 -0.0224  0.0466  False
-     3     14   0.0734  0.001  0.0395  0.1074   True
-     3     21   0.0907  0.001  0.0567  0.1246   True
-     3     28   0.0858  0.001  0.0504  0.1213   True
-     7     14   0.0613  0.001  0.0253  0.0973   True
-     7     21   0.0786  0.001  0.0426  0.1146   True
-     7     28   0.0737  0.001  0.0363  0.1111   True
-    14     21   0.0173 0.7056 -0.0182  0.0527  False
-    14     28   0.0124    0.9 -0.0245  0.0493  False
-    21     28  -0.0048    0.9 -0.0417  0.0321  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0272 0.5001 -0.0172 0.0716  False
-     0      7   0.0283 0.3607 -0.0127 0.0693  False
-     0     14   0.0589  0.001  0.0195 0.0983   True
-     0     21   0.0436 0.0643 -0.0014 0.0887  False
-     0     28   0.0266 0.4798 -0.0161 0.0694  False
-     3      7   0.0011    0.9 -0.0439 0.0462  False
-     3     14   0.0317 0.2983 -0.0118 0.0753  False
-     3     21   0.0165    0.9 -0.0323 0.0652  False
-     3     28  -0.0005    0.9 -0.0472 0.0461  False
-     7     14   0.0306 0.2479 -0.0095 0.0707  False
-     7     21   0.0153    0.9 -0.0304  0.061  False
-     7     28  -0.0017    0.9 -0.0451 0.0418  False
-    14     21  -0.0153    0.9 -0.0595  0.029  False
-    14     28  -0.0323  0.238 -0.0741 0.0096  False
-    21     28   -0.017    0.9 -0.0642 0.0303  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[1.01505933e-08]	Yes
-Stroke	Sham	14	[0.02467788]	Yes
-Stroke	Sham	21	[0.77454459]	No
-Stroke	Sham	28	[0.52926269]	No
-Stroke	Sham	7	[3.91214838e-11]	Yes
-Stroke	Sham	0	[0.97963994]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_1_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_1
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   361      Method:              REML    
+No. Groups:         2        Scale:               0.0161  
+Min. group size:    156      Log-Likelihood:      222.5752
+Max. group size:    205      Converged:           Yes     
+Mean group size:    180.5                                 
+----------------------------------------------------------
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        1.102    0.022 50.186 0.000  1.059  1.145
+merged_timepoint 0.002    0.001  3.331 0.001  0.001  0.004
+Group Var        0.001    0.009                           
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0684 0.2228 -0.1562 0.0193  False
+     0      7  -0.0448 0.7325 -0.1374 0.0479  False
+     0     14   0.0216 0.9838 -0.0697  0.113  False
+     0     21   0.0397 0.8105 -0.0516 0.1311  False
+     0     28   0.0272 0.9623 -0.0676 0.1221  False
+     3      7   0.0237 0.9677 -0.0618 0.1091  False
+     3     14   0.0901 0.0278   0.006 0.1741   True
+     3     21   0.1082 0.0037  0.0241 0.1922   True
+     3     28   0.0957 0.0238  0.0079 0.1835   True
+     7     14   0.0664 0.2688 -0.0227 0.1555  False
+     7     21   0.0845 0.0739 -0.0046 0.1736  False
+     7     28    0.072 0.2255 -0.0206 0.1647  False
+    14     21   0.0181 0.9914 -0.0697 0.1059  False
+    14     28   0.0056    1.0 -0.0858  0.097  False
+    21     28  -0.0125 0.9988 -0.1039 0.0789  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0261 0.9762 -0.0752 0.1273  False
+     0      7   0.0313 0.9281 -0.0622 0.1248  False
+     0     14    0.065 0.2986 -0.0248 0.1547  False
+     0     21   0.0478 0.7597 -0.0549 0.1506  False
+     0     28   0.0313 0.9386 -0.0661 0.1288  False
+     3      7   0.0052    1.0 -0.0975  0.108  False
+     3     14   0.0389 0.8679 -0.0604 0.1383  False
+     3     21   0.0218 0.9931 -0.0894  0.133  False
+     3     28   0.0053    1.0 -0.1011 0.1116  False
+     7     14   0.0337 0.8949 -0.0578 0.1251  False
+     7     21   0.0166 0.9974 -0.0876 0.1208  False
+     7     28   0.0001    1.0 -0.0989 0.0991  False
+    14     21  -0.0171 0.9965  -0.118 0.0837  False
+    14     28  -0.0336 0.9118 -0.1291 0.0619  False
+    21     28  -0.0165 0.9978 -0.1242 0.0912  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00403565]	Yes
+Stroke	Sham	14	[0.29369269]	No
+Stroke	Sham	21	[0.86217643]	No
+Stroke	Sham	28	[0.87499294]	No
+Stroke	Sham	7	[0.00232509]	Yes
+Stroke	Sham	0	[0.99327941]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_2_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_2
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0145
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 89142.059 0.000 1.000 -174715.225 174715.225
-merged_timepoint 0.002     0.000 7.132 0.000       0.002      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  -0.0524  0.001 -0.0878 -0.0169   True
-     0      7  -0.0402 0.0265 -0.0777 -0.0028   True
-     0     14   0.0211 0.5679 -0.0158   0.058  False
-     0     21   0.0383 0.0364  0.0014  0.0752   True
-     0     28   0.0335 0.1254 -0.0048  0.0718  False
-     3      7   0.0121    0.9 -0.0224  0.0466  False
-     3     14   0.0734  0.001  0.0395  0.1074   True
-     3     21   0.0907  0.001  0.0567  0.1246   True
-     3     28   0.0858  0.001  0.0504  0.1213   True
-     7     14   0.0613  0.001  0.0253  0.0973   True
-     7     21   0.0786  0.001  0.0426  0.1146   True
-     7     28   0.0737  0.001  0.0363  0.1111   True
-    14     21   0.0173 0.7056 -0.0182  0.0527  False
-    14     28   0.0124    0.9 -0.0245  0.0493  False
-    21     28  -0.0048    0.9 -0.0417  0.0321  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0272 0.5001 -0.0172 0.0716  False
-     0      7   0.0283 0.3607 -0.0127 0.0693  False
-     0     14   0.0589  0.001  0.0195 0.0983   True
-     0     21   0.0436 0.0643 -0.0014 0.0887  False
-     0     28   0.0266 0.4798 -0.0161 0.0694  False
-     3      7   0.0011    0.9 -0.0439 0.0462  False
-     3     14   0.0317 0.2983 -0.0118 0.0753  False
-     3     21   0.0165    0.9 -0.0323 0.0652  False
-     3     28  -0.0005    0.9 -0.0472 0.0461  False
-     7     14   0.0306 0.2479 -0.0095 0.0707  False
-     7     21   0.0153    0.9 -0.0304  0.061  False
-     7     28  -0.0017    0.9 -0.0451 0.0418  False
-    14     21  -0.0153    0.9 -0.0595  0.029  False
-    14     28  -0.0323  0.238 -0.0741 0.0096  False
-    21     28   -0.017    0.9 -0.0642 0.0303  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[1.01505933e-08]	Yes
-Stroke	Sham	14	[0.02467788]	Yes
-Stroke	Sham	21	[0.77454459]	No
-Stroke	Sham	28	[0.52926269]	No
-Stroke	Sham	7	[3.91214838e-11]	Yes
-Stroke	Sham	0	[0.97963994]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_2_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_2
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0129
+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 221633.035 0.000 1.000 -434392.766 434392.766
+merged_timepoint 0.002      0.001 3.035 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  -0.0374 0.7265 -0.1143 0.0394  False
+     0      7    -0.04 0.7156 -0.1211 0.0411  False
+     0     14   0.0213 0.9727 -0.0587 0.1013  False
+     0     21   0.0364 0.7786 -0.0435 0.1164  False
+     0     28   0.0329 0.8645 -0.0502 0.1159  False
+     3      7  -0.0026    1.0 -0.0774 0.0722  False
+     3     14   0.0587 0.2001 -0.0148 0.1323  False
+     3     21   0.0739 0.0485  0.0003 0.1474   True
+     3     28   0.0703 0.0946 -0.0066 0.1471  False
+     7     14   0.0613 0.2149 -0.0167 0.1393  False
+     7     21   0.0764 0.0585 -0.0016 0.1544  False
+     7     28   0.0728 0.1059 -0.0083 0.1539  False
+    14     21   0.0151 0.9931 -0.0617  0.092  False
+    14     28   0.0115 0.9984 -0.0685 0.0915  False
+    21     28  -0.0036    1.0 -0.0836 0.0764  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0341 0.9038 -0.0606 0.1287  False
+     0      7    0.026 0.9555 -0.0614 0.1134  False
+     0     14    0.056 0.3901 -0.0279 0.1399  False
+     0     21   0.0423 0.7996 -0.0537 0.1384  False
+     0     28   0.0279 0.9498 -0.0632  0.119  False
+     3      7  -0.0081 0.9999 -0.1041  0.088  False
+     3     14   0.0219 0.9837 -0.0709 0.1148  False
+     3     21   0.0082 0.9999 -0.0957 0.1122  False
+     3     28  -0.0062    1.0 -0.1056 0.0932  False
+     7     14     0.03  0.913 -0.0555 0.1155  False
+     7     21   0.0163 0.9967 -0.0811 0.1137  False
+     7     28   0.0019    1.0 -0.0907 0.0944  False
+    14     21  -0.0137 0.9983  -0.108 0.0806  False
+    14     28  -0.0281 0.9436 -0.1174 0.0611  False
+    21     28  -0.0144 0.9984 -0.1152 0.0863  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.01392655]	Yes
+Stroke	Sham	14	[0.30395239]	No
+Stroke	Sham	21	[0.85671888]	No
+Stroke	Sham	28	[0.88758615]	No
+Stroke	Sham	7	[0.00199247]	Yes
+Stroke	Sham	0	[0.92970378]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_3_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_3
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0145
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 89142.059 0.000 1.000 -174715.225 174715.225
-merged_timepoint 0.002     0.000 7.132 0.000       0.002      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  -0.0524  0.001 -0.0878 -0.0169   True
-     0      7  -0.0402 0.0265 -0.0777 -0.0028   True
-     0     14   0.0211 0.5679 -0.0158   0.058  False
-     0     21   0.0383 0.0364  0.0014  0.0752   True
-     0     28   0.0335 0.1254 -0.0048  0.0718  False
-     3      7   0.0121    0.9 -0.0224  0.0466  False
-     3     14   0.0734  0.001  0.0395  0.1074   True
-     3     21   0.0907  0.001  0.0567  0.1246   True
-     3     28   0.0858  0.001  0.0504  0.1213   True
-     7     14   0.0613  0.001  0.0253  0.0973   True
-     7     21   0.0786  0.001  0.0426  0.1146   True
-     7     28   0.0737  0.001  0.0363  0.1111   True
-    14     21   0.0173 0.7056 -0.0182  0.0527  False
-    14     28   0.0124    0.9 -0.0245  0.0493  False
-    21     28  -0.0048    0.9 -0.0417  0.0321  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0272 0.5001 -0.0172 0.0716  False
-     0      7   0.0283 0.3607 -0.0127 0.0693  False
-     0     14   0.0589  0.001  0.0195 0.0983   True
-     0     21   0.0436 0.0643 -0.0014 0.0887  False
-     0     28   0.0266 0.4798 -0.0161 0.0694  False
-     3      7   0.0011    0.9 -0.0439 0.0462  False
-     3     14   0.0317 0.2983 -0.0118 0.0753  False
-     3     21   0.0165    0.9 -0.0323 0.0652  False
-     3     28  -0.0005    0.9 -0.0472 0.0461  False
-     7     14   0.0306 0.2479 -0.0095 0.0707  False
-     7     21   0.0153    0.9 -0.0304  0.061  False
-     7     28  -0.0017    0.9 -0.0451 0.0418  False
-    14     21  -0.0153    0.9 -0.0595  0.029  False
-    14     28  -0.0323  0.238 -0.0741 0.0096  False
-    21     28   -0.017    0.9 -0.0642 0.0303  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[1.01505933e-08]	Yes
-Stroke	Sham	14	[0.02467788]	Yes
-Stroke	Sham	21	[0.77454459]	No
-Stroke	Sham	28	[0.52926269]	No
-Stroke	Sham	7	[3.91214838e-11]	Yes
-Stroke	Sham	0	[0.97963994]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_3_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_3
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   361      Method:              REML    
+No. Groups:         2        Scale:               0.0110  
+Min. group size:    156      Log-Likelihood:      291.3122
+Max. group size:    205      Converged:           Yes     
+Mean group size:    180.5                                 
+----------------------------------------------------------
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        1.096    0.014 78.927 0.000  1.069  1.124
+merged_timepoint 0.002    0.001  2.937 0.003  0.001  0.003
+Group Var        0.000    0.004                           
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0234 0.9212 -0.0917 0.0448  False
+     0      7  -0.0391 0.6248 -0.1111 0.0329  False
+     0     14   0.0201 0.9647 -0.0509 0.0911  False
+     0     21   0.0361 0.6884 -0.0349 0.1071  False
+     0     28   0.0362 0.7189 -0.0375 0.1099  False
+     3      7  -0.0156 0.9843  -0.082 0.0508  False
+     3     14   0.0435 0.3945 -0.0218 0.1089  False
+     3     21   0.0595 0.0966 -0.0058 0.1249  False
+     3     28   0.0596 0.1246 -0.0086 0.1279  False
+     7     14   0.0592 0.1418 -0.0101 0.1284  False
+     7     21   0.0752 0.0248  0.0059 0.1445   True
+     7     28   0.0753 0.0347  0.0033 0.1473   True
+    14     21    0.016 0.9845 -0.0522 0.0843  False
+    14     28   0.0161 0.9867 -0.0549 0.0871  False
+    21     28   0.0001    1.0 -0.0709 0.0711  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0345 0.8856  -0.057  0.126  False
+     0      7   0.0239 0.9644 -0.0607 0.1084  False
+     0     14   0.0486 0.5146 -0.0325 0.1297  False
+     0     21   0.0357 0.8772 -0.0572 0.1285  False
+     0     28   0.0252 0.9624 -0.0629 0.1133  False
+     3      7  -0.0106 0.9995 -0.1035 0.0822  False
+     3     14   0.0141 0.9975 -0.0757 0.1039  False
+     3     21   0.0012    1.0 -0.0993 0.1017  False
+     3     28  -0.0093 0.9998 -0.1054 0.0868  False
+     7     14   0.0247 0.9543 -0.0579 0.1074  False
+     7     21   0.0118 0.9992 -0.0824  0.106  False
+     7     28   0.0013    1.0 -0.0881 0.0908  False
+    14     21   -0.013 0.9985 -0.1041 0.0782  False
+    14     28  -0.0234   0.97 -0.1097 0.0629  False
+    21     28  -0.0105 0.9996 -0.1078 0.0869  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.04120918]	Yes
+Stroke	Sham	14	[0.37230429]	No
+Stroke	Sham	21	[0.99450634]	No
+Stroke	Sham	28	[0.56985638]	No
+Stroke	Sham	7	[0.00149948]	Yes
+Stroke	Sham	0	[0.99311853]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_4_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_4
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0145
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 89142.059 0.000 1.000 -174715.225 174715.225
-merged_timepoint 0.002     0.000 7.132 0.000       0.002      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  -0.0524  0.001 -0.0878 -0.0169   True
-     0      7  -0.0402 0.0265 -0.0777 -0.0028   True
-     0     14   0.0211 0.5679 -0.0158   0.058  False
-     0     21   0.0383 0.0364  0.0014  0.0752   True
-     0     28   0.0335 0.1254 -0.0048  0.0718  False
-     3      7   0.0121    0.9 -0.0224  0.0466  False
-     3     14   0.0734  0.001  0.0395  0.1074   True
-     3     21   0.0907  0.001  0.0567  0.1246   True
-     3     28   0.0858  0.001  0.0504  0.1213   True
-     7     14   0.0613  0.001  0.0253  0.0973   True
-     7     21   0.0786  0.001  0.0426  0.1146   True
-     7     28   0.0737  0.001  0.0363  0.1111   True
-    14     21   0.0173 0.7056 -0.0182  0.0527  False
-    14     28   0.0124    0.9 -0.0245  0.0493  False
-    21     28  -0.0048    0.9 -0.0417  0.0321  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0272 0.5001 -0.0172 0.0716  False
-     0      7   0.0283 0.3607 -0.0127 0.0693  False
-     0     14   0.0589  0.001  0.0195 0.0983   True
-     0     21   0.0436 0.0643 -0.0014 0.0887  False
-     0     28   0.0266 0.4798 -0.0161 0.0694  False
-     3      7   0.0011    0.9 -0.0439 0.0462  False
-     3     14   0.0317 0.2983 -0.0118 0.0753  False
-     3     21   0.0165    0.9 -0.0323 0.0652  False
-     3     28  -0.0005    0.9 -0.0472 0.0461  False
-     7     14   0.0306 0.2479 -0.0095 0.0707  False
-     7     21   0.0153    0.9 -0.0304  0.061  False
-     7     28  -0.0017    0.9 -0.0451 0.0418  False
-    14     21  -0.0153    0.9 -0.0595  0.029  False
-    14     28  -0.0323  0.238 -0.0741 0.0096  False
-    21     28   -0.017    0.9 -0.0642 0.0303  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[1.01505933e-08]	Yes
-Stroke	Sham	14	[0.02467788]	Yes
-Stroke	Sham	21	[0.77454459]	No
-Stroke	Sham	28	[0.52926269]	No
-Stroke	Sham	7	[3.91214838e-11]	Yes
-Stroke	Sham	0	[0.97963994]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_4_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_4
+               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 193867.989 0.000 1.000 -379974.277 379974.277
+merged_timepoint 0.002      0.001 3.278 0.001       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  -0.0157  0.978 -0.0774 0.0461  False
+     0      7  -0.0329 0.6942 -0.0981 0.0323  False
+     0     14   0.0199 0.9486 -0.0444 0.0842  False
+     0     21   0.0417  0.427 -0.0226 0.1059  False
+     0     28   0.0451 0.3787 -0.0216 0.1118  False
+     3      7  -0.0172 0.9625 -0.0773 0.0429  False
+     3     14   0.0356 0.5133 -0.0236 0.0947  False
+     3     21   0.0573 0.0632 -0.0018 0.1165  False
+     3     28   0.0607 0.0569  -0.001 0.1225  False
+     7     14   0.0528 0.1531 -0.0099 0.1155  False
+     7     21   0.0746 0.0097  0.0119 0.1373   True
+     7     28    0.078  0.009  0.0128 0.1432   True
+    14     21   0.0218 0.9126   -0.04 0.0835  False
+    14     28   0.0252 0.8696 -0.0391 0.0895  False
+    21     28   0.0034    1.0 -0.0609 0.0677  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0323 0.9081 -0.0584 0.1229  False
+     0      7   0.0278 0.9301 -0.0559 0.1116  False
+     0     14    0.049 0.4952 -0.0314 0.1294  False
+     0     21   0.0348 0.8845 -0.0572 0.1268  False
+     0     28    0.028 0.9388 -0.0592 0.1153  False
+     3      7  -0.0045    1.0 -0.0965 0.0875  False
+     3     14   0.0167 0.9943 -0.0722 0.1057  False
+     3     21   0.0025    1.0 -0.0971 0.1021  False
+     3     28  -0.0042    1.0 -0.0994  0.091  False
+     7     14   0.0212 0.9756 -0.0607 0.1031  False
+     7     21   0.0069 0.9999 -0.0864 0.1002  False
+     7     28   0.0002    1.0 -0.0884 0.0889  False
+    14     21  -0.0142 0.9975 -0.1045 0.0761  False
+    14     28  -0.0209 0.9808 -0.1064 0.0646  False
+    21     28  -0.0067    1.0 -0.1032 0.0898  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.09507782]	No
+Stroke	Sham	14	[0.36576993]	No
+Stroke	Sham	21	[0.81135811]	No
+Stroke	Sham	28	[0.28143792]	No
+Stroke	Sham	7	[0.00241132]	Yes
+Stroke	Sham	0	[0.8988312]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_cut_0_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_cut_0
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0177
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 98490.369 0.000 1.000 -193037.575 193037.575
-merged_timepoint 0.003     0.000 8.107 0.000       0.002      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  -0.0659  0.001 -0.1047 -0.0271   True
-     0      7  -0.0454 0.0197 -0.0864 -0.0045   True
-     0     14   0.0205 0.6739 -0.0199  0.0609  False
-     0     21   0.0454 0.0171   0.005  0.0858   True
-     0     28    0.048 0.0142  0.0061  0.0899   True
-     3      7   0.0205 0.6147 -0.0173  0.0582  False
-     3     14   0.0864  0.001  0.0492  0.1235   True
-     3     21   0.1113  0.001  0.0742  0.1485   True
-     3     28   0.1139  0.001  0.0751  0.1527   True
-     7     14   0.0659  0.001  0.0265  0.1053   True
-     7     21   0.0909  0.001  0.0515  0.1303   True
-     7     28   0.0934  0.001  0.0525  0.1344   True
-    14     21    0.025 0.4439 -0.0138  0.0638  False
-    14     28   0.0275 0.3761 -0.0129  0.0679  False
-    21     28   0.0025    0.9 -0.0378  0.0429  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3    0.021 0.8065 -0.0283 0.0703  False
-     0      7   0.0282 0.4868 -0.0173 0.0738  False
-     0     14    0.068  0.001  0.0243 0.1117   True
-     0     21   0.0429  0.141 -0.0072 0.0929  False
-     0     28   0.0299 0.4697 -0.0176 0.0773  False
-     3      7   0.0072    0.9 -0.0428 0.0573  False
-     3     14    0.047 0.0627 -0.0014 0.0954  False
-     3     21   0.0219 0.8419 -0.0323 0.0761  False
-     3     28   0.0089    0.9 -0.0429 0.0607  False
-     7     14   0.0398 0.1107 -0.0047 0.0843  False
-     7     21   0.0147    0.9 -0.0361 0.0654  False
-     7     28   0.0016    0.9 -0.0466 0.0499  False
-    14     21  -0.0251 0.6654 -0.0742  0.024  False
-    14     28  -0.0381  0.178 -0.0847 0.0084  False
-    21     28   -0.013    0.9 -0.0655 0.0395  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[5.10126041e-09]	Yes
-Stroke	Sham	14	[0.00548223]	Yes
-Stroke	Sham	21	[0.98891423]	No
-Stroke	Sham	28	[0.24169644]	No
-Stroke	Sham	7	[4.93500796e-11]	Yes
-Stroke	Sham	0	[0.80630424]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_cut_0_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_cut_0
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0263
+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 317240.552 0.000 1.000 -621780.057 621780.057
+merged_timepoint 0.003      0.001 3.851 0.000       0.002      0.005
+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  -0.1388  0.003  -0.245 -0.0326   True
+     0      7  -0.0515  0.773 -0.1636  0.0606  False
+     0     14   0.0164 0.9982 -0.0942  0.1269  False
+     0     21   0.0417 0.8864 -0.0688  0.1523  False
+     0     28   0.0401 0.9155 -0.0746  0.1548  False
+     3      7   0.0873 0.1507  -0.016  0.1907  False
+     3     14   0.1552 0.0003  0.0535  0.2569   True
+     3     21   0.1805    0.0  0.0788  0.2822   True
+     3     28   0.1789    0.0  0.0727  0.2851   True
+     7     14   0.0678 0.4611   -0.04  0.1757  False
+     7     21   0.0932 0.1328 -0.0146   0.201  False
+     7     28   0.0916  0.179 -0.0205  0.2037  False
+    14     21   0.0253 0.9833 -0.0809  0.1316  False
+    14     28   0.0237 0.9896 -0.0868  0.1343  False
+    21     28  -0.0016    1.0 -0.1122  0.1089  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0003    1.0 -0.1349 0.1344  False
+     0      7     0.03 0.9822 -0.0944 0.1543  False
+     0     14   0.0832 0.3406 -0.0362 0.2026  False
+     0     21   0.0519 0.8816 -0.0847 0.1886  False
+     0     28   0.0223 0.9963 -0.1073 0.1519  False
+     3      7   0.0302 0.9878 -0.1064 0.1668  False
+     3     14   0.0835 0.4537 -0.0486 0.2155  False
+     3     21   0.0522 0.9108 -0.0956 0.2001  False
+     3     28   0.0225 0.9974 -0.1189 0.1639  False
+     7     14   0.0532 0.8044 -0.0684 0.1748  False
+     7     21    0.022 0.9974 -0.1166 0.1605  False
+     7     28  -0.0077    1.0 -0.1394 0.1239  False
+    14     21  -0.0312 0.9847 -0.1653 0.1029  False
+    14     28  -0.0609 0.7357 -0.1879  0.066  False
+    21     28  -0.0297  0.991  -0.173 0.1136  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00059078]	Yes
+Stroke	Sham	14	[0.17042771]	No
+Stroke	Sham	21	[0.80578929]	No
+Stroke	Sham	28	[0.70315125]	No
+Stroke	Sham	7	[0.00727771]	Yes
+Stroke	Sham	0	[0.92376634]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_cut_1_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_cut_1
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0177
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 98490.369 0.000 1.000 -193037.575 193037.575
-merged_timepoint 0.003     0.000 8.107 0.000       0.002      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  -0.0659  0.001 -0.1047 -0.0271   True
-     0      7  -0.0454 0.0197 -0.0864 -0.0045   True
-     0     14   0.0205 0.6739 -0.0199  0.0609  False
-     0     21   0.0454 0.0171   0.005  0.0858   True
-     0     28    0.048 0.0142  0.0061  0.0899   True
-     3      7   0.0205 0.6147 -0.0173  0.0582  False
-     3     14   0.0864  0.001  0.0492  0.1235   True
-     3     21   0.1113  0.001  0.0742  0.1485   True
-     3     28   0.1139  0.001  0.0751  0.1527   True
-     7     14   0.0659  0.001  0.0265  0.1053   True
-     7     21   0.0909  0.001  0.0515  0.1303   True
-     7     28   0.0934  0.001  0.0525  0.1344   True
-    14     21    0.025 0.4439 -0.0138  0.0638  False
-    14     28   0.0275 0.3761 -0.0129  0.0679  False
-    21     28   0.0025    0.9 -0.0378  0.0429  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3    0.021 0.8065 -0.0283 0.0703  False
-     0      7   0.0282 0.4868 -0.0173 0.0738  False
-     0     14    0.068  0.001  0.0243 0.1117   True
-     0     21   0.0429  0.141 -0.0072 0.0929  False
-     0     28   0.0299 0.4697 -0.0176 0.0773  False
-     3      7   0.0072    0.9 -0.0428 0.0573  False
-     3     14    0.047 0.0627 -0.0014 0.0954  False
-     3     21   0.0219 0.8419 -0.0323 0.0761  False
-     3     28   0.0089    0.9 -0.0429 0.0607  False
-     7     14   0.0398 0.1107 -0.0047 0.0843  False
-     7     21   0.0147    0.9 -0.0361 0.0654  False
-     7     28   0.0016    0.9 -0.0466 0.0499  False
-    14     21  -0.0251 0.6654 -0.0742  0.024  False
-    14     28  -0.0381  0.178 -0.0847 0.0084  False
-    21     28   -0.013    0.9 -0.0655 0.0395  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[5.10126041e-09]	Yes
-Stroke	Sham	14	[0.00548223]	Yes
-Stroke	Sham	21	[0.98891423]	No
-Stroke	Sham	28	[0.24169644]	No
-Stroke	Sham	7	[4.93500796e-11]	Yes
-Stroke	Sham	0	[0.80630424]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_cut_1_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_cut_1
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0204
+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 279448.631 0.000 1.000 -547709.252 547709.252
+merged_timepoint 0.003      0.001 4.047 0.000       0.002      0.005
+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  -0.0877 0.1058 -0.1853 0.0099  False
+     0      7  -0.0483 0.7563 -0.1513 0.0547  False
+     0     14   0.0236 0.9851  -0.078 0.1252  False
+     0     21   0.0526 0.6717  -0.049 0.1541  False
+     0     28   0.0508 0.7342 -0.0546 0.1563  False
+     3      7   0.0393 0.8404 -0.0556 0.1343  False
+     3     14   0.1113 0.0095  0.0178 0.2047   True
+     3     21   0.1402 0.0004  0.0468 0.2337   True
+     3     28   0.1385 0.0009  0.0409 0.2361   True
+     7     14   0.0719 0.2967 -0.0271  0.171  False
+     7     21   0.1009 0.0432  0.0018    0.2   True
+     7     28   0.0992 0.0664 -0.0038 0.2022  False
+    14     21   0.0289 0.9569 -0.0687 0.1265  False
+    14     28   0.0272  0.972 -0.0744 0.1288  False
+    21     28  -0.0017    1.0 -0.1033 0.0999  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0202 0.9959 -0.0953 0.1358  False
+     0      7   0.0333 0.9456 -0.0734 0.1401  False
+     0     14   0.0804 0.2156 -0.0221 0.1828  False
+     0     21   0.0475 0.8507 -0.0698 0.1647  False
+     0     28   0.0397 0.9069 -0.0715  0.151  False
+     3      7   0.0131 0.9995 -0.1041 0.1304  False
+     3     14   0.0601  0.645 -0.0533 0.1735  False
+     3     21   0.0273 0.9894 -0.0996 0.1542  False
+     3     28   0.0195 0.9973 -0.1019 0.1409  False
+     7     14    0.047 0.7843 -0.0573 0.1514  False
+     7     21   0.0142 0.9994 -0.1048 0.1331  False
+     7     28   0.0064    1.0 -0.1066 0.1194  False
+    14     21  -0.0329 0.9627  -0.148 0.0822  False
+    14     28  -0.0406   0.89 -0.1496 0.0683  False
+    21     28  -0.0078    1.0 -0.1308 0.1152  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00261941]	Yes
+Stroke	Sham	14	[0.17767538]	No
+Stroke	Sham	21	[0.98368511]	No
+Stroke	Sham	28	[0.82726179]	No
+Stroke	Sham	7	[0.00235826]	Yes
+Stroke	Sham	0	[0.88449581]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_cut_2_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_cut_2
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0177
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 98490.369 0.000 1.000 -193037.575 193037.575
-merged_timepoint 0.003     0.000 8.107 0.000       0.002      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  -0.0659  0.001 -0.1047 -0.0271   True
-     0      7  -0.0454 0.0197 -0.0864 -0.0045   True
-     0     14   0.0205 0.6739 -0.0199  0.0609  False
-     0     21   0.0454 0.0171   0.005  0.0858   True
-     0     28    0.048 0.0142  0.0061  0.0899   True
-     3      7   0.0205 0.6147 -0.0173  0.0582  False
-     3     14   0.0864  0.001  0.0492  0.1235   True
-     3     21   0.1113  0.001  0.0742  0.1485   True
-     3     28   0.1139  0.001  0.0751  0.1527   True
-     7     14   0.0659  0.001  0.0265  0.1053   True
-     7     21   0.0909  0.001  0.0515  0.1303   True
-     7     28   0.0934  0.001  0.0525  0.1344   True
-    14     21    0.025 0.4439 -0.0138  0.0638  False
-    14     28   0.0275 0.3761 -0.0129  0.0679  False
-    21     28   0.0025    0.9 -0.0378  0.0429  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3    0.021 0.8065 -0.0283 0.0703  False
-     0      7   0.0282 0.4868 -0.0173 0.0738  False
-     0     14    0.068  0.001  0.0243 0.1117   True
-     0     21   0.0429  0.141 -0.0072 0.0929  False
-     0     28   0.0299 0.4697 -0.0176 0.0773  False
-     3      7   0.0072    0.9 -0.0428 0.0573  False
-     3     14    0.047 0.0627 -0.0014 0.0954  False
-     3     21   0.0219 0.8419 -0.0323 0.0761  False
-     3     28   0.0089    0.9 -0.0429 0.0607  False
-     7     14   0.0398 0.1107 -0.0047 0.0843  False
-     7     21   0.0147    0.9 -0.0361 0.0654  False
-     7     28   0.0016    0.9 -0.0466 0.0499  False
-    14     21  -0.0251 0.6654 -0.0742  0.024  False
-    14     28  -0.0381  0.178 -0.0847 0.0084  False
-    21     28   -0.013    0.9 -0.0655 0.0395  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[5.10126041e-09]	Yes
-Stroke	Sham	14	[0.00548223]	Yes
-Stroke	Sham	21	[0.98891423]	No
-Stroke	Sham	28	[0.24169644]	No
-Stroke	Sham	7	[4.93500796e-11]	Yes
-Stroke	Sham	0	[0.80630424]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_cut_2_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_cut_2
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   361      Method:              REML    
+No. Groups:         2        Scale:               0.0159  
+Min. group size:    156      Log-Likelihood:      225.1317
+Max. group size:    205      Converged:           Yes     
+Mean group size:    180.5                                 
+----------------------------------------------------------
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        1.129    0.020 55.982 0.000  1.089  1.168
+merged_timepoint 0.002    0.001  3.628 0.000  0.001  0.004
+Group Var        0.001    0.008                           
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0495 0.5494 -0.1344 0.0355  False
+     0      7  -0.0433 0.7329 -0.1329 0.0463  False
+     0     14   0.0231 0.9748 -0.0653 0.1115  False
+     0     21   0.0454 0.6777  -0.043 0.1338  False
+     0     28   0.0505 0.6092 -0.0412 0.1423  False
+     3      7   0.0062 0.9999 -0.0765 0.0888  False
+     3     14   0.0726 0.1099 -0.0087 0.1539  False
+     3     21   0.0949 0.0119  0.0136 0.1762   True
+     3     28      0.1 0.0108  0.0151 0.1849   True
+     7     14   0.0664 0.2345 -0.0198 0.1526  False
+     7     21   0.0887 0.0395  0.0025  0.175   True
+     7     28   0.0938 0.0343  0.0042 0.1835   True
+    14     21   0.0223 0.9743 -0.0626 0.1073  False
+    14     28   0.0274  0.948  -0.061 0.1158  False
+    21     28   0.0051    1.0 -0.0833 0.0935  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0319 0.9513 -0.0731 0.1369  False
+     0      7   0.0277 0.9624 -0.0692 0.1247  False
+     0     14   0.0678 0.2913 -0.0253 0.1609  False
+     0     21   0.0447 0.8304 -0.0618 0.1512  False
+     0     28   0.0347   0.92 -0.0663 0.1358  False
+     3      7  -0.0042    1.0 -0.1107 0.1023  False
+     3     14   0.0359 0.9154 -0.0671 0.1389  False
+     3     21   0.0128 0.9995 -0.1025 0.1281  False
+     3     28   0.0028    1.0 -0.1075 0.1131  False
+     7     14   0.0401 0.8262 -0.0547 0.1349  False
+     7     21    0.017 0.9975  -0.091  0.125  False
+     7     28    0.007    1.0 -0.0957 0.1096  False
+    14     21  -0.0231  0.988 -0.1277 0.0815  False
+    14     28  -0.0331 0.9282 -0.1321 0.0659  False
+    21     28    -0.01 0.9998 -0.1217 0.1017  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.01004534]	Yes
+Stroke	Sham	14	[0.20911532]	No
+Stroke	Sham	21	[0.94674776]	No
+Stroke	Sham	28	[0.65545406]	No
+Stroke	Sham	7	[0.00236945]	Yes
+Stroke	Sham	0	[0.87748632]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_cut_3_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_cut_3
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0177
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 98490.369 0.000 1.000 -193037.575 193037.575
-merged_timepoint 0.003     0.000 8.107 0.000       0.002      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  -0.0659  0.001 -0.1047 -0.0271   True
-     0      7  -0.0454 0.0197 -0.0864 -0.0045   True
-     0     14   0.0205 0.6739 -0.0199  0.0609  False
-     0     21   0.0454 0.0171   0.005  0.0858   True
-     0     28    0.048 0.0142  0.0061  0.0899   True
-     3      7   0.0205 0.6147 -0.0173  0.0582  False
-     3     14   0.0864  0.001  0.0492  0.1235   True
-     3     21   0.1113  0.001  0.0742  0.1485   True
-     3     28   0.1139  0.001  0.0751  0.1527   True
-     7     14   0.0659  0.001  0.0265  0.1053   True
-     7     21   0.0909  0.001  0.0515  0.1303   True
-     7     28   0.0934  0.001  0.0525  0.1344   True
-    14     21    0.025 0.4439 -0.0138  0.0638  False
-    14     28   0.0275 0.3761 -0.0129  0.0679  False
-    21     28   0.0025    0.9 -0.0378  0.0429  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3    0.021 0.8065 -0.0283 0.0703  False
-     0      7   0.0282 0.4868 -0.0173 0.0738  False
-     0     14    0.068  0.001  0.0243 0.1117   True
-     0     21   0.0429  0.141 -0.0072 0.0929  False
-     0     28   0.0299 0.4697 -0.0176 0.0773  False
-     3      7   0.0072    0.9 -0.0428 0.0573  False
-     3     14    0.047 0.0627 -0.0014 0.0954  False
-     3     21   0.0219 0.8419 -0.0323 0.0761  False
-     3     28   0.0089    0.9 -0.0429 0.0607  False
-     7     14   0.0398 0.1107 -0.0047 0.0843  False
-     7     21   0.0147    0.9 -0.0361 0.0654  False
-     7     28   0.0016    0.9 -0.0466 0.0499  False
-    14     21  -0.0251 0.6654 -0.0742  0.024  False
-    14     28  -0.0381  0.178 -0.0847 0.0084  False
-    21     28   -0.013    0.9 -0.0655 0.0395  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[5.10126041e-09]	Yes
-Stroke	Sham	14	[0.00548223]	Yes
-Stroke	Sham	21	[0.98891423]	No
-Stroke	Sham	28	[0.24169644]	No
-Stroke	Sham	7	[4.93500796e-11]	Yes
-Stroke	Sham	0	[0.80630424]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_cut_3_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_cut_3
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   361      Method:              REML    
+No. Groups:         2        Scale:               0.0130  
+Min. group size:    156      Log-Likelihood:      260.7140
+Max. group size:    205      Converged:           Yes     
+Mean group size:    180.5                                 
+----------------------------------------------------------
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        1.128    0.015 73.118 0.000  1.098  1.158
+merged_timepoint 0.002    0.001  3.384 0.001  0.001  0.003
+Group Var        0.000    0.005                           
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0319 0.8173 -0.1061 0.0422  False
+     0      7  -0.0439 0.5895 -0.1222 0.0343  False
+     0     14   0.0204 0.9735 -0.0567 0.0976  False
+     0     21   0.0427 0.6046 -0.0345 0.1199  False
+     0     28   0.0485 0.5061 -0.0316 0.1286  False
+     3      7   -0.012 0.9968 -0.0842 0.0602  False
+     3     14   0.0524 0.2801 -0.0186 0.1234  False
+     3     21   0.0746 0.0331  0.0036 0.1456   True
+     3     28   0.0804  0.025  0.0062 0.1546   True
+     7     14   0.0644  0.141 -0.0109 0.1397  False
+     7     21   0.0866 0.0138  0.0114 0.1619   True
+     7     28   0.0924 0.0105  0.0141 0.1707   True
+    14     21   0.0223 0.9545 -0.0519 0.0964  False
+    14     28    0.028  0.902 -0.0492 0.1052  False
+    21     28   0.0058 0.9999 -0.0714  0.083  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0292  0.958 -0.0703 0.1286  False
+     0      7   0.0243 0.9732 -0.0676 0.1161  False
+     0     14   0.0566 0.4358 -0.0316 0.1447  False
+     0     21   0.0354  0.913 -0.0655 0.1363  False
+     0     28   0.0275 0.9614 -0.0682 0.1233  False
+     3      7  -0.0049    1.0 -0.1058  0.096  False
+     3     14   0.0274 0.9653 -0.0702  0.125  False
+     3     21   0.0062    1.0  -0.103 0.1154  False
+     3     28  -0.0016    1.0 -0.1061 0.1028  False
+     7     14   0.0323 0.9044 -0.0575 0.1221  False
+     7     21   0.0111 0.9996 -0.0912 0.1134  False
+     7     28   0.0033    1.0  -0.094 0.1005  False
+    14     21  -0.0212 0.9897 -0.1202 0.0779  False
+    14     28   -0.029 0.9475 -0.1228 0.0647  False
+    21     28  -0.0079 0.9999 -0.1137  0.098  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.04052325]	Yes
+Stroke	Sham	14	[0.26243025]	No
+Stroke	Sham	21	[0.90357504]	No
+Stroke	Sham	28	[0.41288494]	No
+Stroke	Sham	7	[0.00159621]	Yes
+Stroke	Sham	0	[0.92690013]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_cut_4_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_cut_4
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0177
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 98490.369 0.000 1.000 -193037.575 193037.575
-merged_timepoint 0.003     0.000 8.107 0.000       0.002      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  -0.0659  0.001 -0.1047 -0.0271   True
-     0      7  -0.0454 0.0197 -0.0864 -0.0045   True
-     0     14   0.0205 0.6739 -0.0199  0.0609  False
-     0     21   0.0454 0.0171   0.005  0.0858   True
-     0     28    0.048 0.0142  0.0061  0.0899   True
-     3      7   0.0205 0.6147 -0.0173  0.0582  False
-     3     14   0.0864  0.001  0.0492  0.1235   True
-     3     21   0.1113  0.001  0.0742  0.1485   True
-     3     28   0.1139  0.001  0.0751  0.1527   True
-     7     14   0.0659  0.001  0.0265  0.1053   True
-     7     21   0.0909  0.001  0.0515  0.1303   True
-     7     28   0.0934  0.001  0.0525  0.1344   True
-    14     21    0.025 0.4439 -0.0138  0.0638  False
-    14     28   0.0275 0.3761 -0.0129  0.0679  False
-    21     28   0.0025    0.9 -0.0378  0.0429  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3    0.021 0.8065 -0.0283 0.0703  False
-     0      7   0.0282 0.4868 -0.0173 0.0738  False
-     0     14    0.068  0.001  0.0243 0.1117   True
-     0     21   0.0429  0.141 -0.0072 0.0929  False
-     0     28   0.0299 0.4697 -0.0176 0.0773  False
-     3      7   0.0072    0.9 -0.0428 0.0573  False
-     3     14    0.047 0.0627 -0.0014 0.0954  False
-     3     21   0.0219 0.8419 -0.0323 0.0761  False
-     3     28   0.0089    0.9 -0.0429 0.0607  False
-     7     14   0.0398 0.1107 -0.0047 0.0843  False
-     7     21   0.0147    0.9 -0.0361 0.0654  False
-     7     28   0.0016    0.9 -0.0466 0.0499  False
-    14     21  -0.0251 0.6654 -0.0742  0.024  False
-    14     28  -0.0381  0.178 -0.0847 0.0084  False
-    21     28   -0.013    0.9 -0.0655 0.0395  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[5.10126041e-09]	Yes
-Stroke	Sham	14	[0.00548223]	Yes
-Stroke	Sham	21	[0.98891423]	No
-Stroke	Sham	28	[0.24169644]	No
-Stroke	Sham	7	[4.93500796e-11]	Yes
-Stroke	Sham	0	[0.80630424]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_cut_4_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_cut_4
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0116
+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 210756.776 0.000 1.000 -413075.690 413075.690
+merged_timepoint 0.002      0.001 3.395 0.001       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  -0.0217   0.94 -0.0894  0.046  False
+     0      7  -0.0401  0.589 -0.1116 0.0313  False
+     0     14   0.0187 0.9731 -0.0517 0.0892  False
+     0     21   0.0447 0.4511 -0.0257 0.1152  False
+     0     28   0.0499 0.3661 -0.0232 0.1231  False
+     3      7  -0.0184 0.9667 -0.0843 0.0475  False
+     3     14   0.0404 0.4708 -0.0244 0.1053  False
+     3     21   0.0665 0.0409  0.0016 0.1313   True
+     3     28   0.0717 0.0311   0.004 0.1394   True
+     7     14   0.0588 0.1401 -0.0099 0.1275  False
+     7     21   0.0848 0.0062  0.0161 0.1535   True
+     7     28     0.09 0.0048  0.0186 0.1615   True
+    14     21    0.026 0.8786 -0.0417 0.0937  False
+    14     28   0.0312 0.7983 -0.0392 0.1017  False
+    21     28   0.0052 0.9999 -0.0652 0.0757  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0239 0.9808 -0.0737 0.1215  False
+     0      7   0.0257 0.9627 -0.0644 0.1159  False
+     0     14   0.0521 0.5086 -0.0344 0.1387  False
+     0     21   0.0349 0.9118 -0.0642 0.1339  False
+     0     28   0.0251 0.9721 -0.0689  0.119  False
+     3      7   0.0018    1.0 -0.0972 0.1008  False
+     3     14   0.0282 0.9573 -0.0676  0.124  False
+     3     21    0.011 0.9997 -0.0962 0.1181  False
+     3     28   0.0012    1.0 -0.1014 0.1037  False
+     7     14   0.0264 0.9544 -0.0618 0.1145  False
+     7     21   0.0091 0.9998 -0.0913 0.1096  False
+     7     28  -0.0007    1.0 -0.0961 0.0948  False
+    14     21  -0.0172 0.9956 -0.1145   0.08  False
+    14     28  -0.0271 0.9577 -0.1191  0.065  False
+    21     28  -0.0098 0.9998 -0.1137 0.0941  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.1094621]	No
+Stroke	Sham	14	[0.26815861]	No
+Stroke	Sham	21	[0.83962638]	No
+Stroke	Sham	28	[0.26311843]	No
+Stroke	Sham	7	[0.00170419]	Yes
+Stroke	Sham	0	[0.95073457]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_0_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_dilated_0
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0100
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 73917.873 0.000 1.000 -144876.368 144876.368
-merged_timepoint 0.001     0.000 5.955 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   0.0176 0.4416 -0.0097   0.045  False
-     0      7  -0.0313 0.0243 -0.0602 -0.0025   True
-     0     14   0.0293  0.039  0.0009  0.0578   True
-     0     21   0.0496  0.001  0.0211   0.078   True
-     0     28   0.0422  0.001  0.0127  0.0718   True
-     3      7   -0.049  0.001 -0.0756 -0.0223   True
-     3     14   0.0117 0.7722 -0.0145  0.0379  False
-     3     21   0.0319 0.0068  0.0058  0.0581   True
-     3     28   0.0246 0.1065 -0.0028  0.0519  False
-     7     14   0.0607  0.001  0.0329  0.0884   True
-     7     21   0.0809  0.001  0.0531  0.1087   True
-     7     28   0.0735  0.001  0.0447  0.1024   True
-    14     21   0.0202 0.2807 -0.0071  0.0476  False
-    14     28   0.0129 0.7621 -0.0156  0.0413  False
-    21     28  -0.0074    0.9 -0.0358  0.0211  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0396 0.0512 -0.0001 0.0794  False
-     0      7   0.0273 0.2743 -0.0094 0.0641  False
-     0     14    0.045 0.0039  0.0097 0.0802   True
-     0     21   0.0389 0.0665 -0.0015 0.0792  False
-     0     28   0.0298 0.2294 -0.0085  0.068  False
-     3      7  -0.0123    0.9 -0.0527 0.0281  False
-     3     14   0.0053    0.9 -0.0337 0.0443  False
-     3     21  -0.0008    0.9 -0.0444 0.0429  False
-     3     28  -0.0099    0.9 -0.0517 0.0319  False
-     7     14   0.0176 0.6997 -0.0183 0.0535  False
-     7     21   0.0115    0.9 -0.0294 0.0525  False
-     7     28   0.0024    0.9 -0.0365 0.0413  False
-    14     21  -0.0061    0.9 -0.0457 0.0335  False
-    14     28  -0.0152 0.8394 -0.0527 0.0223  False
-    21     28  -0.0091    0.9 -0.0515 0.0332  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.22854221]	No
-Stroke	Sham	14	[0.43480359]	No
-Stroke	Sham	21	[0.33001424]	No
-Stroke	Sham	28	[0.02414372]	Yes
-Stroke	Sham	7	[1.72474068e-09]	Yes
-Stroke	Sham	0	[0.44754138]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_0_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_dilated_0
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   361      Method:              REML    
+No. Groups:         2        Scale:               0.0130  
+Min. group size:    156      Log-Likelihood:      261.8892
+Max. group size:    205      Converged:           Yes     
+Mean group size:    180.5                                 
+----------------------------------------------------------
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        1.133    0.012 98.404 0.000  1.110  1.155
+merged_timepoint 0.002    0.001  3.442 0.001  0.001  0.003
+Group Var        0.000    0.002                           
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0053 0.9999  -0.078 0.0674  False
+     0      7  -0.0359 0.7579 -0.1126 0.0408  False
+     0     14   0.0343 0.7826 -0.0414 0.1099  False
+     0     21   0.0654 0.1324 -0.0102 0.1411  False
+     0     28   0.0503 0.4409 -0.0282 0.1288  False
+     3      7  -0.0306 0.8142 -0.1013 0.0401  False
+     3     14   0.0396 0.5745   -0.03 0.1092  False
+     3     21   0.0708 0.0438  0.0012 0.1404   True
+     3     28   0.0556 0.2418 -0.0171 0.1283  False
+     7     14   0.0702 0.0723 -0.0036  0.144  False
+     7     21   0.1014 0.0015  0.0276 0.1751   True
+     7     28   0.0862 0.0177  0.0095 0.1629   True
+    14     21   0.0311 0.8202 -0.0415 0.1038  False
+    14     28    0.016 0.9903 -0.0597 0.0917  False
+    21     28  -0.0152 0.9925 -0.0908 0.0605  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0212 0.9906 -0.0801 0.1226  False
+     0      7   0.0198   0.99 -0.0738 0.1134  False
+     0     14   0.0527 0.5384 -0.0371 0.1425  False
+     0     21   0.0356 0.9177 -0.0672 0.1384  False
+     0     28   0.0307 0.9438 -0.0668 0.1282  False
+     3      7  -0.0014    1.0 -0.1042 0.1014  False
+     3     14   0.0315 0.9424 -0.0679 0.1309  False
+     3     21   0.0144  0.999 -0.0969 0.1256  False
+     3     28   0.0095 0.9998 -0.0969 0.1159  False
+     7     14   0.0329 0.9048 -0.0587 0.1244  False
+     7     21   0.0157  0.998 -0.0885   0.12  False
+     7     28   0.0109 0.9996 -0.0882 0.1099  False
+    14     21  -0.0171 0.9965 -0.1181 0.0838  False
+    14     28   -0.022 0.9855 -0.1176 0.0735  False
+    21     28  -0.0049    1.0 -0.1127  0.103  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.28390179]	No
+Stroke	Sham	14	[0.39506082]	No
+Stroke	Sham	21	[0.61791987]	No
+Stroke	Sham	28	[0.61496421]	No
+Stroke	Sham	7	[0.00700354]	Yes
+Stroke	Sham	0	[0.7266615]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_1_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_dilated_1
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0100
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 73917.873 0.000 1.000 -144876.368 144876.368
-merged_timepoint 0.001     0.000 5.955 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   0.0176 0.4416 -0.0097   0.045  False
-     0      7  -0.0313 0.0243 -0.0602 -0.0025   True
-     0     14   0.0293  0.039  0.0009  0.0578   True
-     0     21   0.0496  0.001  0.0211   0.078   True
-     0     28   0.0422  0.001  0.0127  0.0718   True
-     3      7   -0.049  0.001 -0.0756 -0.0223   True
-     3     14   0.0117 0.7722 -0.0145  0.0379  False
-     3     21   0.0319 0.0068  0.0058  0.0581   True
-     3     28   0.0246 0.1065 -0.0028  0.0519  False
-     7     14   0.0607  0.001  0.0329  0.0884   True
-     7     21   0.0809  0.001  0.0531  0.1087   True
-     7     28   0.0735  0.001  0.0447  0.1024   True
-    14     21   0.0202 0.2807 -0.0071  0.0476  False
-    14     28   0.0129 0.7621 -0.0156  0.0413  False
-    21     28  -0.0074    0.9 -0.0358  0.0211  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0396 0.0512 -0.0001 0.0794  False
-     0      7   0.0273 0.2743 -0.0094 0.0641  False
-     0     14    0.045 0.0039  0.0097 0.0802   True
-     0     21   0.0389 0.0665 -0.0015 0.0792  False
-     0     28   0.0298 0.2294 -0.0085  0.068  False
-     3      7  -0.0123    0.9 -0.0527 0.0281  False
-     3     14   0.0053    0.9 -0.0337 0.0443  False
-     3     21  -0.0008    0.9 -0.0444 0.0429  False
-     3     28  -0.0099    0.9 -0.0517 0.0319  False
-     7     14   0.0176 0.6997 -0.0183 0.0535  False
-     7     21   0.0115    0.9 -0.0294 0.0525  False
-     7     28   0.0024    0.9 -0.0365 0.0413  False
-    14     21  -0.0061    0.9 -0.0457 0.0335  False
-    14     28  -0.0152 0.8394 -0.0527 0.0223  False
-    21     28  -0.0091    0.9 -0.0515 0.0332  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.22854221]	No
-Stroke	Sham	14	[0.43480359]	No
-Stroke	Sham	21	[0.33001424]	No
-Stroke	Sham	28	[0.02414372]	Yes
-Stroke	Sham	7	[1.72474068e-09]	Yes
-Stroke	Sham	0	[0.44754138]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_1_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_dilated_1
+               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 202563.102 0.000 1.000 -397016.384 397016.384
+merged_timepoint 0.002      0.001 2.665 0.008       0.000      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   0.0236 0.9007 -0.0411 0.0883  False
+     0      7   -0.033  0.733 -0.1013 0.0353  False
+     0     14   0.0334 0.7109  -0.034 0.1007  False
+     0     21   0.0581 0.1335 -0.0092 0.1255  False
+     0     28   0.0412 0.5344 -0.0286 0.1111  False
+     3      7  -0.0566 0.1058 -0.1195 0.0064  False
+     3     14   0.0098 0.9975 -0.0521 0.0717  False
+     3     21   0.0346 0.5954 -0.0274 0.0965  False
+     3     28   0.0177 0.9696  -0.047 0.0824  False
+     7     14   0.0664  0.046  0.0007  0.132   True
+     7     21   0.0911 0.0013  0.0255 0.1568   True
+     7     28   0.0742 0.0244   0.006 0.1425   True
+    14     21   0.0248 0.8802 -0.0399 0.0895  False
+    14     28   0.0079 0.9994 -0.0595 0.0752  False
+    21     28  -0.0169  0.979 -0.0842 0.0504  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0367 0.8685 -0.0572 0.1306  False
+     0      7   0.0227 0.9745  -0.064 0.1094  False
+     0     14   0.0449 0.6268 -0.0383 0.1282  False
+     0     21   0.0369 0.8726 -0.0583 0.1322  False
+     0     28   0.0308 0.9223 -0.0596 0.1212  False
+     3      7  -0.0141 0.9982 -0.1093 0.0812  False
+     3     14   0.0082 0.9998 -0.0839 0.1003  False
+     3     21   0.0002    1.0 -0.1029 0.1033  False
+     3     28  -0.0059    1.0 -0.1045 0.0927  False
+     7     14   0.0223 0.9739 -0.0625 0.1071  False
+     7     21   0.0143 0.9982 -0.0823 0.1109  False
+     7     28   0.0082 0.9998 -0.0836 0.0999  False
+    14     21   -0.008 0.9999 -0.1015 0.0855  False
+    14     28  -0.0141 0.9974 -0.1027 0.0744  False
+    21     28  -0.0061    1.0  -0.106 0.0938  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.63883228]	No
+Stroke	Sham	14	[0.63666676]	No
+Stroke	Sham	21	[0.63543849]	No
+Stroke	Sham	28	[0.63285493]	No
+Stroke	Sham	7	[0.0042443]	Yes
+Stroke	Sham	0	[0.94427977]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_2_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_dilated_2
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0100
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 73917.873 0.000 1.000 -144876.368 144876.368
-merged_timepoint 0.001     0.000 5.955 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   0.0176 0.4416 -0.0097   0.045  False
-     0      7  -0.0313 0.0243 -0.0602 -0.0025   True
-     0     14   0.0293  0.039  0.0009  0.0578   True
-     0     21   0.0496  0.001  0.0211   0.078   True
-     0     28   0.0422  0.001  0.0127  0.0718   True
-     3      7   -0.049  0.001 -0.0756 -0.0223   True
-     3     14   0.0117 0.7722 -0.0145  0.0379  False
-     3     21   0.0319 0.0068  0.0058  0.0581   True
-     3     28   0.0246 0.1065 -0.0028  0.0519  False
-     7     14   0.0607  0.001  0.0329  0.0884   True
-     7     21   0.0809  0.001  0.0531  0.1087   True
-     7     28   0.0735  0.001  0.0447  0.1024   True
-    14     21   0.0202 0.2807 -0.0071  0.0476  False
-    14     28   0.0129 0.7621 -0.0156  0.0413  False
-    21     28  -0.0074    0.9 -0.0358  0.0211  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0396 0.0512 -0.0001 0.0794  False
-     0      7   0.0273 0.2743 -0.0094 0.0641  False
-     0     14    0.045 0.0039  0.0097 0.0802   True
-     0     21   0.0389 0.0665 -0.0015 0.0792  False
-     0     28   0.0298 0.2294 -0.0085  0.068  False
-     3      7  -0.0123    0.9 -0.0527 0.0281  False
-     3     14   0.0053    0.9 -0.0337 0.0443  False
-     3     21  -0.0008    0.9 -0.0444 0.0429  False
-     3     28  -0.0099    0.9 -0.0517 0.0319  False
-     7     14   0.0176 0.6997 -0.0183 0.0535  False
-     7     21   0.0115    0.9 -0.0294 0.0525  False
-     7     28   0.0024    0.9 -0.0365 0.0413  False
-    14     21  -0.0061    0.9 -0.0457 0.0335  False
-    14     28  -0.0152 0.8394 -0.0527 0.0223  False
-    21     28  -0.0091    0.9 -0.0515 0.0332  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.22854221]	No
-Stroke	Sham	14	[0.43480359]	No
-Stroke	Sham	21	[0.33001424]	No
-Stroke	Sham	28	[0.02414372]	Yes
-Stroke	Sham	7	[1.72474068e-09]	Yes
-Stroke	Sham	0	[0.44754138]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_2_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_dilated_2
+               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 188658.996 0.000 1.000 -369764.837 369764.837
+merged_timepoint 0.001      0.001 2.405 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   0.0259 0.8047 -0.0331 0.0848  False
+     0      7  -0.0303 0.7249 -0.0925 0.0318  False
+     0     14   0.0285 0.7646 -0.0329 0.0898  False
+     0     21   0.0469 0.2418 -0.0144 0.1082  False
+     0     28   0.0423 0.3973 -0.0213 0.1059  False
+     3      7  -0.0562 0.0584 -0.1135 0.0012  False
+     3     14   0.0026    1.0 -0.0538  0.059  False
+     3     21    0.021 0.8913 -0.0354 0.0775  False
+     3     28   0.0164 0.9667 -0.0425 0.0754  False
+     7     14   0.0588  0.057  -0.001 0.1186  False
+     7     21   0.0772 0.0035  0.0174  0.137   True
+     7     28   0.0726 0.0118  0.0105 0.1348   True
+    14     21   0.0184  0.946 -0.0405 0.0773  False
+    14     28   0.0138  0.987 -0.0475 0.0752  False
+    21     28  -0.0046 0.9999 -0.0659 0.0567  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0461 0.6672 -0.0429 0.1351  False
+     0      7   0.0285 0.9171 -0.0537 0.1107  False
+     0     14   0.0437 0.6008 -0.0352 0.1226  False
+     0     21   0.0366 0.8505 -0.0537 0.1269  False
+     0     28    0.029 0.9247 -0.0567 0.1146  False
+     3      7  -0.0176 0.9932 -0.1079 0.0726  False
+     3     14  -0.0024    1.0 -0.0897 0.0849  False
+     3     21  -0.0095 0.9998 -0.1072 0.0882  False
+     3     28  -0.0171 0.9949 -0.1106 0.0763  False
+     7     14   0.0152 0.9941 -0.0651 0.0956  False
+     7     21   0.0081 0.9998 -0.0835 0.0997  False
+     7     28   0.0005    1.0 -0.0865 0.0875  False
+    14     21  -0.0071 0.9999 -0.0957 0.0815  False
+    14     28  -0.0147 0.9959 -0.0986 0.0692  False
+    21     28  -0.0076 0.9999 -0.1023 0.0871  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.71079483]	No
+Stroke	Sham	14	[0.8224922]	No
+Stroke	Sham	21	[0.61369955]	No
+Stroke	Sham	28	[0.19579509]	No
+Stroke	Sham	7	[0.00655209]	Yes
+Stroke	Sham	0	[0.59451262]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_3_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_dilated_3
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0100
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 73917.873 0.000 1.000 -144876.368 144876.368
-merged_timepoint 0.001     0.000 5.955 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   0.0176 0.4416 -0.0097   0.045  False
-     0      7  -0.0313 0.0243 -0.0602 -0.0025   True
-     0     14   0.0293  0.039  0.0009  0.0578   True
-     0     21   0.0496  0.001  0.0211   0.078   True
-     0     28   0.0422  0.001  0.0127  0.0718   True
-     3      7   -0.049  0.001 -0.0756 -0.0223   True
-     3     14   0.0117 0.7722 -0.0145  0.0379  False
-     3     21   0.0319 0.0068  0.0058  0.0581   True
-     3     28   0.0246 0.1065 -0.0028  0.0519  False
-     7     14   0.0607  0.001  0.0329  0.0884   True
-     7     21   0.0809  0.001  0.0531  0.1087   True
-     7     28   0.0735  0.001  0.0447  0.1024   True
-    14     21   0.0202 0.2807 -0.0071  0.0476  False
-    14     28   0.0129 0.7621 -0.0156  0.0413  False
-    21     28  -0.0074    0.9 -0.0358  0.0211  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0396 0.0512 -0.0001 0.0794  False
-     0      7   0.0273 0.2743 -0.0094 0.0641  False
-     0     14    0.045 0.0039  0.0097 0.0802   True
-     0     21   0.0389 0.0665 -0.0015 0.0792  False
-     0     28   0.0298 0.2294 -0.0085  0.068  False
-     3      7  -0.0123    0.9 -0.0527 0.0281  False
-     3     14   0.0053    0.9 -0.0337 0.0443  False
-     3     21  -0.0008    0.9 -0.0444 0.0429  False
-     3     28  -0.0099    0.9 -0.0517 0.0319  False
-     7     14   0.0176 0.6997 -0.0183 0.0535  False
-     7     21   0.0115    0.9 -0.0294 0.0525  False
-     7     28   0.0024    0.9 -0.0365 0.0413  False
-    14     21  -0.0061    0.9 -0.0457 0.0335  False
-    14     28  -0.0152 0.8394 -0.0527 0.0223  False
-    21     28  -0.0091    0.9 -0.0515 0.0332  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.22854221]	No
-Stroke	Sham	14	[0.43480359]	No
-Stroke	Sham	21	[0.33001424]	No
-Stroke	Sham	28	[0.02414372]	Yes
-Stroke	Sham	7	[1.72474068e-09]	Yes
-Stroke	Sham	0	[0.44754138]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_3_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_dilated_3
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0086
+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 180799.052 0.000 1.000 -354359.631 354359.631
+merged_timepoint 0.001      0.001 2.435 0.015       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   0.0225 0.8616  -0.034 0.0789  False
+     0      7  -0.0297 0.7058 -0.0892 0.0298  False
+     0     14    0.026 0.7989 -0.0327 0.0847  False
+     0     21   0.0411 0.3379 -0.0176 0.0998  False
+     0     28   0.0415 0.3699 -0.0195 0.1024  False
+     3      7  -0.0521 0.0733  -0.107 0.0028  False
+     3     14   0.0035    1.0 -0.0505 0.0575  False
+     3     21   0.0186 0.9197 -0.0354 0.0726  False
+     3     28    0.019 0.9269 -0.0374 0.0754  False
+     7     14   0.0557 0.0619 -0.0016 0.1129  False
+     7     21   0.0708 0.0062  0.0135  0.128   True
+     7     28   0.0711 0.0091  0.0116 0.1307   True
+    14     21   0.0151 0.9722 -0.0413 0.0715  False
+    14     28   0.0155  0.974 -0.0432 0.0742  False
+    21     28   0.0004    1.0 -0.0583 0.0591  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3    0.045 0.6522 -0.0405 0.1304  False
+     0      7   0.0312 0.8637 -0.0477 0.1101  False
+     0     14   0.0421 0.5982 -0.0337 0.1178  False
+     0     21   0.0398 0.7709 -0.0469 0.1265  False
+     0     28   0.0282 0.9208 -0.0541 0.1104  False
+     3      7  -0.0138 0.9974 -0.1005 0.0729  False
+     3     14  -0.0029    1.0 -0.0868 0.0809  False
+     3     21  -0.0052    1.0  -0.099 0.0886  False
+     3     28  -0.0168 0.9944 -0.1065 0.0729  False
+     7     14   0.0109 0.9985 -0.0663  0.088  False
+     7     21   0.0086 0.9998 -0.0793 0.0965  False
+     7     28   -0.003    1.0 -0.0865 0.0806  False
+    14     21  -0.0023    1.0 -0.0874 0.0828  False
+    14     28  -0.0139 0.9962 -0.0944 0.0667  False
+    21     28  -0.0116 0.9991 -0.1025 0.0793  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.76150079]	No
+Stroke	Sham	14	[0.94215236]	No
+Stroke	Sham	21	[0.67961691]	No
+Stroke	Sham	28	[0.110847]	No
+Stroke	Sham	7	[0.00890305]	Yes
+Stroke	Sham	0	[0.41128626]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_4_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_dilated_4
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0100
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 73917.873 0.000 1.000 -144876.368 144876.368
-merged_timepoint 0.001     0.000 5.955 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   0.0176 0.4416 -0.0097   0.045  False
-     0      7  -0.0313 0.0243 -0.0602 -0.0025   True
-     0     14   0.0293  0.039  0.0009  0.0578   True
-     0     21   0.0496  0.001  0.0211   0.078   True
-     0     28   0.0422  0.001  0.0127  0.0718   True
-     3      7   -0.049  0.001 -0.0756 -0.0223   True
-     3     14   0.0117 0.7722 -0.0145  0.0379  False
-     3     21   0.0319 0.0068  0.0058  0.0581   True
-     3     28   0.0246 0.1065 -0.0028  0.0519  False
-     7     14   0.0607  0.001  0.0329  0.0884   True
-     7     21   0.0809  0.001  0.0531  0.1087   True
-     7     28   0.0735  0.001  0.0447  0.1024   True
-    14     21   0.0202 0.2807 -0.0071  0.0476  False
-    14     28   0.0129 0.7621 -0.0156  0.0413  False
-    21     28  -0.0074    0.9 -0.0358  0.0211  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0396 0.0512 -0.0001 0.0794  False
-     0      7   0.0273 0.2743 -0.0094 0.0641  False
-     0     14    0.045 0.0039  0.0097 0.0802   True
-     0     21   0.0389 0.0665 -0.0015 0.0792  False
-     0     28   0.0298 0.2294 -0.0085  0.068  False
-     3      7  -0.0123    0.9 -0.0527 0.0281  False
-     3     14   0.0053    0.9 -0.0337 0.0443  False
-     3     21  -0.0008    0.9 -0.0444 0.0429  False
-     3     28  -0.0099    0.9 -0.0517 0.0319  False
-     7     14   0.0176 0.6997 -0.0183 0.0535  False
-     7     21   0.0115    0.9 -0.0294 0.0525  False
-     7     28   0.0024    0.9 -0.0365 0.0413  False
-    14     21  -0.0061    0.9 -0.0457 0.0335  False
-    14     28  -0.0152 0.8394 -0.0527 0.0223  False
-    21     28  -0.0091    0.9 -0.0515 0.0332  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.22854221]	No
-Stroke	Sham	14	[0.43480359]	No
-Stroke	Sham	21	[0.33001424]	No
-Stroke	Sham	28	[0.02414372]	Yes
-Stroke	Sham	7	[1.72474068e-09]	Yes
-Stroke	Sham	0	[0.44754138]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_4_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_dilated_4
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0081
+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 175550.129 0.000 1.000 -344071.930 344071.930
+merged_timepoint 0.001      0.000 2.276 0.023       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   0.0216 0.8662 -0.0332 0.0764  False
+     0      7  -0.0277 0.7387 -0.0855 0.0301  False
+     0     14   0.0245 0.8177 -0.0325 0.0815  False
+     0     21   0.0363  0.447 -0.0207 0.0933  False
+     0     28   0.0358 0.5065 -0.0234 0.0949  False
+     3      7  -0.0493 0.0873 -0.1026  0.004  False
+     3     14   0.0029    1.0 -0.0495 0.0554  False
+     3     21   0.0147  0.966 -0.0377 0.0671  False
+     3     28   0.0142 0.9759 -0.0406  0.069  False
+     7     14   0.0522 0.0788 -0.0033 0.1078  False
+     7     21    0.064 0.0137  0.0084 0.1196   True
+     7     28   0.0635  0.022  0.0057 0.1213   True
+    14     21   0.0118 0.9895  -0.043 0.0666  False
+    14     28   0.0113 0.9929 -0.0457 0.0683  False
+    21     28  -0.0005    1.0 -0.0575 0.0565  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0492 0.5264 -0.0338 0.1322  False
+     0      7   0.0346 0.7833 -0.0421 0.1113  False
+     0     14   0.0414 0.5831 -0.0322  0.115  False
+     0     21   0.0456 0.6251 -0.0387 0.1298  False
+     0     28   0.0301 0.8856 -0.0498   0.11  False
+     3      7  -0.0146 0.9961 -0.0988 0.0696  False
+     3     14  -0.0078 0.9998 -0.0892 0.0737  False
+     3     21  -0.0037    1.0 -0.0948 0.0875  False
+     3     28  -0.0191 0.9884 -0.1063 0.0681  False
+     7     14   0.0069 0.9998 -0.0681 0.0818  False
+     7     21    0.011 0.9991 -0.0745 0.0964  False
+     7     28  -0.0045    1.0 -0.0856 0.0767  False
+    14     21   0.0041    1.0 -0.0786 0.0868  False
+    14     28  -0.0113 0.9983 -0.0896 0.0669  False
+    21     28  -0.0154 0.9959 -0.1038 0.0729  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.71253822]	No
+Stroke	Sham	14	[0.96636213]	No
+Stroke	Sham	21	[0.81385935]	No
+Stroke	Sham	28	[0.16070625]	No
+Stroke	Sham	7	[0.01010442]	Yes
+Stroke	Sham	0	[0.28743553]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_cut_0_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_dilated_cut_0
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0140
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 87476.795 0.000 1.000 -171451.368 171451.368
-merged_timepoint 0.002     0.000 7.622 0.000       0.002      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  -0.0042    0.9 -0.0369  0.0286  False
-     0      7  -0.0452 0.0027 -0.0798 -0.0106   True
-     0     14   0.0283 0.1694 -0.0058  0.0624  False
-     0     21   0.0632  0.001  0.0291  0.0973   True
-     0     28   0.0512  0.001  0.0158  0.0866   True
-     3      7   -0.041 0.0034 -0.0729 -0.0091   True
-     3     14   0.0324 0.0378  0.0011  0.0638   True
-     3     21   0.0673  0.001   0.036  0.0987   True
-     3     28   0.0554  0.001  0.0226  0.0882   True
-     7     14   0.0734  0.001  0.0402  0.1067   True
-     7     21   0.1083  0.001  0.0751  0.1416   True
-     7     28   0.0964  0.001  0.0618   0.131   True
-    14     21   0.0349  0.029  0.0021  0.0677   True
-    14     28    0.023 0.3901 -0.0111  0.0571  False
-    21     28  -0.0119    0.9  -0.046  0.0222  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0191 0.8323 -0.0275 0.0657  False
-     0      7   0.0201 0.7377 -0.0229 0.0631  False
-     0     14   0.0534 0.0032  0.0121 0.0947   True
-     0     21   0.0377  0.203 -0.0095  0.085  False
-     0     28   0.0327 0.2976 -0.0122 0.0775  False
-     3      7    0.001    0.9 -0.0462 0.0483  False
-     3     14   0.0343 0.2666 -0.0114   0.08  False
-     3     21   0.0186    0.9 -0.0325 0.0698  False
-     3     28   0.0136    0.9 -0.0353 0.0625  False
-     7     14   0.0333 0.2124 -0.0088 0.0753  False
-     7     21   0.0176    0.9 -0.0303 0.0656  False
-     7     28   0.0126    0.9  -0.033 0.0581  False
-    14     21  -0.0156    0.9  -0.062 0.0308  False
-    14     28  -0.0207 0.7317 -0.0646 0.0232  False
-    21     28  -0.0051    0.9 -0.0546 0.0445  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.10866128]	No
-Stroke	Sham	14	[0.07702347]	No
-Stroke	Sham	21	[0.20595589]	No
-Stroke	Sham	28	[0.09363094]	No
-Stroke	Sham	7	[1.22920063e-09]	Yes
-Stroke	Sham	0	[0.99408357]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_cut_0_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_dilated_cut_0
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   361      Method:              REML    
+No. Groups:         2        Scale:               0.0194  
+Min. group size:    156      Log-Likelihood:      189.1498
+Max. group size:    205      Converged:           Yes     
+Mean group size:    180.5                                 
+----------------------------------------------------------
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        1.182    0.018 64.750 0.000  1.147  1.218
+merged_timepoint 0.004    0.001  4.906 0.000  0.002  0.005
+Group Var        0.000    0.005                           
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0712 0.1926 -0.1598 0.0173  False
+     0      7  -0.0555 0.5269 -0.1489 0.0379  False
+     0     14   0.0342 0.8929 -0.0579 0.1264  False
+     0     21   0.0801 0.1287 -0.0121 0.1722  False
+     0     28   0.0721  0.256 -0.0235 0.1678  False
+     3      7   0.0157 0.9951 -0.0704 0.1019  False
+     3     14   0.1055 0.0057  0.0207 0.1902   True
+     3     21   0.1513    0.0  0.0666 0.2361   True
+     3     28   0.1434 0.0001  0.0549 0.2319   True
+     7     14   0.0898 0.0505 -0.0001 0.1796  False
+     7     21   0.1356 0.0003  0.0457 0.2255   True
+     7     28   0.1277 0.0016  0.0342 0.2211   True
+    14     21   0.0458  0.671 -0.0427 0.1344  False
+    14     28   0.0379 0.8443 -0.0542   0.13  False
+    21     28  -0.0079 0.9999 -0.1001 0.0842  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   -0.002    1.0 -0.1233 0.1193  False
+     0      7    0.018 0.9973 -0.0941   0.13  False
+     0     14    0.075 0.3395 -0.0325 0.1826  False
+     0     21   0.0461 0.8878 -0.0769 0.1692  False
+     0     28   0.0372  0.941 -0.0796  0.154  False
+     3      7     0.02 0.9971 -0.1031  0.143  False
+     3     14    0.077 0.4256  -0.042 0.1961  False
+     3     21   0.0481 0.9024 -0.0851 0.1814  False
+     3     28   0.0392 0.9488 -0.0882 0.1666  False
+     7     14   0.0571 0.6624 -0.0525 0.1666  False
+     7     21   0.0282 0.9867 -0.0966  0.153  False
+     7     28   0.0192 0.9971 -0.0994 0.1378  False
+    14     21  -0.0289 0.9828 -0.1497 0.0919  False
+    14     28  -0.0378 0.9312 -0.1522 0.0766  False
+    21     28  -0.0089    1.0  -0.138 0.1201  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.04099001]	Yes
+Stroke	Sham	14	[0.21577427]	No
+Stroke	Sham	21	[0.59172602]	No
+Stroke	Sham	28	[0.366086]	No
+Stroke	Sham	7	[0.00703377]	Yes
+Stroke	Sham	0	[0.8027824]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_cut_1_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_dilated_cut_1
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0140
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 87476.795 0.000 1.000 -171451.368 171451.368
-merged_timepoint 0.002     0.000 7.622 0.000       0.002      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  -0.0042    0.9 -0.0369  0.0286  False
-     0      7  -0.0452 0.0027 -0.0798 -0.0106   True
-     0     14   0.0283 0.1694 -0.0058  0.0624  False
-     0     21   0.0632  0.001  0.0291  0.0973   True
-     0     28   0.0512  0.001  0.0158  0.0866   True
-     3      7   -0.041 0.0034 -0.0729 -0.0091   True
-     3     14   0.0324 0.0378  0.0011  0.0638   True
-     3     21   0.0673  0.001   0.036  0.0987   True
-     3     28   0.0554  0.001  0.0226  0.0882   True
-     7     14   0.0734  0.001  0.0402  0.1067   True
-     7     21   0.1083  0.001  0.0751  0.1416   True
-     7     28   0.0964  0.001  0.0618   0.131   True
-    14     21   0.0349  0.029  0.0021  0.0677   True
-    14     28    0.023 0.3901 -0.0111  0.0571  False
-    21     28  -0.0119    0.9  -0.046  0.0222  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0191 0.8323 -0.0275 0.0657  False
-     0      7   0.0201 0.7377 -0.0229 0.0631  False
-     0     14   0.0534 0.0032  0.0121 0.0947   True
-     0     21   0.0377  0.203 -0.0095  0.085  False
-     0     28   0.0327 0.2976 -0.0122 0.0775  False
-     3      7    0.001    0.9 -0.0462 0.0483  False
-     3     14   0.0343 0.2666 -0.0114   0.08  False
-     3     21   0.0186    0.9 -0.0325 0.0698  False
-     3     28   0.0136    0.9 -0.0353 0.0625  False
-     7     14   0.0333 0.2124 -0.0088 0.0753  False
-     7     21   0.0176    0.9 -0.0303 0.0656  False
-     7     28   0.0126    0.9  -0.033 0.0581  False
-    14     21  -0.0156    0.9  -0.062 0.0308  False
-    14     28  -0.0207 0.7317 -0.0646 0.0232  False
-    21     28  -0.0051    0.9 -0.0546 0.0445  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.10866128]	No
-Stroke	Sham	14	[0.07702347]	No
-Stroke	Sham	21	[0.20595589]	No
-Stroke	Sham	28	[0.09363094]	No
-Stroke	Sham	7	[1.22920063e-09]	Yes
-Stroke	Sham	0	[0.99408357]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_cut_1_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_dilated_cut_1
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0156
+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 243896.525 0.000 1.000 -478028.405 478028.405
+merged_timepoint 0.003      0.001 4.054 0.000       0.001      0.004
+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  -0.0122 0.9978 -0.0917 0.0672  False
+     0      7  -0.0485 0.5576 -0.1323 0.0354  False
+     0     14   0.0342 0.8407 -0.0485 0.1169  False
+     0     21   0.0781 0.0764 -0.0046 0.1608  False
+     0     28   0.0621 0.3011 -0.0237 0.1479  False
+     3      7  -0.0362 0.7571 -0.1136 0.0411  False
+     3     14   0.0465 0.4958 -0.0296 0.1225  False
+     3     21   0.0903 0.0099  0.0142 0.1664   True
+     3     28   0.0743 0.0816 -0.0052 0.1538  False
+     7     14   0.0827 0.0408  0.0021 0.1633   True
+     7     21   0.1265 0.0002  0.0459 0.2072   True
+     7     28   0.1105 0.0027  0.0267 0.1944   True
+    14     21   0.0438 0.6074 -0.0356 0.1233  False
+    14     28   0.0278 0.9272 -0.0548 0.1105  False
+    21     28   -0.016 0.9936 -0.0987 0.0667  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0171 0.9978 -0.0938  0.128  False
+     0      7   0.0167 0.9971 -0.0857 0.1191  False
+     0     14   0.0601 0.4914 -0.0382 0.1584  False
+     0     21   0.0384 0.9224 -0.0742 0.1509  False
+     0     28   0.0414  0.873 -0.0654 0.1481  False
+     3      7  -0.0004    1.0 -0.1129 0.1121  False
+     3     14    0.043 0.8631 -0.0658 0.1518  False
+     3     21   0.0213  0.996 -0.1005 0.1431  False
+     3     28   0.0243 0.9908 -0.0922 0.1407  False
+     7     14   0.0434 0.8102 -0.0567 0.1436  False
+     7     21   0.0217  0.994 -0.0924 0.1358  False
+     7     28   0.0247 0.9862 -0.0837 0.1331  False
+    14     21  -0.0218 0.9929 -0.1322 0.0887  False
+    14     28  -0.0188 0.9954 -0.1233 0.0858  False
+    21     28    0.003    1.0  -0.115  0.121  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.31430403]	No
+Stroke	Sham	14	[0.35080466]	No
+Stroke	Sham	21	[0.4732268]	No
+Stroke	Sham	28	[0.58372046]	No
+Stroke	Sham	7	[0.00614384]	Yes
+Stroke	Sham	0	[0.81115249]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_cut_2_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_dilated_cut_2
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0140
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 87476.795 0.000 1.000 -171451.368 171451.368
-merged_timepoint 0.002     0.000 7.622 0.000       0.002      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  -0.0042    0.9 -0.0369  0.0286  False
-     0      7  -0.0452 0.0027 -0.0798 -0.0106   True
-     0     14   0.0283 0.1694 -0.0058  0.0624  False
-     0     21   0.0632  0.001  0.0291  0.0973   True
-     0     28   0.0512  0.001  0.0158  0.0866   True
-     3      7   -0.041 0.0034 -0.0729 -0.0091   True
-     3     14   0.0324 0.0378  0.0011  0.0638   True
-     3     21   0.0673  0.001   0.036  0.0987   True
-     3     28   0.0554  0.001  0.0226  0.0882   True
-     7     14   0.0734  0.001  0.0402  0.1067   True
-     7     21   0.1083  0.001  0.0751  0.1416   True
-     7     28   0.0964  0.001  0.0618   0.131   True
-    14     21   0.0349  0.029  0.0021  0.0677   True
-    14     28    0.023 0.3901 -0.0111  0.0571  False
-    21     28  -0.0119    0.9  -0.046  0.0222  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0191 0.8323 -0.0275 0.0657  False
-     0      7   0.0201 0.7377 -0.0229 0.0631  False
-     0     14   0.0534 0.0032  0.0121 0.0947   True
-     0     21   0.0377  0.203 -0.0095  0.085  False
-     0     28   0.0327 0.2976 -0.0122 0.0775  False
-     3      7    0.001    0.9 -0.0462 0.0483  False
-     3     14   0.0343 0.2666 -0.0114   0.08  False
-     3     21   0.0186    0.9 -0.0325 0.0698  False
-     3     28   0.0136    0.9 -0.0353 0.0625  False
-     7     14   0.0333 0.2124 -0.0088 0.0753  False
-     7     21   0.0176    0.9 -0.0303 0.0656  False
-     7     28   0.0126    0.9  -0.033 0.0581  False
-    14     21  -0.0156    0.9  -0.062 0.0308  False
-    14     28  -0.0207 0.7317 -0.0646 0.0232  False
-    21     28  -0.0051    0.9 -0.0546 0.0445  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.10866128]	No
-Stroke	Sham	14	[0.07702347]	No
-Stroke	Sham	21	[0.20595589]	No
-Stroke	Sham	28	[0.09363094]	No
-Stroke	Sham	7	[1.22920063e-09]	Yes
-Stroke	Sham	0	[0.99408357]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_cut_2_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_dilated_cut_2
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0125
+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 218852.180 0.000 1.000 -428942.391 428942.391
+merged_timepoint 0.002      0.001 3.134 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   0.0146 0.9909 -0.0554 0.0845  False
+     0      7  -0.0443 0.5148 -0.1181 0.0295  False
+     0     14   0.0283  0.873 -0.0445 0.1011  False
+     0     21   0.0617 0.1476 -0.0111 0.1345  False
+     0     28   0.0493 0.4184 -0.0262 0.1249  False
+     3      7  -0.0589 0.1318  -0.127 0.0092  False
+     3     14   0.0137 0.9916 -0.0532 0.0807  False
+     3     21   0.0471 0.3313 -0.0198 0.1141  False
+     3     28   0.0347 0.7094 -0.0352 0.1047  False
+     7     14   0.0726 0.0416  0.0016 0.1436   True
+     7     21   0.1061 0.0004  0.0351  0.177   True
+     7     28   0.0936 0.0045  0.0198 0.1674   True
+    14     21   0.0334 0.7418 -0.0365 0.1034  False
+    14     28    0.021 0.9616 -0.0518 0.0938  False
+    21     28  -0.0124 0.9964 -0.0852 0.0604  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0261 0.9761 -0.0753 0.1274  False
+     0      7   0.0189 0.9921 -0.0747 0.1125  False
+     0     14   0.0512 0.5697 -0.0386 0.1411  False
+     0     21    0.035 0.9224 -0.0678 0.1379  False
+     0     28   0.0343 0.9125 -0.0633 0.1318  False
+     3      7  -0.0072    1.0   -0.11 0.0956  False
+     3     14   0.0251  0.978 -0.0743 0.1246  False
+     3     21    0.009 0.9999 -0.1023 0.1202  False
+     3     28   0.0082 0.9999 -0.0982 0.1146  False
+     7     14   0.0324 0.9104 -0.0592 0.1239  False
+     7     21   0.0162 0.9977 -0.0881 0.1205  False
+     7     28   0.0154 0.9977 -0.0837 0.1145  False
+    14     21  -0.0162 0.9973 -0.1171 0.0848  False
+    14     28  -0.0169 0.9957 -0.1125 0.0786  False
+    21     28  -0.0008    1.0 -0.1086 0.1071  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.73097578]	No
+Stroke	Sham	14	[0.45192858]	No
+Stroke	Sham	21	[0.54191969]	No
+Stroke	Sham	28	[0.48503716]	No
+Stroke	Sham	7	[0.00527242]	Yes
+Stroke	Sham	0	[0.98800637]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_cut_3_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_dilated_cut_3
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0140
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 87476.795 0.000 1.000 -171451.368 171451.368
-merged_timepoint 0.002     0.000 7.622 0.000       0.002      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  -0.0042    0.9 -0.0369  0.0286  False
-     0      7  -0.0452 0.0027 -0.0798 -0.0106   True
-     0     14   0.0283 0.1694 -0.0058  0.0624  False
-     0     21   0.0632  0.001  0.0291  0.0973   True
-     0     28   0.0512  0.001  0.0158  0.0866   True
-     3      7   -0.041 0.0034 -0.0729 -0.0091   True
-     3     14   0.0324 0.0378  0.0011  0.0638   True
-     3     21   0.0673  0.001   0.036  0.0987   True
-     3     28   0.0554  0.001  0.0226  0.0882   True
-     7     14   0.0734  0.001  0.0402  0.1067   True
-     7     21   0.1083  0.001  0.0751  0.1416   True
-     7     28   0.0964  0.001  0.0618   0.131   True
-    14     21   0.0349  0.029  0.0021  0.0677   True
-    14     28    0.023 0.3901 -0.0111  0.0571  False
-    21     28  -0.0119    0.9  -0.046  0.0222  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0191 0.8323 -0.0275 0.0657  False
-     0      7   0.0201 0.7377 -0.0229 0.0631  False
-     0     14   0.0534 0.0032  0.0121 0.0947   True
-     0     21   0.0377  0.203 -0.0095  0.085  False
-     0     28   0.0327 0.2976 -0.0122 0.0775  False
-     3      7    0.001    0.9 -0.0462 0.0483  False
-     3     14   0.0343 0.2666 -0.0114   0.08  False
-     3     21   0.0186    0.9 -0.0325 0.0698  False
-     3     28   0.0136    0.9 -0.0353 0.0625  False
-     7     14   0.0333 0.2124 -0.0088 0.0753  False
-     7     21   0.0176    0.9 -0.0303 0.0656  False
-     7     28   0.0126    0.9  -0.033 0.0581  False
-    14     21  -0.0156    0.9  -0.062 0.0308  False
-    14     28  -0.0207 0.7317 -0.0646 0.0232  False
-    21     28  -0.0051    0.9 -0.0546 0.0445  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.10866128]	No
-Stroke	Sham	14	[0.07702347]	No
-Stroke	Sham	21	[0.20595589]	No
-Stroke	Sham	28	[0.09363094]	No
-Stroke	Sham	7	[1.22920063e-09]	Yes
-Stroke	Sham	0	[0.99408357]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_cut_3_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_dilated_cut_3
+               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 201778.792 0.000 1.000 -395479.165 395479.165
+merged_timepoint 0.001      0.001 2.547 0.011       0.000      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   0.0228 0.9049 -0.0404   0.086  False
+     0      7  -0.0409 0.4917 -0.1075  0.0258  False
+     0     14   0.0242 0.8962 -0.0415    0.09  False
+     0     21   0.0516 0.2162 -0.0141  0.1174  False
+     0     28   0.0393 0.5627  -0.029  0.1075  False
+     3      7  -0.0636 0.0378 -0.1251 -0.0021   True
+     3     14   0.0015    1.0  -0.059   0.062  False
+     3     21   0.0288 0.7436 -0.0316  0.0893  False
+     3     28   0.0165 0.9751 -0.0467  0.0797  False
+     7     14   0.0651 0.0444   0.001  0.1292   True
+     7     21   0.0925 0.0007  0.0283  0.1566   True
+     7     28   0.0801 0.0086  0.0135  0.1468   True
+    14     21   0.0274 0.8131 -0.0358  0.0906  False
+    14     28    0.015 0.9862 -0.0507  0.0808  False
+    21     28  -0.0124 0.9944 -0.0781  0.0534  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0251 0.9735   -0.07 0.1201  False
+     0      7   0.0209 0.9832 -0.0669 0.1086  False
+     0     14   0.0418 0.7082 -0.0425  0.126  False
+     0     21   0.0336 0.9154 -0.0628   0.13  False
+     0     28   0.0265   0.96 -0.0649  0.118  False
+     3      7  -0.0042    1.0 -0.1006 0.0922  False
+     3     14   0.0167 0.9954 -0.0765 0.1099  False
+     3     21   0.0085 0.9999 -0.0958 0.1129  False
+     3     28   0.0015    1.0 -0.0983 0.1013  False
+     7     14   0.0209 0.9814 -0.0649 0.1067  False
+     7     21   0.0127  0.999 -0.0851 0.1105  False
+     7     28   0.0057    1.0 -0.0873 0.0986  False
+    14     21  -0.0082 0.9999 -0.1028 0.0865  False
+    14     28  -0.0152 0.9964 -0.1048 0.0744  False
+    21     28  -0.0071    1.0 -0.1082 0.0941  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.95790412]	No
+Stroke	Sham	14	[0.61628702]	No
+Stroke	Sham	21	[0.60080212]	No
+Stroke	Sham	28	[0.37427385]	No
+Stroke	Sham	7	[0.00485843]	Yes
+Stroke	Sham	0	[0.84398151]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_cut_4_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_dilated_cut_4
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0140
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 87476.795 0.000 1.000 -171451.368 171451.368
-merged_timepoint 0.002     0.000 7.622 0.000       0.002      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  -0.0042    0.9 -0.0369  0.0286  False
-     0      7  -0.0452 0.0027 -0.0798 -0.0106   True
-     0     14   0.0283 0.1694 -0.0058  0.0624  False
-     0     21   0.0632  0.001  0.0291  0.0973   True
-     0     28   0.0512  0.001  0.0158  0.0866   True
-     3      7   -0.041 0.0034 -0.0729 -0.0091   True
-     3     14   0.0324 0.0378  0.0011  0.0638   True
-     3     21   0.0673  0.001   0.036  0.0987   True
-     3     28   0.0554  0.001  0.0226  0.0882   True
-     7     14   0.0734  0.001  0.0402  0.1067   True
-     7     21   0.1083  0.001  0.0751  0.1416   True
-     7     28   0.0964  0.001  0.0618   0.131   True
-    14     21   0.0349  0.029  0.0021  0.0677   True
-    14     28    0.023 0.3901 -0.0111  0.0571  False
-    21     28  -0.0119    0.9  -0.046  0.0222  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0191 0.8323 -0.0275 0.0657  False
-     0      7   0.0201 0.7377 -0.0229 0.0631  False
-     0     14   0.0534 0.0032  0.0121 0.0947   True
-     0     21   0.0377  0.203 -0.0095  0.085  False
-     0     28   0.0327 0.2976 -0.0122 0.0775  False
-     3      7    0.001    0.9 -0.0462 0.0483  False
-     3     14   0.0343 0.2666 -0.0114   0.08  False
-     3     21   0.0186    0.9 -0.0325 0.0698  False
-     3     28   0.0136    0.9 -0.0353 0.0625  False
-     7     14   0.0333 0.2124 -0.0088 0.0753  False
-     7     21   0.0176    0.9 -0.0303 0.0656  False
-     7     28   0.0126    0.9  -0.033 0.0581  False
-    14     21  -0.0156    0.9  -0.062 0.0308  False
-    14     28  -0.0207 0.7317 -0.0646 0.0232  False
-    21     28  -0.0051    0.9 -0.0546 0.0445  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.10866128]	No
-Stroke	Sham	14	[0.07702347]	No
-Stroke	Sham	21	[0.20595589]	No
-Stroke	Sham	28	[0.09363094]	No
-Stroke	Sham	7	[1.22920063e-09]	Yes
-Stroke	Sham	0	[0.99408357]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_cut_4_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_dilated_cut_4
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0095
+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 190655.997 0.000 1.000 -373678.888 373678.888
+merged_timepoint 0.001      0.001 2.171 0.030       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   0.0252 0.8232 -0.0339  0.0842  False
+     0      7  -0.0368 0.5342 -0.0991  0.0255  False
+     0     14   0.0203 0.9333 -0.0412  0.0817  False
+     0     21   0.0443  0.306 -0.0172  0.1057  False
+     0     28   0.0333 0.6635 -0.0305  0.0971  False
+     3      7   -0.062 0.0263 -0.1194 -0.0045   True
+     3     14  -0.0049 0.9999 -0.0615  0.0516  False
+     3     21   0.0191 0.9265 -0.0375  0.0756  False
+     3     28   0.0081 0.9987 -0.0509  0.0672  False
+     7     14    0.057 0.0723 -0.0029   0.117  False
+     7     21   0.0811 0.0019  0.0211   0.141   True
+     7     28   0.0701 0.0176  0.0078  0.1324   True
+    14     21    0.024 0.8506  -0.035  0.0831  False
+    14     28    0.013 0.9902 -0.0484  0.0745  False
+    21     28   -0.011 0.9956 -0.0724  0.0505  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0293 0.9376 -0.0614 0.1199  False
+     0      7   0.0262 0.9455 -0.0576 0.1099  False
+     0     14   0.0387 0.7323 -0.0416 0.1191  False
+     0     21   0.0355 0.8743 -0.0564 0.1275  False
+     0     28    0.024 0.9679 -0.0632 0.1113  False
+     3      7  -0.0031    1.0 -0.0951 0.0889  False
+     3     14   0.0095 0.9996 -0.0795 0.0984  False
+     3     21   0.0063    1.0 -0.0933 0.1058  False
+     3     28  -0.0052    1.0 -0.1004   0.09  False
+     7     14   0.0126 0.9978 -0.0693 0.0944  False
+     7     21   0.0094 0.9997 -0.0839 0.1026  False
+     7     28  -0.0021    1.0 -0.0907 0.0865  False
+    14     21  -0.0032    1.0 -0.0935 0.0871  False
+    14     28  -0.0147 0.9962 -0.1001 0.0708  False
+    21     28  -0.0115 0.9994 -0.1079 0.0849  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.87305439]	No
+Stroke	Sham	14	[0.69558331]	No
+Stroke	Sham	21	[0.66759955]	No
+Stroke	Sham	28	[0.28435608]	No
+Stroke	Sham	7	[0.00507773]	Yes
+Stroke	Sham	0	[0.64753185]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_0_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOs-MOs_0
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0164
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 94593.791 0.000 1.000 -185400.424 185400.424
-merged_timepoint 0.002     0.000 5.539 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  -0.0353   0.11 -0.0748 0.0042  False
-     0      7  -0.0183 0.7836   -0.06 0.0233  False
-     0     14   0.0328  0.204 -0.0083 0.0739  False
-     0     21   0.0338 0.1763 -0.0073 0.0749  False
-     0     28   0.0244 0.5668 -0.0183  0.067  False
-     3      7    0.017 0.7797 -0.0214 0.0554  False
-     3     14   0.0681  0.001  0.0303 0.1059   True
-     3     21   0.0691  0.001  0.0313 0.1069   True
-     3     28   0.0597  0.001  0.0202 0.0992   True
-     7     14   0.0511 0.0039   0.011 0.0912   True
-     7     21   0.0521  0.003   0.012 0.0922   True
-     7     28   0.0427 0.0409   0.001 0.0844   True
-    14     21    0.001    0.9 -0.0385 0.0405  False
-    14     28  -0.0084    0.9 -0.0495 0.0327  False
-    21     28  -0.0094    0.9 -0.0505 0.0317  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0531   0.01  0.0082  0.098   True
-     0      7   0.0302  0.299 -0.0113 0.0717  False
-     0     14   0.0453  0.015  0.0055 0.0851   True
-     0     21   0.0724  0.001  0.0269  0.118   True
-     0     28   0.0342 0.2124  -0.009 0.0774  False
-     3      7  -0.0229 0.6805 -0.0684 0.0227  False
-     3     14  -0.0077    0.9 -0.0518 0.0363  False
-     3     21   0.0194 0.8599 -0.0299 0.0687  False
-     3     28  -0.0189 0.8477  -0.066 0.0283  False
-     7     14   0.0151 0.8921 -0.0254 0.0557  False
-     7     21   0.0423 0.0951 -0.0039 0.0885  False
-     7     28    0.004    0.9 -0.0399 0.0479  False
-    14     21   0.0271 0.5091 -0.0176 0.0718  False
-    14     28  -0.0112    0.9 -0.0535 0.0312  False
-    21     28  -0.0383 0.1998 -0.0861 0.0095  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[1.47006851e-11]	Yes
-Stroke	Sham	14	[0.26327967]	No
-Stroke	Sham	21	[0.01605402]	Yes
-Stroke	Sham	28	[0.11218774]	No
-Stroke	Sham	7	[6.16982408e-07]	Yes
-Stroke	Sham	0	[0.45465261]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_0_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOs-MOs_0
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   361      Method:              REML    
+No. Groups:         2        Scale:               0.0272  
+Min. group size:    156      Log-Likelihood:      128.3486
+Max. group size:    205      Converged:           Yes     
+Mean group size:    180.5                                 
+----------------------------------------------------------
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        1.084    0.030 36.625 0.000  1.026  1.142
+merged_timepoint 0.003    0.001  3.226 0.001  0.001  0.005
+Group Var        0.001    0.013                           
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   -0.081 0.3426 -0.1971 0.0352  False
+     0      7  -0.0052    1.0 -0.1278 0.1173  False
+     0     14   0.0489 0.8529 -0.0719 0.1698  False
+     0     21   0.0541 0.7913 -0.0668  0.175  False
+     0     28   0.0341 0.9701 -0.0913 0.1596  False
+     3      7   0.0757 0.3881 -0.0373 0.1887  False
+     3     14   0.1299 0.0118  0.0187 0.2411   True
+     3     21   0.1351 0.0076  0.0239 0.2462   True
+     3     28   0.1151 0.0536  -0.001 0.2312  False
+     7     14   0.0542 0.7724 -0.0637  0.172  False
+     7     21   0.0593 0.6972 -0.0585 0.1772  False
+     7     28   0.0394 0.9398 -0.0832 0.1619  False
+    14     21   0.0052    1.0  -0.111 0.1213  False
+    14     28  -0.0148 0.9993 -0.1357 0.1061  False
+    21     28    -0.02  0.997 -0.1408 0.1009  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0452 0.9148 -0.0843 0.1747  False
+     0      7   0.0421 0.9115 -0.0774 0.1617  False
+     0     14   0.0616 0.6335 -0.0532 0.1764  False
+     0     21   0.0987 0.2588 -0.0327 0.2301  False
+     0     28     0.05 0.8553 -0.0746 0.1747  False
+     3      7  -0.0031    1.0 -0.1344 0.1283  False
+     3     14   0.0164  0.999 -0.1107 0.1434  False
+     3     21   0.0535 0.8864 -0.0887 0.1957  False
+     3     28   0.0048    1.0 -0.1311 0.1408  False
+     7     14   0.0194 0.9968 -0.0975 0.1364  False
+     7     21   0.0565 0.8241 -0.0767 0.1898  False
+     7     28   0.0079    1.0 -0.1187 0.1345  False
+    14     21   0.0371 0.9614 -0.0919 0.1661  False
+    14     28  -0.0115 0.9998 -0.1336 0.1106  False
+    21     28  -0.0486  0.911 -0.1864 0.0892  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00049223]	Yes
+Stroke	Sham	14	[0.65651701]	No
+Stroke	Sham	21	[0.27601683]	No
+Stroke	Sham	28	[0.44305664]	No
+Stroke	Sham	7	[0.06033843]	No
+Stroke	Sham	0	[0.67578668]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_1_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOs-MOs_1
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0164
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 94593.791 0.000 1.000 -185400.424 185400.424
-merged_timepoint 0.002     0.000 5.539 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  -0.0353   0.11 -0.0748 0.0042  False
-     0      7  -0.0183 0.7836   -0.06 0.0233  False
-     0     14   0.0328  0.204 -0.0083 0.0739  False
-     0     21   0.0338 0.1763 -0.0073 0.0749  False
-     0     28   0.0244 0.5668 -0.0183  0.067  False
-     3      7    0.017 0.7797 -0.0214 0.0554  False
-     3     14   0.0681  0.001  0.0303 0.1059   True
-     3     21   0.0691  0.001  0.0313 0.1069   True
-     3     28   0.0597  0.001  0.0202 0.0992   True
-     7     14   0.0511 0.0039   0.011 0.0912   True
-     7     21   0.0521  0.003   0.012 0.0922   True
-     7     28   0.0427 0.0409   0.001 0.0844   True
-    14     21    0.001    0.9 -0.0385 0.0405  False
-    14     28  -0.0084    0.9 -0.0495 0.0327  False
-    21     28  -0.0094    0.9 -0.0505 0.0317  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0531   0.01  0.0082  0.098   True
-     0      7   0.0302  0.299 -0.0113 0.0717  False
-     0     14   0.0453  0.015  0.0055 0.0851   True
-     0     21   0.0724  0.001  0.0269  0.118   True
-     0     28   0.0342 0.2124  -0.009 0.0774  False
-     3      7  -0.0229 0.6805 -0.0684 0.0227  False
-     3     14  -0.0077    0.9 -0.0518 0.0363  False
-     3     21   0.0194 0.8599 -0.0299 0.0687  False
-     3     28  -0.0189 0.8477  -0.066 0.0283  False
-     7     14   0.0151 0.8921 -0.0254 0.0557  False
-     7     21   0.0423 0.0951 -0.0039 0.0885  False
-     7     28    0.004    0.9 -0.0399 0.0479  False
-    14     21   0.0271 0.5091 -0.0176 0.0718  False
-    14     28  -0.0112    0.9 -0.0535 0.0312  False
-    21     28  -0.0383 0.1998 -0.0861 0.0095  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[1.47006851e-11]	Yes
-Stroke	Sham	14	[0.26327967]	No
-Stroke	Sham	21	[0.01605402]	Yes
-Stroke	Sham	28	[0.11218774]	No
-Stroke	Sham	7	[6.16982408e-07]	Yes
-Stroke	Sham	0	[0.45465261]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_1_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOs-MOs_1
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0174
+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 257688.429 0.000 1.000 -505060.041 505060.041
+merged_timepoint 0.002      0.001 2.318 0.020       0.000      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  -0.0436 0.7711 -0.1384 0.0512  False
+     0      7  -0.0147 0.9982 -0.1147 0.0853  False
+     0     14   0.0318 0.9391 -0.0669 0.1304  False
+     0     21    0.031 0.9453 -0.0677 0.1296  False
+     0     28   0.0128 0.9992 -0.0896 0.1152  False
+     3      7   0.0289 0.9456 -0.0633 0.1211  False
+     3     14   0.0754 0.1642 -0.0153 0.1662  False
+     3     21   0.0746 0.1735 -0.0161 0.1653  False
+     3     28   0.0564 0.5248 -0.0384 0.1512  False
+     7     14   0.0465 0.7324 -0.0497 0.1427  False
+     7     21   0.0457 0.7468 -0.0505 0.1419  False
+     7     28   0.0275 0.9687 -0.0725 0.1275  False
+    14     21  -0.0008    1.0 -0.0956  0.094  False
+    14     28   -0.019 0.9937 -0.1176 0.0797  False
+    21     28  -0.0182 0.9949 -0.1168 0.0805  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0609 0.5138 -0.0407 0.1624  False
+     0      7   0.0341 0.9005 -0.0597 0.1279  False
+     0     14    0.042 0.7588 -0.0481  0.132  False
+     0     21    0.087 0.1504 -0.0161   0.19  False
+     0     28    0.038 0.8719 -0.0598 0.1357  False
+     3      7  -0.0268  0.975 -0.1299 0.0762  False
+     3     14  -0.0189  0.994 -0.1185 0.0807  False
+     3     21   0.0261 0.9844 -0.0854 0.1376  False
+     3     28  -0.0229 0.9894 -0.1296 0.0837  False
+     7     14   0.0079 0.9999 -0.0838 0.0996  False
+     7     21   0.0529 0.6891 -0.0516 0.1574  False
+     7     28   0.0039    1.0 -0.0954 0.1032  False
+    14     21    0.045 0.7933 -0.0562 0.1461  False
+    14     28   -0.004    1.0 -0.0998 0.0917  False
+    21     28   -0.049 0.7796 -0.1571 0.0591  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00128221]	Yes
+Stroke	Sham	14	[0.75363289]	No
+Stroke	Sham	21	[0.19029083]	No
+Stroke	Sham	28	[0.25397517]	No
+Stroke	Sham	7	[0.06261855]	No
+Stroke	Sham	0	[0.89267327]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_2_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOs-MOs_2
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0164
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 94593.791 0.000 1.000 -185400.424 185400.424
-merged_timepoint 0.002     0.000 5.539 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  -0.0353   0.11 -0.0748 0.0042  False
-     0      7  -0.0183 0.7836   -0.06 0.0233  False
-     0     14   0.0328  0.204 -0.0083 0.0739  False
-     0     21   0.0338 0.1763 -0.0073 0.0749  False
-     0     28   0.0244 0.5668 -0.0183  0.067  False
-     3      7    0.017 0.7797 -0.0214 0.0554  False
-     3     14   0.0681  0.001  0.0303 0.1059   True
-     3     21   0.0691  0.001  0.0313 0.1069   True
-     3     28   0.0597  0.001  0.0202 0.0992   True
-     7     14   0.0511 0.0039   0.011 0.0912   True
-     7     21   0.0521  0.003   0.012 0.0922   True
-     7     28   0.0427 0.0409   0.001 0.0844   True
-    14     21    0.001    0.9 -0.0385 0.0405  False
-    14     28  -0.0084    0.9 -0.0495 0.0327  False
-    21     28  -0.0094    0.9 -0.0505 0.0317  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0531   0.01  0.0082  0.098   True
-     0      7   0.0302  0.299 -0.0113 0.0717  False
-     0     14   0.0453  0.015  0.0055 0.0851   True
-     0     21   0.0724  0.001  0.0269  0.118   True
-     0     28   0.0342 0.2124  -0.009 0.0774  False
-     3      7  -0.0229 0.6805 -0.0684 0.0227  False
-     3     14  -0.0077    0.9 -0.0518 0.0363  False
-     3     21   0.0194 0.8599 -0.0299 0.0687  False
-     3     28  -0.0189 0.8477  -0.066 0.0283  False
-     7     14   0.0151 0.8921 -0.0254 0.0557  False
-     7     21   0.0423 0.0951 -0.0039 0.0885  False
-     7     28    0.004    0.9 -0.0399 0.0479  False
-    14     21   0.0271 0.5091 -0.0176 0.0718  False
-    14     28  -0.0112    0.9 -0.0535 0.0312  False
-    21     28  -0.0383 0.1998 -0.0861 0.0095  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[1.47006851e-11]	Yes
-Stroke	Sham	14	[0.26327967]	No
-Stroke	Sham	21	[0.01605402]	Yes
-Stroke	Sham	28	[0.11218774]	No
-Stroke	Sham	7	[6.16982408e-07]	Yes
-Stroke	Sham	0	[0.45465261]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_2_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOs-MOs_2
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0145
+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 235360.280 0.000 1.000 -461297.673 461297.673
+merged_timepoint 0.001      0.001 2.075 0.038       0.000      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  -0.0251 0.9586 -0.1105 0.0603  False
+     0      7   -0.023 0.9774 -0.1131 0.0671  False
+     0     14   0.0308  0.918  -0.058 0.1197  False
+     0     21   0.0241 0.9706 -0.0648  0.113  False
+     0     28   0.0166 0.9955 -0.0757 0.1088  False
+     3      7   0.0021    1.0  -0.081 0.0851  False
+     3     14   0.0559 0.3645 -0.0258 0.1377  False
+     3     21   0.0492 0.5132 -0.0326 0.1309  False
+     3     28   0.0416 0.7251 -0.0437  0.127  False
+     7     14   0.0538 0.4759 -0.0328 0.1405  False
+     7     21   0.0471 0.6231 -0.0396 0.1338  False
+     7     28   0.0396 0.8042 -0.0505 0.1297  False
+    14     21  -0.0067 0.9999 -0.0921 0.0786  False
+    14     28  -0.0143 0.9973 -0.1031 0.0746  False
+    21     28  -0.0075 0.9999 -0.0964 0.0813  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0587 0.4823 -0.0366  0.154  False
+     0      7   0.0235 0.9718 -0.0645 0.1115  False
+     0     14   0.0401 0.7448 -0.0444 0.1245  False
+     0     21   0.0722  0.264 -0.0244 0.1689  False
+     0     28   0.0301 0.9335 -0.0616 0.1218  False
+     3      7  -0.0352 0.8997 -0.1318 0.0615  False
+     3     14  -0.0186 0.9925 -0.1121 0.0748  False
+     3     21   0.0135  0.999 -0.0911 0.1181  False
+     3     28  -0.0286 0.9622 -0.1287 0.0714  False
+     7     14   0.0166 0.9936 -0.0695 0.1026  False
+     7     21   0.0487 0.7059 -0.0493 0.1467  False
+     7     28   0.0065    1.0 -0.0866 0.0997  False
+    14     21   0.0322 0.9242 -0.0627  0.127  False
+    14     28    -0.01 0.9995 -0.0998 0.0798  False
+    21     28  -0.0422 0.8359 -0.1435 0.0592  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00244342]	Yes
+Stroke	Sham	14	[0.64225776]	No
+Stroke	Sham	21	[0.17726149]	No
+Stroke	Sham	28	[0.32639953]	No
+Stroke	Sham	7	[0.03008994]	Yes
+Stroke	Sham	0	[0.72639033]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_3_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOs-MOs_3
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0164
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 94593.791 0.000 1.000 -185400.424 185400.424
-merged_timepoint 0.002     0.000 5.539 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  -0.0353   0.11 -0.0748 0.0042  False
-     0      7  -0.0183 0.7836   -0.06 0.0233  False
-     0     14   0.0328  0.204 -0.0083 0.0739  False
-     0     21   0.0338 0.1763 -0.0073 0.0749  False
-     0     28   0.0244 0.5668 -0.0183  0.067  False
-     3      7    0.017 0.7797 -0.0214 0.0554  False
-     3     14   0.0681  0.001  0.0303 0.1059   True
-     3     21   0.0691  0.001  0.0313 0.1069   True
-     3     28   0.0597  0.001  0.0202 0.0992   True
-     7     14   0.0511 0.0039   0.011 0.0912   True
-     7     21   0.0521  0.003   0.012 0.0922   True
-     7     28   0.0427 0.0409   0.001 0.0844   True
-    14     21    0.001    0.9 -0.0385 0.0405  False
-    14     28  -0.0084    0.9 -0.0495 0.0327  False
-    21     28  -0.0094    0.9 -0.0505 0.0317  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0531   0.01  0.0082  0.098   True
-     0      7   0.0302  0.299 -0.0113 0.0717  False
-     0     14   0.0453  0.015  0.0055 0.0851   True
-     0     21   0.0724  0.001  0.0269  0.118   True
-     0     28   0.0342 0.2124  -0.009 0.0774  False
-     3      7  -0.0229 0.6805 -0.0684 0.0227  False
-     3     14  -0.0077    0.9 -0.0518 0.0363  False
-     3     21   0.0194 0.8599 -0.0299 0.0687  False
-     3     28  -0.0189 0.8477  -0.066 0.0283  False
-     7     14   0.0151 0.8921 -0.0254 0.0557  False
-     7     21   0.0423 0.0951 -0.0039 0.0885  False
-     7     28    0.004    0.9 -0.0399 0.0479  False
-    14     21   0.0271 0.5091 -0.0176 0.0718  False
-    14     28  -0.0112    0.9 -0.0535 0.0312  False
-    21     28  -0.0383 0.1998 -0.0861 0.0095  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[1.47006851e-11]	Yes
-Stroke	Sham	14	[0.26327967]	No
-Stroke	Sham	21	[0.01605402]	Yes
-Stroke	Sham	28	[0.11218774]	No
-Stroke	Sham	7	[6.16982408e-07]	Yes
-Stroke	Sham	0	[0.45465261]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_3_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOs-MOs_3
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0119
+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 212975.232 0.000 1.000 -417423.785 417423.785
+merged_timepoint 0.001      0.001 2.216 0.027       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  -0.0148 0.9928 -0.0891 0.0596  False
+     0      7  -0.0247 0.9449 -0.1031 0.0538  False
+     0     14   0.0263 0.9245 -0.0511 0.1037  False
+     0     21   0.0285 0.8971 -0.0489 0.1058  False
+     0     28    0.026 0.9381 -0.0543 0.1063  False
+     3      7  -0.0099 0.9988 -0.0823 0.0624  False
+     3     14    0.041 0.5601 -0.0301 0.1122  False
+     3     21   0.0432 0.5024  -0.028 0.1144  False
+     3     28   0.0407 0.6148 -0.0336 0.1151  False
+     7     14    0.051 0.3788 -0.0245 0.1264  False
+     7     21   0.0531 0.3312 -0.0223 0.1286  False
+     7     28   0.0506 0.4312 -0.0278 0.1291  False
+    14     21   0.0022    1.0 -0.0722 0.0765  False
+    14     28  -0.0003    1.0 -0.0777 0.0771  False
+    21     28  -0.0025    1.0 -0.0798 0.0749  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0528 0.5525 -0.0384 0.1439  False
+     0      7   0.0253 0.9537 -0.0589 0.1095  False
+     0     14   0.0411 0.6856 -0.0397 0.1219  False
+     0     21    0.056 0.5025 -0.0365 0.1485  False
+     0     28   0.0263 0.9542 -0.0615  0.114  False
+     3      7  -0.0275 0.9557   -0.12  0.065  False
+     3     14  -0.0117  0.999 -0.1011 0.0777  False
+     3     21   0.0032    1.0 -0.0969 0.1033  False
+     3     28  -0.0265 0.9673 -0.1222 0.0692  False
+     7     14   0.0158 0.9937 -0.0665 0.0981  False
+     7     21   0.0307  0.934 -0.0631 0.1245  False
+     7     28    0.001    1.0 -0.0881 0.0901  False
+    14     21   0.0149  0.997 -0.0759 0.1057  False
+    14     28  -0.0148 0.9962 -0.1007 0.0712  False
+    21     28  -0.0297 0.9497 -0.1267 0.0673  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00690785]	Yes
+Stroke	Sham	14	[0.47176737]	No
+Stroke	Sham	21	[0.35118055]	No
+Stroke	Sham	28	[0.61084008]	No
+Stroke	Sham	7	[0.0046389]	Yes
+Stroke	Sham	0	[0.65928703]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_4_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOs-MOs_4
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      1805         Method:                  REML  
-No. Groups:            2            Scale:                   0.0164
-Min. group size:       780          Log-Likelihood:          inf   
-Max. group size:       1025         Converged:               Yes   
-Mean group size:       902.5                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 94593.791 0.000 1.000 -185400.424 185400.424
-merged_timepoint 0.002     0.000 5.539 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  -0.0353   0.11 -0.0748 0.0042  False
-     0      7  -0.0183 0.7836   -0.06 0.0233  False
-     0     14   0.0328  0.204 -0.0083 0.0739  False
-     0     21   0.0338 0.1763 -0.0073 0.0749  False
-     0     28   0.0244 0.5668 -0.0183  0.067  False
-     3      7    0.017 0.7797 -0.0214 0.0554  False
-     3     14   0.0681  0.001  0.0303 0.1059   True
-     3     21   0.0691  0.001  0.0313 0.1069   True
-     3     28   0.0597  0.001  0.0202 0.0992   True
-     7     14   0.0511 0.0039   0.011 0.0912   True
-     7     21   0.0521  0.003   0.012 0.0922   True
-     7     28   0.0427 0.0409   0.001 0.0844   True
-    14     21    0.001    0.9 -0.0385 0.0405  False
-    14     28  -0.0084    0.9 -0.0495 0.0327  False
-    21     28  -0.0094    0.9 -0.0505 0.0317  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0531   0.01  0.0082  0.098   True
-     0      7   0.0302  0.299 -0.0113 0.0717  False
-     0     14   0.0453  0.015  0.0055 0.0851   True
-     0     21   0.0724  0.001  0.0269  0.118   True
-     0     28   0.0342 0.2124  -0.009 0.0774  False
-     3      7  -0.0229 0.6805 -0.0684 0.0227  False
-     3     14  -0.0077    0.9 -0.0518 0.0363  False
-     3     21   0.0194 0.8599 -0.0299 0.0687  False
-     3     28  -0.0189 0.8477  -0.066 0.0283  False
-     7     14   0.0151 0.8921 -0.0254 0.0557  False
-     7     21   0.0423 0.0951 -0.0039 0.0885  False
-     7     28    0.004    0.9 -0.0399 0.0479  False
-    14     21   0.0271 0.5091 -0.0176 0.0718  False
-    14     28  -0.0112    0.9 -0.0535 0.0312  False
-    21     28  -0.0383 0.1998 -0.0861 0.0095  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[1.47006851e-11]	Yes
-Stroke	Sham	14	[0.26327967]	No
-Stroke	Sham	21	[0.01605402]	Yes
-Stroke	Sham	28	[0.11218774]	No
-Stroke	Sham	7	[6.16982408e-07]	Yes
-Stroke	Sham	0	[0.45465261]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_4_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOs-MOs_4
+               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:          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 199677.988 0.000 1.000 -391361.666 391361.666
+merged_timepoint 0.001      0.001 2.494 0.013       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  -0.0122 0.9956 -0.0801 0.0558  False
+     0      7   -0.024 0.9291 -0.0957 0.0477  False
+     0     14   0.0261  0.896 -0.0446 0.0968  False
+     0     21   0.0313 0.7998 -0.0394 0.1019  False
+     0     28   0.0324 0.8012  -0.041 0.1057  False
+     3      7  -0.0118 0.9956 -0.0779 0.0543  False
+     3     14   0.0382 0.5389 -0.0268 0.1033  False
+     3     21   0.0434 0.3924 -0.0216 0.1084  False
+     3     28   0.0445 0.4137 -0.0234 0.1124  False
+     7     14   0.0501 0.2971 -0.0189  0.119  False
+     7     21   0.0552 0.1967 -0.0137 0.1242  False
+     7     28   0.0563 0.2147 -0.0153  0.128  False
+    14     21   0.0052 0.9999 -0.0627 0.0731  False
+    14     28   0.0063 0.9998 -0.0644  0.077  False
+    21     28   0.0011    1.0 -0.0696 0.0718  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0477 0.6237 -0.0404 0.1358  False
+     0      7   0.0259 0.9411 -0.0555 0.1073  False
+     0     14   0.0419 0.6323 -0.0362 0.1201  False
+     0     21   0.0483 0.6256 -0.0411 0.1377  False
+     0     28   0.0265 0.9456 -0.0583 0.1113  False
+     3      7  -0.0218 0.9812 -0.1112 0.0676  False
+     3     14  -0.0058    1.0 -0.0922 0.0807  False
+     3     21   0.0006    1.0 -0.0961 0.0974  False
+     3     28  -0.0212 0.9857 -0.1138 0.0713  False
+     7     14    0.016 0.9921 -0.0635 0.0956  False
+     7     21   0.0224   0.98 -0.0682 0.1131  False
+     7     28   0.0006    1.0 -0.0856 0.0867  False
+    14     21   0.0064 0.9999 -0.0814 0.0941  False
+    14     28  -0.0155 0.9945 -0.0985 0.0676  False
+    21     28  -0.0218 0.9847 -0.1156 0.0719  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.01435751]	Yes
+Stroke	Sham	14	[0.48315099]	No
+Stroke	Sham	21	[0.5394724]	No
+Stroke	Sham	28	[0.96495406]	No
+Stroke	Sham	7	[0.00344298]	Yes
+Stroke	Sham	0	[0.75102905]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_cut_0_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOs-MOs_cut_0
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       1805         Method:                  REML  
-No. Groups:             2            Scale:                   0.0236
-Min. group size:        780          Log-Likelihood:          inf   
-Max. group size:        1025         Converged:               Yes   
-Mean group size:        902.5                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 113631.846 0.000 1.000 -222714.326 222714.326
-merged_timepoint 0.002      0.000 5.969 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  -0.0572 0.0055 -0.1034 -0.0111   True
-     0      7  -0.0212 0.7919 -0.0698  0.0275  False
-     0     14   0.0364 0.2551 -0.0116  0.0844  False
-     0     21   0.0366 0.2498 -0.0114  0.0846  False
-     0     28   0.0326 0.4235 -0.0172  0.0825  False
-     3      7   0.0361 0.1975 -0.0088   0.081  False
-     3     14   0.0936  0.001  0.0495  0.1378   True
-     3     21   0.0938  0.001  0.0496   0.138   True
-     3     28   0.0899  0.001  0.0437   0.136   True
-     7     14   0.0576 0.0062  0.0107  0.1044   True
-     7     21   0.0578  0.006  0.0109  0.1046   True
-     7     28   0.0538 0.0205  0.0051  0.1025   True
-    14     21   0.0002    0.9 -0.0459  0.0463  False
-    14     28  -0.0038    0.9 -0.0518  0.0442  False
-    21     28   -0.004    0.9  -0.052  0.0441  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0531 0.0741 -0.0028 0.1091  False
-     0      7   0.0219 0.8078 -0.0297 0.0736  False
-     0     14    0.056 0.0164  0.0064 0.1056   True
-     0     21   0.0677 0.0091  0.0109 0.1244   True
-     0     28   0.0403 0.2693 -0.0136 0.0941  False
-     3      7  -0.0312 0.6032 -0.0879 0.0256  False
-     3     14   0.0029    0.9  -0.052 0.0578  False
-     3     21   0.0145    0.9 -0.0469  0.076  False
-     3     28  -0.0128    0.9 -0.0716 0.0459  False
-     7     14   0.0341 0.3877 -0.0164 0.0846  False
-     7     21   0.0457 0.2084 -0.0119 0.1033  False
-     7     28   0.0183    0.9 -0.0364  0.073  False
-    14     21   0.0116    0.9 -0.0441 0.0673  False
-    14     28  -0.0157    0.9 -0.0685  0.037  False
-    21     28  -0.0274 0.7502 -0.0869 0.0322  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[1.85051974e-12]	Yes
-Stroke	Sham	14	[0.10157331]	No
-Stroke	Sham	21	[0.03008135]	Yes
-Stroke	Sham	28	[0.12962971]	No
-Stroke	Sham	7	[9.68052183e-06]	Yes
-Stroke	Sham	0	[0.25738922]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_cut_0_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOs-MOs_cut_0
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0402
+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 391787.523 0.000 1.000 -767889.435 767889.435
+merged_timepoint 0.004      0.001 3.427 0.001       0.002      0.006
+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  -0.1233  0.075 -0.2536 0.0069  False
+     0      7  -0.0066    1.0 -0.1441 0.1308  False
+     0     14    0.043 0.9429 -0.0926 0.1786  False
+     0     21   0.0555 0.8465   -0.08 0.1911  False
+     0     28   0.0368 0.9748 -0.1039 0.1775  False
+     3      7   0.1167 0.0905 -0.0101 0.2434  False
+     3     14   0.1663 0.0023  0.0416  0.291   True
+     3     21   0.1788 0.0008  0.0541 0.3035   True
+     3     28   0.1601 0.0066  0.0299 0.2904   True
+     7     14   0.0496 0.8888 -0.0826 0.1818  False
+     7     21   0.0622 0.7548   -0.07 0.1944  False
+     7     28   0.0434 0.9437  -0.094 0.1809  False
+    14     21   0.0125 0.9998 -0.1177 0.1428  False
+    14     28  -0.0062    1.0 -0.1417 0.1294  False
+    21     28  -0.0187 0.9987 -0.1543 0.1168  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0591 0.9233 -0.1147 0.2329  False
+     0      7   0.0189 0.9994 -0.1416 0.1794  False
+     0     14    0.082 0.6411 -0.0721 0.2361  False
+     0     21   0.0989 0.5871 -0.0774 0.2753  False
+     0     28    0.073 0.8061 -0.0943 0.2403  False
+     3      7  -0.0401 0.9862 -0.2165 0.1362  False
+     3     14    0.023 0.9988 -0.1476 0.1935  False
+     3     21   0.0399 0.9907  -0.151 0.2307  False
+     3     28    0.014 0.9999 -0.1686 0.1965  False
+     7     14   0.0631 0.8545 -0.0938 0.2201  False
+     7     21     0.08 0.7894 -0.0988 0.2589  False
+     7     28   0.0541 0.9411 -0.1158  0.224  False
+    14     21   0.0169 0.9998 -0.1562   0.19  False
+    14     28   -0.009    1.0 -0.1729 0.1549  False
+    21     28  -0.0259 0.9986 -0.2109 0.1591  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00032929]	Yes
+Stroke	Sham	14	[0.34635843]	No
+Stroke	Sham	21	[0.28321631]	No
+Stroke	Sham	28	[0.29641034]	No
+Stroke	Sham	7	[0.22004862]	No
+Stroke	Sham	0	[0.60602126]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_cut_1_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOs-MOs_cut_1
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       1805         Method:                  REML  
-No. Groups:             2            Scale:                   0.0236
-Min. group size:        780          Log-Likelihood:          inf   
-Max. group size:        1025         Converged:               Yes   
-Mean group size:        902.5                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 113631.846 0.000 1.000 -222714.326 222714.326
-merged_timepoint 0.002      0.000 5.969 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  -0.0572 0.0055 -0.1034 -0.0111   True
-     0      7  -0.0212 0.7919 -0.0698  0.0275  False
-     0     14   0.0364 0.2551 -0.0116  0.0844  False
-     0     21   0.0366 0.2498 -0.0114  0.0846  False
-     0     28   0.0326 0.4235 -0.0172  0.0825  False
-     3      7   0.0361 0.1975 -0.0088   0.081  False
-     3     14   0.0936  0.001  0.0495  0.1378   True
-     3     21   0.0938  0.001  0.0496   0.138   True
-     3     28   0.0899  0.001  0.0437   0.136   True
-     7     14   0.0576 0.0062  0.0107  0.1044   True
-     7     21   0.0578  0.006  0.0109  0.1046   True
-     7     28   0.0538 0.0205  0.0051  0.1025   True
-    14     21   0.0002    0.9 -0.0459  0.0463  False
-    14     28  -0.0038    0.9 -0.0518  0.0442  False
-    21     28   -0.004    0.9  -0.052  0.0441  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0531 0.0741 -0.0028 0.1091  False
-     0      7   0.0219 0.8078 -0.0297 0.0736  False
-     0     14    0.056 0.0164  0.0064 0.1056   True
-     0     21   0.0677 0.0091  0.0109 0.1244   True
-     0     28   0.0403 0.2693 -0.0136 0.0941  False
-     3      7  -0.0312 0.6032 -0.0879 0.0256  False
-     3     14   0.0029    0.9  -0.052 0.0578  False
-     3     21   0.0145    0.9 -0.0469  0.076  False
-     3     28  -0.0128    0.9 -0.0716 0.0459  False
-     7     14   0.0341 0.3877 -0.0164 0.0846  False
-     7     21   0.0457 0.2084 -0.0119 0.1033  False
-     7     28   0.0183    0.9 -0.0364  0.073  False
-    14     21   0.0116    0.9 -0.0441 0.0673  False
-    14     28  -0.0157    0.9 -0.0685  0.037  False
-    21     28  -0.0274 0.7502 -0.0869 0.0322  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[1.85051974e-12]	Yes
-Stroke	Sham	14	[0.10157331]	No
-Stroke	Sham	21	[0.03008135]	Yes
-Stroke	Sham	28	[0.12962971]	No
-Stroke	Sham	7	[9.68052183e-06]	Yes
-Stroke	Sham	0	[0.25738922]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_cut_1_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOs-MOs_cut_1
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0251
+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 309797.470 0.000 1.000 -607191.884 607191.884
+merged_timepoint 0.002      0.001 2.746 0.006       0.001      0.004
+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  -0.0718 0.4353 -0.1833 0.0398  False
+     0      7  -0.0149 0.9991 -0.1326 0.1028  False
+     0     14   0.0393 0.9257 -0.0768 0.1554  False
+     0     21    0.039 0.9277 -0.0771 0.1551  False
+     0     28   0.0248 0.9915 -0.0957 0.1453  False
+     3      7   0.0569 0.6599 -0.0517 0.1654  False
+     3     14   0.1111 0.0363  0.0043 0.2179   True
+     3     21   0.1108  0.037   0.004 0.2176   True
+     3     28   0.0966 0.1317  -0.015 0.2081  False
+     7     14   0.0542 0.7404  -0.059 0.1674  False
+     7     21   0.0539 0.7444 -0.0593 0.1672  False
+     7     28   0.0397 0.9268  -0.078 0.1574  False
+    14     21  -0.0003    1.0 -0.1118 0.1113  False
+    14     28  -0.0145 0.9992 -0.1306 0.1016  False
+    21     28  -0.0142 0.9993 -0.1303 0.1019  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0616 0.7196 -0.0643 0.1875  False
+     0      7   0.0258 0.9877 -0.0905 0.1421  False
+     0     14   0.0551 0.7113 -0.0565 0.1668  False
+     0     21   0.0794 0.4728 -0.0484 0.2071  False
+     0     28   0.0477 0.8654 -0.0735 0.1689  False
+     3      7  -0.0358 0.9656 -0.1635  0.092  False
+     3     14  -0.0065    1.0   -0.13 0.1171  False
+     3     21   0.0178 0.9991 -0.1205  0.156  False
+     3     28  -0.0139 0.9997 -0.1461 0.1183  False
+     7     14   0.0293  0.976 -0.0844  0.143  False
+     7     21   0.0535 0.8395  -0.076 0.1831  False
+     7     28   0.0219 0.9956 -0.1012  0.145  False
+    14     21   0.0242 0.9935 -0.1012 0.1496  False
+    14     28  -0.0074    1.0 -0.1261 0.1113  False
+    21     28  -0.0317 0.9837 -0.1656 0.1023  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00045419]	Yes
+Stroke	Sham	14	[0.54298307]	No
+Stroke	Sham	21	[0.26442461]	No
+Stroke	Sham	28	[0.26413149]	No
+Stroke	Sham	7	[0.08576433]	No
+Stroke	Sham	0	[0.6552648]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_cut_2_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOs-MOs_cut_2
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       1805         Method:                  REML  
-No. Groups:             2            Scale:                   0.0236
-Min. group size:        780          Log-Likelihood:          inf   
-Max. group size:        1025         Converged:               Yes   
-Mean group size:        902.5                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 113631.846 0.000 1.000 -222714.326 222714.326
-merged_timepoint 0.002      0.000 5.969 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  -0.0572 0.0055 -0.1034 -0.0111   True
-     0      7  -0.0212 0.7919 -0.0698  0.0275  False
-     0     14   0.0364 0.2551 -0.0116  0.0844  False
-     0     21   0.0366 0.2498 -0.0114  0.0846  False
-     0     28   0.0326 0.4235 -0.0172  0.0825  False
-     3      7   0.0361 0.1975 -0.0088   0.081  False
-     3     14   0.0936  0.001  0.0495  0.1378   True
-     3     21   0.0938  0.001  0.0496   0.138   True
-     3     28   0.0899  0.001  0.0437   0.136   True
-     7     14   0.0576 0.0062  0.0107  0.1044   True
-     7     21   0.0578  0.006  0.0109  0.1046   True
-     7     28   0.0538 0.0205  0.0051  0.1025   True
-    14     21   0.0002    0.9 -0.0459  0.0463  False
-    14     28  -0.0038    0.9 -0.0518  0.0442  False
-    21     28   -0.004    0.9  -0.052  0.0441  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0531 0.0741 -0.0028 0.1091  False
-     0      7   0.0219 0.8078 -0.0297 0.0736  False
-     0     14    0.056 0.0164  0.0064 0.1056   True
-     0     21   0.0677 0.0091  0.0109 0.1244   True
-     0     28   0.0403 0.2693 -0.0136 0.0941  False
-     3      7  -0.0312 0.6032 -0.0879 0.0256  False
-     3     14   0.0029    0.9  -0.052 0.0578  False
-     3     21   0.0145    0.9 -0.0469  0.076  False
-     3     28  -0.0128    0.9 -0.0716 0.0459  False
-     7     14   0.0341 0.3877 -0.0164 0.0846  False
-     7     21   0.0457 0.2084 -0.0119 0.1033  False
-     7     28   0.0183    0.9 -0.0364  0.073  False
-    14     21   0.0116    0.9 -0.0441 0.0673  False
-    14     28  -0.0157    0.9 -0.0685  0.037  False
-    21     28  -0.0274 0.7502 -0.0869 0.0322  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[1.85051974e-12]	Yes
-Stroke	Sham	14	[0.10157331]	No
-Stroke	Sham	21	[0.03008135]	Yes
-Stroke	Sham	28	[0.12962971]	No
-Stroke	Sham	7	[9.68052183e-06]	Yes
-Stroke	Sham	0	[0.25738922]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_cut_2_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOs-MOs_cut_2
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0202
+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 277890.242 0.000 1.000 -544654.866 544654.866
+merged_timepoint 0.002      0.001 2.364 0.018       0.000      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  -0.0419 0.8447 -0.1439 0.0601  False
+     0      7  -0.0273 0.9779 -0.1349 0.0803  False
+     0     14   0.0389  0.898 -0.0672 0.1451  False
+     0     21   0.0269 0.9781 -0.0792  0.133  False
+     0     28   0.0284 0.9763 -0.0817 0.1386  False
+     3      7   0.0146 0.9983 -0.0847 0.1138  False
+     3     14   0.0809 0.1672 -0.0168 0.1785  False
+     3     21   0.0688 0.3303 -0.0288 0.1664  False
+     3     28   0.0703 0.3547 -0.0316 0.1723  False
+     7     14   0.0663  0.441 -0.0372 0.1698  False
+     7     21   0.0542 0.6599 -0.0493 0.1577  False
+     7     28   0.0558 0.6705 -0.0519 0.1634  False
+    14     21  -0.0121 0.9994  -0.114 0.0899  False
+    14     28  -0.0105 0.9997 -0.1167 0.0956  False
+    21     28   0.0015    1.0 -0.1046 0.1077  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0576 0.6619 -0.0529 0.1681  False
+     0      7   0.0186 0.9951 -0.0835 0.1206  False
+     0     14   0.0491 0.6986 -0.0489  0.147  False
+     0     21   0.0675 0.5092 -0.0446 0.1796  False
+     0     28   0.0326 0.9496 -0.0738  0.139  False
+     3      7   -0.039 0.9157 -0.1511 0.0731  False
+     3     14  -0.0085 0.9999 -0.1169 0.0999  False
+     3     21   0.0099 0.9999 -0.1114 0.1312  False
+     3     28   -0.025 0.9893  -0.141  0.091  False
+     7     14   0.0305 0.9501 -0.0693 0.1303  False
+     7     21   0.0489 0.8154 -0.0648 0.1626  False
+     7     28    0.014  0.999  -0.094 0.1221  False
+    14     21   0.0184 0.9967 -0.0916 0.1285  False
+    14     28  -0.0165 0.9975 -0.1207 0.0877  False
+    21     28  -0.0349  0.956 -0.1525 0.0827  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00127238]	Yes
+Stroke	Sham	14	[0.56742245]	No
+Stroke	Sham	21	[0.20981999]	No
+Stroke	Sham	28	[0.46960941]	No
+Stroke	Sham	7	[0.03310928]	Yes
+Stroke	Sham	0	[0.59477908]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_cut_3_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOs-MOs_cut_3
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       1805         Method:                  REML  
-No. Groups:             2            Scale:                   0.0236
-Min. group size:        780          Log-Likelihood:          inf   
-Max. group size:        1025         Converged:               Yes   
-Mean group size:        902.5                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 113631.846 0.000 1.000 -222714.326 222714.326
-merged_timepoint 0.002      0.000 5.969 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  -0.0572 0.0055 -0.1034 -0.0111   True
-     0      7  -0.0212 0.7919 -0.0698  0.0275  False
-     0     14   0.0364 0.2551 -0.0116  0.0844  False
-     0     21   0.0366 0.2498 -0.0114  0.0846  False
-     0     28   0.0326 0.4235 -0.0172  0.0825  False
-     3      7   0.0361 0.1975 -0.0088   0.081  False
-     3     14   0.0936  0.001  0.0495  0.1378   True
-     3     21   0.0938  0.001  0.0496   0.138   True
-     3     28   0.0899  0.001  0.0437   0.136   True
-     7     14   0.0576 0.0062  0.0107  0.1044   True
-     7     21   0.0578  0.006  0.0109  0.1046   True
-     7     28   0.0538 0.0205  0.0051  0.1025   True
-    14     21   0.0002    0.9 -0.0459  0.0463  False
-    14     28  -0.0038    0.9 -0.0518  0.0442  False
-    21     28   -0.004    0.9  -0.052  0.0441  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0531 0.0741 -0.0028 0.1091  False
-     0      7   0.0219 0.8078 -0.0297 0.0736  False
-     0     14    0.056 0.0164  0.0064 0.1056   True
-     0     21   0.0677 0.0091  0.0109 0.1244   True
-     0     28   0.0403 0.2693 -0.0136 0.0941  False
-     3      7  -0.0312 0.6032 -0.0879 0.0256  False
-     3     14   0.0029    0.9  -0.052 0.0578  False
-     3     21   0.0145    0.9 -0.0469  0.076  False
-     3     28  -0.0128    0.9 -0.0716 0.0459  False
-     7     14   0.0341 0.3877 -0.0164 0.0846  False
-     7     21   0.0457 0.2084 -0.0119 0.1033  False
-     7     28   0.0183    0.9 -0.0364  0.073  False
-    14     21   0.0116    0.9 -0.0441 0.0673  False
-    14     28  -0.0157    0.9 -0.0685  0.037  False
-    21     28  -0.0274 0.7502 -0.0869 0.0322  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[1.85051974e-12]	Yes
-Stroke	Sham	14	[0.10157331]	No
-Stroke	Sham	21	[0.03008135]	Yes
-Stroke	Sham	28	[0.12962971]	No
-Stroke	Sham	7	[9.68052183e-06]	Yes
-Stroke	Sham	0	[0.25738922]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_cut_3_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOs-MOs_cut_3
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0161
+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 247730.322 0.000 1.000 -485542.510 485542.510
+merged_timepoint 0.002      0.001 2.325 0.020       0.000      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  -0.0272 0.9496 -0.1156 0.0612  False
+     0      7  -0.0292 0.9463 -0.1224 0.0641  False
+     0     14   0.0312  0.925 -0.0608 0.1232  False
+     0     21   0.0286 0.9472 -0.0634 0.1206  False
+     0     28   0.0338 0.9112 -0.0617 0.1293  False
+     3      7  -0.0019    1.0  -0.088 0.0841  False
+     3     14   0.0584 0.3538 -0.0262 0.1431  False
+     3     21   0.0558 0.4059 -0.0288 0.1405  False
+     3     28    0.061 0.3539 -0.0274 0.1494  False
+     7     14   0.0604 0.3833 -0.0294 0.1501  False
+     7     21   0.0578  0.434 -0.0319 0.1475  False
+     7     28    0.063 0.3797 -0.0303 0.1562  False
+    14     21  -0.0026    1.0  -0.091 0.0858  False
+    14     28   0.0026    1.0 -0.0894 0.0946  False
+    21     28   0.0052    1.0 -0.0868 0.0972  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0466 0.7827 -0.0566 0.1497  False
+     0      7   0.0232 0.9812  -0.072 0.1185  False
+     0     14   0.0472 0.6701 -0.0442 0.1387  False
+     0     21     0.05 0.7399 -0.0547 0.1546  False
+     0     28    0.025 0.9785 -0.0743 0.1242  False
+     3      7  -0.0233 0.9874  -0.128 0.0813  False
+     3     14   0.0007    1.0 -0.1005 0.1019  False
+     3     21   0.0034    1.0 -0.1099 0.1166  False
+     3     28  -0.0216 0.9924 -0.1299 0.0867  False
+     7     14    0.024  0.976 -0.0691 0.1171  False
+     7     21   0.0267 0.9783 -0.0794 0.1328  False
+     7     28   0.0017    1.0 -0.0991 0.1026  False
+    14     21   0.0027    1.0    -0.1 0.1054  False
+    14     28  -0.0223 0.9858 -0.1195 0.0749  False
+    21     28   -0.025 0.9861 -0.1348 0.0847  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.0056592]	Yes
+Stroke	Sham	14	[0.44581797]	No
+Stroke	Sham	21	[0.39837925]	No
+Stroke	Sham	28	[0.78236573]	No
+Stroke	Sham	7	[0.00494418]	Yes
+Stroke	Sham	0	[0.56904576]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_cut_4_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOs-MOs_cut_4
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       1805         Method:                  REML  
-No. Groups:             2            Scale:                   0.0236
-Min. group size:        780          Log-Likelihood:          inf   
-Max. group size:        1025         Converged:               Yes   
-Mean group size:        902.5                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 113631.846 0.000 1.000 -222714.326 222714.326
-merged_timepoint 0.002      0.000 5.969 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  -0.0572 0.0055 -0.1034 -0.0111   True
-     0      7  -0.0212 0.7919 -0.0698  0.0275  False
-     0     14   0.0364 0.2551 -0.0116  0.0844  False
-     0     21   0.0366 0.2498 -0.0114  0.0846  False
-     0     28   0.0326 0.4235 -0.0172  0.0825  False
-     3      7   0.0361 0.1975 -0.0088   0.081  False
-     3     14   0.0936  0.001  0.0495  0.1378   True
-     3     21   0.0938  0.001  0.0496   0.138   True
-     3     28   0.0899  0.001  0.0437   0.136   True
-     7     14   0.0576 0.0062  0.0107  0.1044   True
-     7     21   0.0578  0.006  0.0109  0.1046   True
-     7     28   0.0538 0.0205  0.0051  0.1025   True
-    14     21   0.0002    0.9 -0.0459  0.0463  False
-    14     28  -0.0038    0.9 -0.0518  0.0442  False
-    21     28   -0.004    0.9  -0.052  0.0441  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0531 0.0741 -0.0028 0.1091  False
-     0      7   0.0219 0.8078 -0.0297 0.0736  False
-     0     14    0.056 0.0164  0.0064 0.1056   True
-     0     21   0.0677 0.0091  0.0109 0.1244   True
-     0     28   0.0403 0.2693 -0.0136 0.0941  False
-     3      7  -0.0312 0.6032 -0.0879 0.0256  False
-     3     14   0.0029    0.9  -0.052 0.0578  False
-     3     21   0.0145    0.9 -0.0469  0.076  False
-     3     28  -0.0128    0.9 -0.0716 0.0459  False
-     7     14   0.0341 0.3877 -0.0164 0.0846  False
-     7     21   0.0457 0.2084 -0.0119 0.1033  False
-     7     28   0.0183    0.9 -0.0364  0.073  False
-    14     21   0.0116    0.9 -0.0441 0.0673  False
-    14     28  -0.0157    0.9 -0.0685  0.037  False
-    21     28  -0.0274 0.7502 -0.0869 0.0322  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[1.85051974e-12]	Yes
-Stroke	Sham	14	[0.10157331]	No
-Stroke	Sham	21	[0.03008135]	Yes
-Stroke	Sham	28	[0.12962971]	No
-Stroke	Sham	7	[9.68052183e-06]	Yes
-Stroke	Sham	0	[0.25738922]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_cut_4_log_significant.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOs-MOs_cut_4
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       361          Method:                  REML  
+No. Groups:             2            Scale:                   0.0137
+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 228858.167 0.000 1.000 -448553.765 448553.765
+merged_timepoint 0.002      0.001 2.546 0.011       0.000      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  -0.0219 0.9678 -0.1011 0.0573  False
+     0      7  -0.0278 0.9307 -0.1114 0.0558  False
+     0     14   0.0296 0.9064 -0.0529  0.112  False
+     0     21   0.0329 0.8609 -0.0496 0.1153  False
+     0     28   0.0393 0.7723 -0.0462 0.1249  False
+     3      7  -0.0059 0.9999  -0.083 0.0712  False
+     3     14   0.0515 0.3723 -0.0243 0.1274  False
+     3     21   0.0548 0.3024  -0.021 0.1306  False
+     3     28   0.0613 0.2309  -0.018 0.1405  False
+     7     14   0.0574 0.3159  -0.023 0.1378  False
+     7     21   0.0607 0.2558 -0.0197 0.1411  False
+     7     28   0.0671 0.1945 -0.0165 0.1507  False
+    14     21   0.0033    1.0 -0.0759 0.0825  False
+    14     28   0.0097 0.9994 -0.0727 0.0922  False
+    21     28   0.0065 0.9999  -0.076 0.0889  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0408 0.8419 -0.0583 0.1398  False
+     0      7   0.0232 0.9776 -0.0683 0.1146  False
+     0     14   0.0466 0.6435 -0.0412 0.1344  False
+     0     21   0.0425 0.8257  -0.058  0.143  False
+     0     28   0.0231 0.9817 -0.0722 0.1184  False
+     3      7  -0.0176 0.9959  -0.118 0.0829  False
+     3     14   0.0059    1.0 -0.0913  0.103  False
+     3     21   0.0018    1.0  -0.107 0.1105  False
+     3     28  -0.0176 0.9965 -0.1216 0.0864  False
+     7     14   0.0234 0.9742  -0.066 0.1128  False
+     7     21   0.0193 0.9941 -0.0826 0.1212  False
+     7     28  -0.0001    1.0 -0.0969 0.0967  False
+    14     21  -0.0041    1.0 -0.1027 0.0945  False
+    14     28  -0.0235 0.9784 -0.1169 0.0699  False
+    21     28  -0.0194 0.9948 -0.1248  0.086  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.01195224]	Yes
+Stroke	Sham	14	[0.43791305]	No
+Stroke	Sham	21	[0.59526014]	No
+Stroke	Sham	28	[0.87651062]	No
+Stroke	Sham	7	[0.00381174]	Yes
+Stroke	Sham	0	[0.60913213]	No