[DATALAD] Recorded changes

code/correlation_between_bahavior_and_DTI.py

@@ -31,18 +31,18 @@ for dd in df["dialation_amount"].unique():
                     # Filter the DataFrame for the current combination of 'Group', 'merged_timepoint', 'Qtype', and 'mask_name'
                     df_f2 = df[(df["Group"] == ss) & (df["merged_timepoint"] == time_point) & (df["Qtype"] == qq) & (df["mask_name"] == mm) &  (df["dialation_amount"] == dd)]
     
-                    # Remove rows with NaN values in 'Value' or 'hindlimb_dropZ-score' columns
-                    df_f2 = df_f2.dropna(subset=['Value', 'hindlimb_dropZ-score'])
+                    # 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["hindlimb_dropZ-score"])
+                        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["hindlimb_dropZ-score"])
+                            correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2["averageScore"])
                         else:
-                            correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2["hindlimb_dropZ-score"])
+                            correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2["averageScore"])
                        
     
                         # Store the results in a dictionary

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, output_folder):
+def PlotBoxplot(filtered_df, qq, mm,dd, output_folder):
     """
     Plot boxplots for filtered dataframe and save as images.
 
@@ -41,7 +41,7 @@ def PlotBoxplot(filtered_df, qq, mm, output_folder):
     plt.legend(title=None, frameon=False)
     
     # Save the plot as an image
-    output_path = os.path.join(output_folder, f'{qq}_{mm}_mixedlm_significant.png')
+    output_path = os.path.join(output_folder, f'{qq}_{mm}_{dd}_mixedlm_significant.png')
     plt.savefig(output_path, dpi=100)
     
     # Close the plot to avoid displaying it
@@ -66,7 +66,7 @@ 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["dialation_amount"] == 3) & (~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)
 
@@ -80,57 +80,59 @@ df_f1 = df_f1.dropna(axis=1, how="all")
 results = []
 
 # Iterate over unique values of "Qtype" and "mask_name"
-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)]
-        
-        # Fit the mixed-effects model
-        model_name = f"{qq}_{mm}"
-        md = smf.mixedlm("Value ~ merged_timepoint", filtered_df, groups=filtered_df["Group"])
-        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, mixed_model_dir)
-                
-                # 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()
+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)]
+            
+            # Fit the mixed-effects model
+            model_name = f"{qq}_{mm}_{dd}"
+            md = smf.mixedlm("Value ~ merged_timepoint", filtered_df, groups=filtered_df["Group"])
+            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 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, 'p_value': mdf.pvalues['merged_timepoint']})
+                    # 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)
+                    
+                    # 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")
+            
+            # Append the results to the list
+            results.append({'Qtype': qq, 'mask_name': mm,'dialation': dd,'p_value': mdf.pvalues['merged_timepoint']})
 
 # Create a DataFrame from results
 results_df = pd.DataFrame(results)

output/Final_Quantitative_output/Quantitative_results_from_dwi_processing.csv

@@ -1 +1 @@
-/annex/objects/MD5E-s37872731--c159287b385b232ea255a85bb27ee1e4.csv
+/annex/objects/MD5E-s42286741--9ef25abde24b4b9d51748d61db131110.csv

output/Final_Quantitative_output/Quantitative_results_from_dwi_processing_merged_with_behavior_data.csv

@@ -1 +1 @@
-/annex/objects/MD5E-s50295933--0597d65c759f1df6e8b8aa918c76b5ea.csv
+/annex/objects/MD5E-s55846190--48323fd86e44c9e00c346b7e20a3b9d6.csv

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_0_log.txt

@@ -0,0 +1,67 @@
+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_1_log.txt

@@ -0,0 +1,67 @@
+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_2_log.txt

@@ -0,0 +1,67 @@
+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_3_log.txt

@@ -0,0 +1,67 @@
+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_4_log.txt

@@ -0,0 +1,67 @@
+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_cut_0_log.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:      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.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:      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.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:      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.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:      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.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:      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_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_cut
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       361          Method:                  REML  
-No. Groups:             2            Scale:                   0.0098
-Min. group size:        156          Log-Likelihood:          inf   
-Max. group size:        205          Converged:               Yes   
-Mean group size:        180.5                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 193575.274 0.000 1.000 -379400.566 379400.566
-merged_timepoint 0.001      0.001 2.573 0.010       0.000      0.002
-Group Var        0.000                                              
-====================================================================
-
-Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3  -0.0013    0.9 -0.0643 0.0617  False
-     0      7  -0.0333 0.6775 -0.0998 0.0332  False
-     0     14   0.0241 0.8967 -0.0415 0.0897  False
-     0     21    0.033 0.6719 -0.0325 0.0986  False
-     0     28    0.043  0.457  -0.025 0.1111  False
-     3      7  -0.0319 0.6441 -0.0932 0.0294  False
-     3     14   0.0255  0.807 -0.0349 0.0858  False
-     3     21   0.0344 0.5626 -0.0259 0.0947  False
-     3     28   0.0444 0.3306 -0.0186 0.1074  False
-     7     14   0.0574 0.1066 -0.0066 0.1213  False
-     7     21   0.0663 0.0372  0.0024 0.1303   True
-     7     28   0.0763 0.0142  0.0098 0.1428   True
-    14     21   0.0089    0.9 -0.0541 0.0719  False
-    14     28   0.0189    0.9 -0.0466 0.0845  False
-    21     28     0.01    0.9 -0.0556 0.0756  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3    0.056 0.4534 -0.0325 0.1444  False
-     0      7   0.0255    0.9 -0.0562 0.1072  False
-     0     14   0.0385 0.6912 -0.0399 0.1169  False
-     0     21    0.045 0.6734 -0.0447 0.1348  False
-     0     28   0.0246    0.9 -0.0605 0.1098  False
-     3      7  -0.0305    0.9 -0.1202 0.0593  False
-     3     14  -0.0175    0.9 -0.1043 0.0693  False
-     3     21   -0.011    0.9 -0.1081 0.0862  False
-     3     28  -0.0314    0.9 -0.1243 0.0615  False
-     7     14    0.013    0.9 -0.0669 0.0928  False
-     7     21   0.0195    0.9 -0.0715 0.1105  False
-     7     28  -0.0009    0.9 -0.0874 0.0856  False
-    14     21   0.0065    0.9 -0.0816 0.0946  False
-    14     28  -0.0139    0.9 -0.0973 0.0695  False
-    21     28  -0.0204    0.9 -0.1145 0.0737  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.0378204]	Yes
-Stroke	Sham	14	[0.66421351]	No
-Stroke	Sham	21	[0.78907715]	No
-Stroke	Sham	28	[0.25846633]	No
-Stroke	Sham	7	[0.00060319]	Yes
-Stroke	Sham	0	[0.94690315]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_0_log.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:      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.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:      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.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:      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.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:      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.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:      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_cut_0_log.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:      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.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:      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.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:      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.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:      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.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:      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_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp-MOp_dilated_cut
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       361          Method:                  REML  
-No. Groups:             2            Scale:                   0.0088
-Min. group size:        156          Log-Likelihood:          inf   
-Max. group size:        205          Converged:               Yes   
-Mean group size:        180.5                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 182887.871 0.000 1.000 -358453.640 358453.640
-merged_timepoint 0.001      0.001 2.183 0.029       0.000      0.002
-Group Var        0.000                                              
-====================================================================
-
-Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05 
-====================================================
-group1 group2 meandiff p-adj   lower   upper  reject
-----------------------------------------------------
-     0      3   0.0353 0.4518 -0.0203   0.091  False
-     0      7   -0.033 0.5774 -0.0917  0.0258  False
-     0     14   0.0336 0.5456 -0.0243  0.0915  False
-     0     21   0.0468 0.1889 -0.0111  0.1047  False
-     0     28   0.0409 0.3717 -0.0192   0.101  False
-     3      7  -0.0683 0.0048 -0.1224 -0.0142   True
-     3     14  -0.0017    0.9  -0.055  0.0515  False
-     3     21   0.0114    0.9 -0.0418  0.0647  False
-     3     28   0.0055    0.9 -0.0501  0.0612  False
-     7     14   0.0666 0.0107  0.0101   0.123   True
-     7     21   0.0797  0.001  0.0233  0.1362   True
-     7     28   0.0738  0.005  0.0151  0.1325   True
-    14     21   0.0132    0.9 -0.0425  0.0688  False
-    14     28   0.0073    0.9 -0.0506  0.0652  False
-    21     28  -0.0059    0.9 -0.0638   0.052  False
-----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0525 0.5058 -0.0346 0.1395  False
-     0      7    0.025    0.9 -0.0554 0.1053  False
-     0     14   0.0327 0.8012 -0.0444 0.1099  False
-     0     21    0.041 0.7347 -0.0473 0.1293  False
-     0     28   0.0265    0.9 -0.0573 0.1103  False
-     3      7  -0.0275    0.9 -0.1158 0.0608  False
-     3     14  -0.0198    0.9 -0.1052 0.0656  False
-     3     21  -0.0115    0.9 -0.1071 0.0841  False
-     3     28   -0.026    0.9 -0.1174 0.0654  False
-     7     14   0.0078    0.9 -0.0708 0.0864  False
-     7     21    0.016    0.9 -0.0735 0.1056  False
-     7     28   0.0015    0.9 -0.0836 0.0866  False
-    14     21   0.0083    0.9 -0.0784  0.095  False
-    14     28  -0.0062    0.9 -0.0883 0.0759  False
-    21     28  -0.0145    0.9 -0.1071 0.0781  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.63702768]	No
-Stroke	Sham	14	[0.82523409]	No
-Stroke	Sham	21	[0.79268718]	No
-Stroke	Sham	28	[0.2189166]	No
-Stroke	Sham	7	[0.0011087]	Yes
-Stroke	Sham	0	[0.76334283]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_0_log.txt

@@ -0,0 +1,67 @@
+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_1_log.txt

@@ -0,0 +1,67 @@
+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_2_log.txt

@@ -0,0 +1,67 @@
+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_3_log.txt

@@ -0,0 +1,67 @@
+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_4_log.txt

@@ -0,0 +1,67 @@
+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_cut_0_log.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:       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.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:       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.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:       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.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:       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.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:       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_SSp_ll-SSp_ll_cut_0_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_SSp_ll-SSp_ll_cut_0
+                Mixed Linear Model Regression Results
+======================================================================
+Model:                  MixedLM       Dependent Variable:       Value 
+No. Observations:       1805          Method:                   REML  
+No. Groups:             2             Scale:                    0.0249
+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 116788.789 -0.000 1.000 -228901.820 228901.820
+merged_timepoint -0.001      0.000 -3.788 0.000      -0.002     -0.001
+Group Var         0.000                                               
+======================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.2274  0.001    0.18  0.2747   True
+     0      7   -0.022 0.7814  -0.072  0.0279  False
+     0     14   0.0605 0.0063  0.0112  0.1098   True
+     0     21   0.0763  0.001   0.027  0.1256   True
+     0     28   0.0049    0.9 -0.0463   0.056  False
+     3      7  -0.2494  0.001 -0.2955 -0.2034   True
+     3     14  -0.1669  0.001 -0.2122 -0.1215   True
+     3     21  -0.1511  0.001 -0.1964 -0.1058   True
+     3     28  -0.2225  0.001 -0.2699 -0.1752   True
+     7     14   0.0826  0.001  0.0345  0.1306   True
+     7     21   0.0983  0.001  0.0503  0.1464   True
+     7     28   0.0269 0.6209 -0.0231  0.0769  False
+    14     21   0.0158    0.9 -0.0316  0.0631  False
+    14     28  -0.0556 0.0164 -0.1049 -0.0064   True
+    21     28  -0.0714  0.001 -0.1207 -0.0221   True
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0721  0.001  0.0261  0.1181   True
+     0      7   0.0341 0.1973 -0.0084  0.0766  False
+     0     14   0.0163 0.8499 -0.0245  0.0571  False
+     0     21   0.0511 0.0225  0.0044  0.0978   True
+     0     28   0.0167 0.8847 -0.0275   0.061  False
+     3      7  -0.0379 0.1863 -0.0846  0.0087  False
+     3     14  -0.0558 0.0059 -0.1009 -0.0106   True
+     3     21   -0.021 0.8239 -0.0715  0.0295  False
+     3     28  -0.0553 0.0142 -0.1036  -0.007   True
+     7     14  -0.0178 0.8003 -0.0594  0.0237  False
+     7     21    0.017    0.9 -0.0304  0.0643  False
+     7     28  -0.0174  0.871 -0.0624  0.0276  False
+    14     21   0.0348 0.2529  -0.011  0.0806  False
+    14     28   0.0005    0.9 -0.0429  0.0438  False
+    21     28  -0.0343 0.3408 -0.0833  0.0146  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[4.02216038e-09]	Yes
+Stroke	Sham	14	[1.07462353e-06]	Yes
+Stroke	Sham	21	[0.0609449]	No
+Stroke	Sham	28	[0.6972035]	No
+Stroke	Sham	7	[9.72308112e-05]	Yes
+Stroke	Sham	0	[0.0839076]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_SSp_ll-SSp_ll_cut_1_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_SSp_ll-SSp_ll_cut_1
+                Mixed Linear Model Regression Results
+======================================================================
+Model:                  MixedLM       Dependent Variable:       Value 
+No. Observations:       1805          Method:                   REML  
+No. Groups:             2             Scale:                    0.0249
+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 116788.789 -0.000 1.000 -228901.820 228901.820
+merged_timepoint -0.001      0.000 -3.788 0.000      -0.002     -0.001
+Group Var         0.000                                               
+======================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.2274  0.001    0.18  0.2747   True
+     0      7   -0.022 0.7814  -0.072  0.0279  False
+     0     14   0.0605 0.0063  0.0112  0.1098   True
+     0     21   0.0763  0.001   0.027  0.1256   True
+     0     28   0.0049    0.9 -0.0463   0.056  False
+     3      7  -0.2494  0.001 -0.2955 -0.2034   True
+     3     14  -0.1669  0.001 -0.2122 -0.1215   True
+     3     21  -0.1511  0.001 -0.1964 -0.1058   True
+     3     28  -0.2225  0.001 -0.2699 -0.1752   True
+     7     14   0.0826  0.001  0.0345  0.1306   True
+     7     21   0.0983  0.001  0.0503  0.1464   True
+     7     28   0.0269 0.6209 -0.0231  0.0769  False
+    14     21   0.0158    0.9 -0.0316  0.0631  False
+    14     28  -0.0556 0.0164 -0.1049 -0.0064   True
+    21     28  -0.0714  0.001 -0.1207 -0.0221   True
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0721  0.001  0.0261  0.1181   True
+     0      7   0.0341 0.1973 -0.0084  0.0766  False
+     0     14   0.0163 0.8499 -0.0245  0.0571  False
+     0     21   0.0511 0.0225  0.0044  0.0978   True
+     0     28   0.0167 0.8847 -0.0275   0.061  False
+     3      7  -0.0379 0.1863 -0.0846  0.0087  False
+     3     14  -0.0558 0.0059 -0.1009 -0.0106   True
+     3     21   -0.021 0.8239 -0.0715  0.0295  False
+     3     28  -0.0553 0.0142 -0.1036  -0.007   True
+     7     14  -0.0178 0.8003 -0.0594  0.0237  False
+     7     21    0.017    0.9 -0.0304  0.0643  False
+     7     28  -0.0174  0.871 -0.0624  0.0276  False
+    14     21   0.0348 0.2529  -0.011  0.0806  False
+    14     28   0.0005    0.9 -0.0429  0.0438  False
+    21     28  -0.0343 0.3408 -0.0833  0.0146  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[4.02216038e-09]	Yes
+Stroke	Sham	14	[1.07462353e-06]	Yes
+Stroke	Sham	21	[0.0609449]	No
+Stroke	Sham	28	[0.6972035]	No
+Stroke	Sham	7	[9.72308112e-05]	Yes
+Stroke	Sham	0	[0.0839076]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_SSp_ll-SSp_ll_cut_2_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_SSp_ll-SSp_ll_cut_2
+                Mixed Linear Model Regression Results
+======================================================================
+Model:                  MixedLM       Dependent Variable:       Value 
+No. Observations:       1805          Method:                   REML  
+No. Groups:             2             Scale:                    0.0249
+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 116788.789 -0.000 1.000 -228901.820 228901.820
+merged_timepoint -0.001      0.000 -3.788 0.000      -0.002     -0.001
+Group Var         0.000                                               
+======================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.2274  0.001    0.18  0.2747   True
+     0      7   -0.022 0.7814  -0.072  0.0279  False
+     0     14   0.0605 0.0063  0.0112  0.1098   True
+     0     21   0.0763  0.001   0.027  0.1256   True
+     0     28   0.0049    0.9 -0.0463   0.056  False
+     3      7  -0.2494  0.001 -0.2955 -0.2034   True
+     3     14  -0.1669  0.001 -0.2122 -0.1215   True
+     3     21  -0.1511  0.001 -0.1964 -0.1058   True
+     3     28  -0.2225  0.001 -0.2699 -0.1752   True
+     7     14   0.0826  0.001  0.0345  0.1306   True
+     7     21   0.0983  0.001  0.0503  0.1464   True
+     7     28   0.0269 0.6209 -0.0231  0.0769  False
+    14     21   0.0158    0.9 -0.0316  0.0631  False
+    14     28  -0.0556 0.0164 -0.1049 -0.0064   True
+    21     28  -0.0714  0.001 -0.1207 -0.0221   True
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0721  0.001  0.0261  0.1181   True
+     0      7   0.0341 0.1973 -0.0084  0.0766  False
+     0     14   0.0163 0.8499 -0.0245  0.0571  False
+     0     21   0.0511 0.0225  0.0044  0.0978   True
+     0     28   0.0167 0.8847 -0.0275   0.061  False
+     3      7  -0.0379 0.1863 -0.0846  0.0087  False
+     3     14  -0.0558 0.0059 -0.1009 -0.0106   True
+     3     21   -0.021 0.8239 -0.0715  0.0295  False
+     3     28  -0.0553 0.0142 -0.1036  -0.007   True
+     7     14  -0.0178 0.8003 -0.0594  0.0237  False
+     7     21    0.017    0.9 -0.0304  0.0643  False
+     7     28  -0.0174  0.871 -0.0624  0.0276  False
+    14     21   0.0348 0.2529  -0.011  0.0806  False
+    14     28   0.0005    0.9 -0.0429  0.0438  False
+    21     28  -0.0343 0.3408 -0.0833  0.0146  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[4.02216038e-09]	Yes
+Stroke	Sham	14	[1.07462353e-06]	Yes
+Stroke	Sham	21	[0.0609449]	No
+Stroke	Sham	28	[0.6972035]	No
+Stroke	Sham	7	[9.72308112e-05]	Yes
+Stroke	Sham	0	[0.0839076]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_SSp_ll-SSp_ll_cut_3_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_SSp_ll-SSp_ll_cut_3
+                Mixed Linear Model Regression Results
+======================================================================
+Model:                  MixedLM       Dependent Variable:       Value 
+No. Observations:       1805          Method:                   REML  
+No. Groups:             2             Scale:                    0.0249
+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 116788.789 -0.000 1.000 -228901.820 228901.820
+merged_timepoint -0.001      0.000 -3.788 0.000      -0.002     -0.001
+Group Var         0.000                                               
+======================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.2274  0.001    0.18  0.2747   True
+     0      7   -0.022 0.7814  -0.072  0.0279  False
+     0     14   0.0605 0.0063  0.0112  0.1098   True
+     0     21   0.0763  0.001   0.027  0.1256   True
+     0     28   0.0049    0.9 -0.0463   0.056  False
+     3      7  -0.2494  0.001 -0.2955 -0.2034   True
+     3     14  -0.1669  0.001 -0.2122 -0.1215   True
+     3     21  -0.1511  0.001 -0.1964 -0.1058   True
+     3     28  -0.2225  0.001 -0.2699 -0.1752   True
+     7     14   0.0826  0.001  0.0345  0.1306   True
+     7     21   0.0983  0.001  0.0503  0.1464   True
+     7     28   0.0269 0.6209 -0.0231  0.0769  False
+    14     21   0.0158    0.9 -0.0316  0.0631  False
+    14     28  -0.0556 0.0164 -0.1049 -0.0064   True
+    21     28  -0.0714  0.001 -0.1207 -0.0221   True
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0721  0.001  0.0261  0.1181   True
+     0      7   0.0341 0.1973 -0.0084  0.0766  False
+     0     14   0.0163 0.8499 -0.0245  0.0571  False
+     0     21   0.0511 0.0225  0.0044  0.0978   True
+     0     28   0.0167 0.8847 -0.0275   0.061  False
+     3      7  -0.0379 0.1863 -0.0846  0.0087  False
+     3     14  -0.0558 0.0059 -0.1009 -0.0106   True
+     3     21   -0.021 0.8239 -0.0715  0.0295  False
+     3     28  -0.0553 0.0142 -0.1036  -0.007   True
+     7     14  -0.0178 0.8003 -0.0594  0.0237  False
+     7     21    0.017    0.9 -0.0304  0.0643  False
+     7     28  -0.0174  0.871 -0.0624  0.0276  False
+    14     21   0.0348 0.2529  -0.011  0.0806  False
+    14     28   0.0005    0.9 -0.0429  0.0438  False
+    21     28  -0.0343 0.3408 -0.0833  0.0146  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[4.02216038e-09]	Yes
+Stroke	Sham	14	[1.07462353e-06]	Yes
+Stroke	Sham	21	[0.0609449]	No
+Stroke	Sham	28	[0.6972035]	No
+Stroke	Sham	7	[9.72308112e-05]	Yes
+Stroke	Sham	0	[0.0839076]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_SSp_ll-SSp_ll_cut_4_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_SSp_ll-SSp_ll_cut_4
+                Mixed Linear Model Regression Results
+======================================================================
+Model:                  MixedLM       Dependent Variable:       Value 
+No. Observations:       1805          Method:                   REML  
+No. Groups:             2             Scale:                    0.0249
+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 116788.789 -0.000 1.000 -228901.820 228901.820
+merged_timepoint -0.001      0.000 -3.788 0.000      -0.002     -0.001
+Group Var         0.000                                               
+======================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.2274  0.001    0.18  0.2747   True
+     0      7   -0.022 0.7814  -0.072  0.0279  False
+     0     14   0.0605 0.0063  0.0112  0.1098   True
+     0     21   0.0763  0.001   0.027  0.1256   True
+     0     28   0.0049    0.9 -0.0463   0.056  False
+     3      7  -0.2494  0.001 -0.2955 -0.2034   True
+     3     14  -0.1669  0.001 -0.2122 -0.1215   True
+     3     21  -0.1511  0.001 -0.1964 -0.1058   True
+     3     28  -0.2225  0.001 -0.2699 -0.1752   True
+     7     14   0.0826  0.001  0.0345  0.1306   True
+     7     21   0.0983  0.001  0.0503  0.1464   True
+     7     28   0.0269 0.6209 -0.0231  0.0769  False
+    14     21   0.0158    0.9 -0.0316  0.0631  False
+    14     28  -0.0556 0.0164 -0.1049 -0.0064   True
+    21     28  -0.0714  0.001 -0.1207 -0.0221   True
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0721  0.001  0.0261  0.1181   True
+     0      7   0.0341 0.1973 -0.0084  0.0766  False
+     0     14   0.0163 0.8499 -0.0245  0.0571  False
+     0     21   0.0511 0.0225  0.0044  0.0978   True
+     0     28   0.0167 0.8847 -0.0275   0.061  False
+     3      7  -0.0379 0.1863 -0.0846  0.0087  False
+     3     14  -0.0558 0.0059 -0.1009 -0.0106   True
+     3     21   -0.021 0.8239 -0.0715  0.0295  False
+     3     28  -0.0553 0.0142 -0.1036  -0.007   True
+     7     14  -0.0178 0.8003 -0.0594  0.0237  False
+     7     21    0.017    0.9 -0.0304  0.0643  False
+     7     28  -0.0174  0.871 -0.0624  0.0276  False
+    14     21   0.0348 0.2529  -0.011  0.0806  False
+    14     28   0.0005    0.9 -0.0429  0.0438  False
+    21     28  -0.0343 0.3408 -0.0833  0.0146  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[4.02216038e-09]	Yes
+Stroke	Sham	14	[1.07462353e-06]	Yes
+Stroke	Sham	21	[0.0609449]	No
+Stroke	Sham	28	[0.6972035]	No
+Stroke	Sham	7	[9.72308112e-05]	Yes
+Stroke	Sham	0	[0.0839076]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_SSp_ul-SSp_ul_cut_0_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_SSp_ul-SSp_ul_cut_0
+                Mixed Linear Model Regression Results
+======================================================================
+Model:                  MixedLM       Dependent Variable:       Value 
+No. Observations:       1805          Method:                   REML  
+No. Groups:             2             Scale:                    0.0216
+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 108711.854 -0.000 1.000 -213071.318 213071.318
+merged_timepoint -0.001      0.000 -2.744 0.006      -0.002     -0.000
+Group Var         0.000                                               
+======================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.2094  0.001  0.1656  0.2531   True
+     0      7  -0.0093    0.9 -0.0555  0.0368  False
+     0     14   0.0623 0.0014  0.0167  0.1078   True
+     0     21   0.0736  0.001  0.0281  0.1192   True
+     0     28   0.0291 0.4942 -0.0182  0.0764  False
+     3      7  -0.2187  0.001 -0.2613 -0.1761   True
+     3     14  -0.1471  0.001  -0.189 -0.1052   True
+     3     21  -0.1357  0.001 -0.1776 -0.0938   True
+     3     28  -0.1803  0.001  -0.224 -0.1365   True
+     7     14   0.0716  0.001  0.0272   0.116   True
+     7     21    0.083  0.001  0.0386  0.1274   True
+     7     28   0.0384 0.1658 -0.0078  0.0846  False
+    14     21   0.0114    0.9 -0.0324  0.0551  False
+    14     28  -0.0332 0.2989 -0.0787  0.0124  False
+    21     28  -0.0445 0.0595 -0.0901   0.001  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0574 0.0037  0.0126  0.1023   True
+     0      7   0.0266 0.4446 -0.0148  0.0681  False
+     0     14   0.0076    0.9 -0.0322  0.0474  False
+     0     21   0.0399 0.1239 -0.0056  0.0854  False
+     0     28   0.0154    0.9 -0.0277  0.0586  False
+     3      7  -0.0308 0.3838 -0.0763  0.0147  False
+     3     14  -0.0498 0.0159 -0.0939 -0.0058   True
+     3     21  -0.0175    0.9 -0.0668  0.0317  False
+     3     28   -0.042 0.1122 -0.0891  0.0051  False
+     7     14   -0.019 0.7332 -0.0596  0.0215  False
+     7     21   0.0133    0.9 -0.0329  0.0594  False
+     7     28  -0.0112    0.9 -0.0551  0.0327  False
+    14     21   0.0323 0.3056 -0.0123   0.077  False
+    14     28   0.0078    0.9 -0.0344  0.0501  False
+    21     28  -0.0245 0.6627 -0.0722  0.0232  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[7.29267979e-10]	Yes
+Stroke	Sham	14	[2.99931915e-08]	Yes
+Stroke	Sham	21	[0.04196674]	Yes
+Stroke	Sham	28	[0.01108557]	Yes
+Stroke	Sham	7	[0.01193809]	Yes
+Stroke	Sham	0	[0.18879961]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_SSp_ul-SSp_ul_cut_1_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_SSp_ul-SSp_ul_cut_1
+                Mixed Linear Model Regression Results
+======================================================================
+Model:                  MixedLM       Dependent Variable:       Value 
+No. Observations:       1805          Method:                   REML  
+No. Groups:             2             Scale:                    0.0216
+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 108711.854 -0.000 1.000 -213071.318 213071.318
+merged_timepoint -0.001      0.000 -2.744 0.006      -0.002     -0.000
+Group Var         0.000                                               
+======================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.2094  0.001  0.1656  0.2531   True
+     0      7  -0.0093    0.9 -0.0555  0.0368  False
+     0     14   0.0623 0.0014  0.0167  0.1078   True
+     0     21   0.0736  0.001  0.0281  0.1192   True
+     0     28   0.0291 0.4942 -0.0182  0.0764  False
+     3      7  -0.2187  0.001 -0.2613 -0.1761   True
+     3     14  -0.1471  0.001  -0.189 -0.1052   True
+     3     21  -0.1357  0.001 -0.1776 -0.0938   True
+     3     28  -0.1803  0.001  -0.224 -0.1365   True
+     7     14   0.0716  0.001  0.0272   0.116   True
+     7     21    0.083  0.001  0.0386  0.1274   True
+     7     28   0.0384 0.1658 -0.0078  0.0846  False
+    14     21   0.0114    0.9 -0.0324  0.0551  False
+    14     28  -0.0332 0.2989 -0.0787  0.0124  False
+    21     28  -0.0445 0.0595 -0.0901   0.001  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0574 0.0037  0.0126  0.1023   True
+     0      7   0.0266 0.4446 -0.0148  0.0681  False
+     0     14   0.0076    0.9 -0.0322  0.0474  False
+     0     21   0.0399 0.1239 -0.0056  0.0854  False
+     0     28   0.0154    0.9 -0.0277  0.0586  False
+     3      7  -0.0308 0.3838 -0.0763  0.0147  False
+     3     14  -0.0498 0.0159 -0.0939 -0.0058   True
+     3     21  -0.0175    0.9 -0.0668  0.0317  False
+     3     28   -0.042 0.1122 -0.0891  0.0051  False
+     7     14   -0.019 0.7332 -0.0596  0.0215  False
+     7     21   0.0133    0.9 -0.0329  0.0594  False
+     7     28  -0.0112    0.9 -0.0551  0.0327  False
+    14     21   0.0323 0.3056 -0.0123   0.077  False
+    14     28   0.0078    0.9 -0.0344  0.0501  False
+    21     28  -0.0245 0.6627 -0.0722  0.0232  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[7.29267979e-10]	Yes
+Stroke	Sham	14	[2.99931915e-08]	Yes
+Stroke	Sham	21	[0.04196674]	Yes
+Stroke	Sham	28	[0.01108557]	Yes
+Stroke	Sham	7	[0.01193809]	Yes
+Stroke	Sham	0	[0.18879961]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_SSp_ul-SSp_ul_cut_2_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_SSp_ul-SSp_ul_cut_2
+                Mixed Linear Model Regression Results
+======================================================================
+Model:                  MixedLM       Dependent Variable:       Value 
+No. Observations:       1805          Method:                   REML  
+No. Groups:             2             Scale:                    0.0216
+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 108711.854 -0.000 1.000 -213071.318 213071.318
+merged_timepoint -0.001      0.000 -2.744 0.006      -0.002     -0.000
+Group Var         0.000                                               
+======================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.2094  0.001  0.1656  0.2531   True
+     0      7  -0.0093    0.9 -0.0555  0.0368  False
+     0     14   0.0623 0.0014  0.0167  0.1078   True
+     0     21   0.0736  0.001  0.0281  0.1192   True
+     0     28   0.0291 0.4942 -0.0182  0.0764  False
+     3      7  -0.2187  0.001 -0.2613 -0.1761   True
+     3     14  -0.1471  0.001  -0.189 -0.1052   True
+     3     21  -0.1357  0.001 -0.1776 -0.0938   True
+     3     28  -0.1803  0.001  -0.224 -0.1365   True
+     7     14   0.0716  0.001  0.0272   0.116   True
+     7     21    0.083  0.001  0.0386  0.1274   True
+     7     28   0.0384 0.1658 -0.0078  0.0846  False
+    14     21   0.0114    0.9 -0.0324  0.0551  False
+    14     28  -0.0332 0.2989 -0.0787  0.0124  False
+    21     28  -0.0445 0.0595 -0.0901   0.001  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0574 0.0037  0.0126  0.1023   True
+     0      7   0.0266 0.4446 -0.0148  0.0681  False
+     0     14   0.0076    0.9 -0.0322  0.0474  False
+     0     21   0.0399 0.1239 -0.0056  0.0854  False
+     0     28   0.0154    0.9 -0.0277  0.0586  False
+     3      7  -0.0308 0.3838 -0.0763  0.0147  False
+     3     14  -0.0498 0.0159 -0.0939 -0.0058   True
+     3     21  -0.0175    0.9 -0.0668  0.0317  False
+     3     28   -0.042 0.1122 -0.0891  0.0051  False
+     7     14   -0.019 0.7332 -0.0596  0.0215  False
+     7     21   0.0133    0.9 -0.0329  0.0594  False
+     7     28  -0.0112    0.9 -0.0551  0.0327  False
+    14     21   0.0323 0.3056 -0.0123   0.077  False
+    14     28   0.0078    0.9 -0.0344  0.0501  False
+    21     28  -0.0245 0.6627 -0.0722  0.0232  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[7.29267979e-10]	Yes
+Stroke	Sham	14	[2.99931915e-08]	Yes
+Stroke	Sham	21	[0.04196674]	Yes
+Stroke	Sham	28	[0.01108557]	Yes
+Stroke	Sham	7	[0.01193809]	Yes
+Stroke	Sham	0	[0.18879961]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_SSp_ul-SSp_ul_cut_3_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_SSp_ul-SSp_ul_cut_3
+                Mixed Linear Model Regression Results
+======================================================================
+Model:                  MixedLM       Dependent Variable:       Value 
+No. Observations:       1805          Method:                   REML  
+No. Groups:             2             Scale:                    0.0216
+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 108711.854 -0.000 1.000 -213071.318 213071.318
+merged_timepoint -0.001      0.000 -2.744 0.006      -0.002     -0.000
+Group Var         0.000                                               
+======================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.2094  0.001  0.1656  0.2531   True
+     0      7  -0.0093    0.9 -0.0555  0.0368  False
+     0     14   0.0623 0.0014  0.0167  0.1078   True
+     0     21   0.0736  0.001  0.0281  0.1192   True
+     0     28   0.0291 0.4942 -0.0182  0.0764  False
+     3      7  -0.2187  0.001 -0.2613 -0.1761   True
+     3     14  -0.1471  0.001  -0.189 -0.1052   True
+     3     21  -0.1357  0.001 -0.1776 -0.0938   True
+     3     28  -0.1803  0.001  -0.224 -0.1365   True
+     7     14   0.0716  0.001  0.0272   0.116   True
+     7     21    0.083  0.001  0.0386  0.1274   True
+     7     28   0.0384 0.1658 -0.0078  0.0846  False
+    14     21   0.0114    0.9 -0.0324  0.0551  False
+    14     28  -0.0332 0.2989 -0.0787  0.0124  False
+    21     28  -0.0445 0.0595 -0.0901   0.001  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0574 0.0037  0.0126  0.1023   True
+     0      7   0.0266 0.4446 -0.0148  0.0681  False
+     0     14   0.0076    0.9 -0.0322  0.0474  False
+     0     21   0.0399 0.1239 -0.0056  0.0854  False
+     0     28   0.0154    0.9 -0.0277  0.0586  False
+     3      7  -0.0308 0.3838 -0.0763  0.0147  False
+     3     14  -0.0498 0.0159 -0.0939 -0.0058   True
+     3     21  -0.0175    0.9 -0.0668  0.0317  False
+     3     28   -0.042 0.1122 -0.0891  0.0051  False
+     7     14   -0.019 0.7332 -0.0596  0.0215  False
+     7     21   0.0133    0.9 -0.0329  0.0594  False
+     7     28  -0.0112    0.9 -0.0551  0.0327  False
+    14     21   0.0323 0.3056 -0.0123   0.077  False
+    14     28   0.0078    0.9 -0.0344  0.0501  False
+    21     28  -0.0245 0.6627 -0.0722  0.0232  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[7.29267979e-10]	Yes
+Stroke	Sham	14	[2.99931915e-08]	Yes
+Stroke	Sham	21	[0.04196674]	Yes
+Stroke	Sham	28	[0.01108557]	Yes
+Stroke	Sham	7	[0.01193809]	Yes
+Stroke	Sham	0	[0.18879961]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_SSp_ul-SSp_ul_cut_4_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_SSp_ul-SSp_ul_cut_4
+                Mixed Linear Model Regression Results
+======================================================================
+Model:                  MixedLM       Dependent Variable:       Value 
+No. Observations:       1805          Method:                   REML  
+No. Groups:             2             Scale:                    0.0216
+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 108711.854 -0.000 1.000 -213071.318 213071.318
+merged_timepoint -0.001      0.000 -2.744 0.006      -0.002     -0.000
+Group Var         0.000                                               
+======================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.2094  0.001  0.1656  0.2531   True
+     0      7  -0.0093    0.9 -0.0555  0.0368  False
+     0     14   0.0623 0.0014  0.0167  0.1078   True
+     0     21   0.0736  0.001  0.0281  0.1192   True
+     0     28   0.0291 0.4942 -0.0182  0.0764  False
+     3      7  -0.2187  0.001 -0.2613 -0.1761   True
+     3     14  -0.1471  0.001  -0.189 -0.1052   True
+     3     21  -0.1357  0.001 -0.1776 -0.0938   True
+     3     28  -0.1803  0.001  -0.224 -0.1365   True
+     7     14   0.0716  0.001  0.0272   0.116   True
+     7     21    0.083  0.001  0.0386  0.1274   True
+     7     28   0.0384 0.1658 -0.0078  0.0846  False
+    14     21   0.0114    0.9 -0.0324  0.0551  False
+    14     28  -0.0332 0.2989 -0.0787  0.0124  False
+    21     28  -0.0445 0.0595 -0.0901   0.001  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0574 0.0037  0.0126  0.1023   True
+     0      7   0.0266 0.4446 -0.0148  0.0681  False
+     0     14   0.0076    0.9 -0.0322  0.0474  False
+     0     21   0.0399 0.1239 -0.0056  0.0854  False
+     0     28   0.0154    0.9 -0.0277  0.0586  False
+     3      7  -0.0308 0.3838 -0.0763  0.0147  False
+     3     14  -0.0498 0.0159 -0.0939 -0.0058   True
+     3     21  -0.0175    0.9 -0.0668  0.0317  False
+     3     28   -0.042 0.1122 -0.0891  0.0051  False
+     7     14   -0.019 0.7332 -0.0596  0.0215  False
+     7     21   0.0133    0.9 -0.0329  0.0594  False
+     7     28  -0.0112    0.9 -0.0551  0.0327  False
+    14     21   0.0323 0.3056 -0.0123   0.077  False
+    14     28   0.0078    0.9 -0.0344  0.0501  False
+    21     28  -0.0245 0.6627 -0.0722  0.0232  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[7.29267979e-10]	Yes
+Stroke	Sham	14	[2.99931915e-08]	Yes
+Stroke	Sham	21	[0.04196674]	Yes
+Stroke	Sham	28	[0.01108557]	Yes
+Stroke	Sham	7	[0.01193809]	Yes
+Stroke	Sham	0	[0.18879961]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CReT_MOp-TRN_contralesional_CCcut_0_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CReT_MOp-TRN_contralesional_CCcut_0
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      1805         Method:                  REML  
+No. Groups:            2            Scale:                   0.0125
+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 82678.620 0.000 1.000 -162047.118 162047.118
+merged_timepoint 0.001     0.000 4.874 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  -0.0494  0.001 -0.0813 -0.0176   True
+     0      7  -0.0389 0.0124 -0.0725 -0.0053   True
+     0     14  -0.0079    0.9 -0.0411  0.0252  False
+     0     21  -0.0061    0.9 -0.0392   0.027  False
+     0     28   0.0209 0.5062 -0.0135  0.0553  False
+     3      7   0.0105    0.9 -0.0205  0.0415  False
+     3     14   0.0415 0.0015   0.011   0.072   True
+     3     21   0.0433  0.001  0.0128  0.0738   True
+     3     28   0.0703  0.001  0.0385  0.1022   True
+     7     14    0.031 0.0686 -0.0013  0.0633  False
+     7     21   0.0328  0.044  0.0005  0.0651   True
+     7     28   0.0598  0.001  0.0263  0.0934   True
+    14     21   0.0018    0.9   -0.03  0.0336  False
+    14     28   0.0288 0.1292 -0.0043   0.062  False
+    21     28    0.027 0.1834 -0.0061  0.0602  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0187 0.7939 -0.0244 0.0618  False
+     0      7     0.01    0.9 -0.0298 0.0498  False
+     0     14   0.0498 0.0029  0.0116  0.088   True
+     0     21   0.0396 0.1025 -0.0042 0.0833  False
+     0     28   0.0154 0.8947 -0.0261  0.057  False
+     3      7  -0.0087    0.9 -0.0525 0.0351  False
+     3     14   0.0311 0.2884 -0.0112 0.0734  False
+     3     21   0.0209 0.7812 -0.0265 0.0683  False
+     3     28  -0.0032    0.9 -0.0485 0.0421  False
+     7     14   0.0398 0.0419  0.0009 0.0788   True
+     7     21   0.0296 0.4018 -0.0148  0.074  False
+     7     28   0.0055    0.9 -0.0367 0.0476  False
+    14     21  -0.0102    0.9 -0.0532 0.0327  False
+    14     28  -0.0343  0.153  -0.075 0.0063  False
+    21     28  -0.0241 0.6417   -0.07 0.0218  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00074341]	Yes
+Stroke	Sham	14	[0.05657858]	No
+Stroke	Sham	21	[0.46579048]	No
+Stroke	Sham	28	[0.00316567]	Yes
+Stroke	Sham	7	[0.03031475]	Yes
+Stroke	Sham	0	[0.00881509]	Yes

output/Final_Quantitative_output/mixed_model_analysis/ad_CReT_MOp-TRN_contralesional_CCcut_1_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CReT_MOp-TRN_contralesional_CCcut_1
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      1805         Method:                  REML  
+No. Groups:            2            Scale:                   0.0125
+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 82678.620 0.000 1.000 -162047.118 162047.118
+merged_timepoint 0.001     0.000 4.874 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  -0.0494  0.001 -0.0813 -0.0176   True
+     0      7  -0.0389 0.0124 -0.0725 -0.0053   True
+     0     14  -0.0079    0.9 -0.0411  0.0252  False
+     0     21  -0.0061    0.9 -0.0392   0.027  False
+     0     28   0.0209 0.5062 -0.0135  0.0553  False
+     3      7   0.0105    0.9 -0.0205  0.0415  False
+     3     14   0.0415 0.0015   0.011   0.072   True
+     3     21   0.0433  0.001  0.0128  0.0738   True
+     3     28   0.0703  0.001  0.0385  0.1022   True
+     7     14    0.031 0.0686 -0.0013  0.0633  False
+     7     21   0.0328  0.044  0.0005  0.0651   True
+     7     28   0.0598  0.001  0.0263  0.0934   True
+    14     21   0.0018    0.9   -0.03  0.0336  False
+    14     28   0.0288 0.1292 -0.0043   0.062  False
+    21     28    0.027 0.1834 -0.0061  0.0602  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0187 0.7939 -0.0244 0.0618  False
+     0      7     0.01    0.9 -0.0298 0.0498  False
+     0     14   0.0498 0.0029  0.0116  0.088   True
+     0     21   0.0396 0.1025 -0.0042 0.0833  False
+     0     28   0.0154 0.8947 -0.0261  0.057  False
+     3      7  -0.0087    0.9 -0.0525 0.0351  False
+     3     14   0.0311 0.2884 -0.0112 0.0734  False
+     3     21   0.0209 0.7812 -0.0265 0.0683  False
+     3     28  -0.0032    0.9 -0.0485 0.0421  False
+     7     14   0.0398 0.0419  0.0009 0.0788   True
+     7     21   0.0296 0.4018 -0.0148  0.074  False
+     7     28   0.0055    0.9 -0.0367 0.0476  False
+    14     21  -0.0102    0.9 -0.0532 0.0327  False
+    14     28  -0.0343  0.153  -0.075 0.0063  False
+    21     28  -0.0241 0.6417   -0.07 0.0218  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00074341]	Yes
+Stroke	Sham	14	[0.05657858]	No
+Stroke	Sham	21	[0.46579048]	No
+Stroke	Sham	28	[0.00316567]	Yes
+Stroke	Sham	7	[0.03031475]	Yes
+Stroke	Sham	0	[0.00881509]	Yes

output/Final_Quantitative_output/mixed_model_analysis/ad_CReT_MOp-TRN_contralesional_CCcut_2_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CReT_MOp-TRN_contralesional_CCcut_2
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      1805         Method:                  REML  
+No. Groups:            2            Scale:                   0.0125
+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 82678.620 0.000 1.000 -162047.118 162047.118
+merged_timepoint 0.001     0.000 4.874 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  -0.0494  0.001 -0.0813 -0.0176   True
+     0      7  -0.0389 0.0124 -0.0725 -0.0053   True
+     0     14  -0.0079    0.9 -0.0411  0.0252  False
+     0     21  -0.0061    0.9 -0.0392   0.027  False
+     0     28   0.0209 0.5062 -0.0135  0.0553  False
+     3      7   0.0105    0.9 -0.0205  0.0415  False
+     3     14   0.0415 0.0015   0.011   0.072   True
+     3     21   0.0433  0.001  0.0128  0.0738   True
+     3     28   0.0703  0.001  0.0385  0.1022   True
+     7     14    0.031 0.0686 -0.0013  0.0633  False
+     7     21   0.0328  0.044  0.0005  0.0651   True
+     7     28   0.0598  0.001  0.0263  0.0934   True
+    14     21   0.0018    0.9   -0.03  0.0336  False
+    14     28   0.0288 0.1292 -0.0043   0.062  False
+    21     28    0.027 0.1834 -0.0061  0.0602  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0187 0.7939 -0.0244 0.0618  False
+     0      7     0.01    0.9 -0.0298 0.0498  False
+     0     14   0.0498 0.0029  0.0116  0.088   True
+     0     21   0.0396 0.1025 -0.0042 0.0833  False
+     0     28   0.0154 0.8947 -0.0261  0.057  False
+     3      7  -0.0087    0.9 -0.0525 0.0351  False
+     3     14   0.0311 0.2884 -0.0112 0.0734  False
+     3     21   0.0209 0.7812 -0.0265 0.0683  False
+     3     28  -0.0032    0.9 -0.0485 0.0421  False
+     7     14   0.0398 0.0419  0.0009 0.0788   True
+     7     21   0.0296 0.4018 -0.0148  0.074  False
+     7     28   0.0055    0.9 -0.0367 0.0476  False
+    14     21  -0.0102    0.9 -0.0532 0.0327  False
+    14     28  -0.0343  0.153  -0.075 0.0063  False
+    21     28  -0.0241 0.6417   -0.07 0.0218  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00074341]	Yes
+Stroke	Sham	14	[0.05657858]	No
+Stroke	Sham	21	[0.46579048]	No
+Stroke	Sham	28	[0.00316567]	Yes
+Stroke	Sham	7	[0.03031475]	Yes
+Stroke	Sham	0	[0.00881509]	Yes

output/Final_Quantitative_output/mixed_model_analysis/ad_CReT_MOp-TRN_contralesional_CCcut_3_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CReT_MOp-TRN_contralesional_CCcut_3
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      1805         Method:                  REML  
+No. Groups:            2            Scale:                   0.0125
+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 82678.620 0.000 1.000 -162047.118 162047.118
+merged_timepoint 0.001     0.000 4.874 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  -0.0494  0.001 -0.0813 -0.0176   True
+     0      7  -0.0389 0.0124 -0.0725 -0.0053   True
+     0     14  -0.0079    0.9 -0.0411  0.0252  False
+     0     21  -0.0061    0.9 -0.0392   0.027  False
+     0     28   0.0209 0.5062 -0.0135  0.0553  False
+     3      7   0.0105    0.9 -0.0205  0.0415  False
+     3     14   0.0415 0.0015   0.011   0.072   True
+     3     21   0.0433  0.001  0.0128  0.0738   True
+     3     28   0.0703  0.001  0.0385  0.1022   True
+     7     14    0.031 0.0686 -0.0013  0.0633  False
+     7     21   0.0328  0.044  0.0005  0.0651   True
+     7     28   0.0598  0.001  0.0263  0.0934   True
+    14     21   0.0018    0.9   -0.03  0.0336  False
+    14     28   0.0288 0.1292 -0.0043   0.062  False
+    21     28    0.027 0.1834 -0.0061  0.0602  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0187 0.7939 -0.0244 0.0618  False
+     0      7     0.01    0.9 -0.0298 0.0498  False
+     0     14   0.0498 0.0029  0.0116  0.088   True
+     0     21   0.0396 0.1025 -0.0042 0.0833  False
+     0     28   0.0154 0.8947 -0.0261  0.057  False
+     3      7  -0.0087    0.9 -0.0525 0.0351  False
+     3     14   0.0311 0.2884 -0.0112 0.0734  False
+     3     21   0.0209 0.7812 -0.0265 0.0683  False
+     3     28  -0.0032    0.9 -0.0485 0.0421  False
+     7     14   0.0398 0.0419  0.0009 0.0788   True
+     7     21   0.0296 0.4018 -0.0148  0.074  False
+     7     28   0.0055    0.9 -0.0367 0.0476  False
+    14     21  -0.0102    0.9 -0.0532 0.0327  False
+    14     28  -0.0343  0.153  -0.075 0.0063  False
+    21     28  -0.0241 0.6417   -0.07 0.0218  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00074341]	Yes
+Stroke	Sham	14	[0.05657858]	No
+Stroke	Sham	21	[0.46579048]	No
+Stroke	Sham	28	[0.00316567]	Yes
+Stroke	Sham	7	[0.03031475]	Yes
+Stroke	Sham	0	[0.00881509]	Yes

output/Final_Quantitative_output/mixed_model_analysis/ad_CReT_MOp-TRN_contralesional_CCcut_4_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CReT_MOp-TRN_contralesional_CCcut_4
+               Mixed Linear Model Regression Results
+===================================================================
+Model:                 MixedLM      Dependent Variable:      Value 
+No. Observations:      1805         Method:                  REML  
+No. Groups:            2            Scale:                   0.0125
+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 82678.620 0.000 1.000 -162047.118 162047.118
+merged_timepoint 0.001     0.000 4.874 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  -0.0494  0.001 -0.0813 -0.0176   True
+     0      7  -0.0389 0.0124 -0.0725 -0.0053   True
+     0     14  -0.0079    0.9 -0.0411  0.0252  False
+     0     21  -0.0061    0.9 -0.0392   0.027  False
+     0     28   0.0209 0.5062 -0.0135  0.0553  False
+     3      7   0.0105    0.9 -0.0205  0.0415  False
+     3     14   0.0415 0.0015   0.011   0.072   True
+     3     21   0.0433  0.001  0.0128  0.0738   True
+     3     28   0.0703  0.001  0.0385  0.1022   True
+     7     14    0.031 0.0686 -0.0013  0.0633  False
+     7     21   0.0328  0.044  0.0005  0.0651   True
+     7     28   0.0598  0.001  0.0263  0.0934   True
+    14     21   0.0018    0.9   -0.03  0.0336  False
+    14     28   0.0288 0.1292 -0.0043   0.062  False
+    21     28    0.027 0.1834 -0.0061  0.0602  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0187 0.7939 -0.0244 0.0618  False
+     0      7     0.01    0.9 -0.0298 0.0498  False
+     0     14   0.0498 0.0029  0.0116  0.088   True
+     0     21   0.0396 0.1025 -0.0042 0.0833  False
+     0     28   0.0154 0.8947 -0.0261  0.057  False
+     3      7  -0.0087    0.9 -0.0525 0.0351  False
+     3     14   0.0311 0.2884 -0.0112 0.0734  False
+     3     21   0.0209 0.7812 -0.0265 0.0683  False
+     3     28  -0.0032    0.9 -0.0485 0.0421  False
+     7     14   0.0398 0.0419  0.0009 0.0788   True
+     7     21   0.0296 0.4018 -0.0148  0.074  False
+     7     28   0.0055    0.9 -0.0367 0.0476  False
+    14     21  -0.0102    0.9 -0.0532 0.0327  False
+    14     28  -0.0343  0.153  -0.075 0.0063  False
+    21     28  -0.0241 0.6417   -0.07 0.0218  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00074341]	Yes
+Stroke	Sham	14	[0.05657858]	No
+Stroke	Sham	21	[0.46579048]	No
+Stroke	Sham	28	[0.00316567]	Yes
+Stroke	Sham	7	[0.03031475]	Yes
+Stroke	Sham	0	[0.00881509]	Yes