final results

code/correlation_between_bahavior_and_DTI.py

@@ -1,6 +1,6 @@
 import os
 import pandas as pd
-from scipy.stats import spearmanr, shapiro
+from scipy.stats import spearmanr, shapiro, pearsonr
 import numpy as np
 from statsmodels.stats.multitest import multipletests
 
@@ -13,64 +13,72 @@ parent_dir = os.path.dirname(code_dir)
 # Step 4: Save the resulting dataframe to a CSV file
 input_file_path = os.path.join(parent_dir, 'output', "Final_Quantitative_output", 'Quantitative_results_from_dwi_processing_merged_with_behavior_data.csv')
 
+
 df = pd.read_csv(input_file_path)
 
+df = df[(df["merged_timepoint"]<40)]
 
-df_f1 = (df["dialation_amount"] == 2)
 
+#%%
 # Empty list to store the results
 results = []
-
-# Iterate over unique values of 'Group', 'merged_timepoint', 'Qtype', and 'mask_name'
-for ss in df["Group"].unique():
-    for time_point in df["merged_timepoint"].unique():
-        for qq in df["Qtype"].unique():
-            for mm in df["mask_name"].unique():
-                # Filter the DataFrame for the current combination of 'Group', 'merged_timepoint', 'Qtype', and 'mask_name'
-                df_f2 = df[df_f1 & (df["Group"] == ss) & (df["merged_timepoint"] == time_point) & (df["Qtype"] == qq) & (df["mask_name"] == mm)]
-
-                # Remove rows with NaN values in 'Value' or 'averageScore' columns
-                df_f2 = df_f2.dropna(subset=['Value', 'averageScore'])
-
-                if not df_f2.empty:
-
-                    correlation_coefficient, p_value = spearmanr(df_f2["Value"], df_f2["averageScore"])
-                    # Calculate Shapiro-Wilk test for normality
-                    shapiro_statValue, shapiro_pvalueQValue = shapiro(df_f2["Value"])
-                    shapiro_statScore, shapiro_pvalueBehavior = shapiro(df_f2["averageScore"])
-                    
-
-                    # Store the results in a dictionary
-                    result = {'Group': ss, 'merged_timepoint': time_point, 'Qtype': qq, 'mask_name': mm, 
-                              'Pval_corr': p_value, 'R_corr': correlation_coefficient,
-                              'shapiro-wilk_pvalue_qtype': shapiro_pvalueQValue,'shapiro-wilk_pvalue_behavior': shapiro_pvalueBehavior}
-
-                    # Append the dictionary to the results list
-                    results.append(result)
-                else:
-                    print(
-                        f"No valid data found for Group: {ss}, merged_timepoint: {time_point}, Qtype: {qq}, and mask_name: {mm}. Skipping.")
+for dd in df["dialation_amount"].unique():
+    # Iterate over unique values of 'Group', 'merged_timepoint', 'Qtype', and 'mask_name'
+    for ss in df["Group"].unique():
+        for time_point in df["merged_timepoint"].unique():
+            for qq in df["Qtype"].unique():
+                for mm in df["mask_name"].unique():
+                    # Filter the DataFrame for the current combination of 'Group', 'merged_timepoint', 'Qtype', and 'mask_name'
+                    df_f2 = df[(df["Group"] == ss) & (df["merged_timepoint"] == time_point) & (df["Qtype"] == qq) & (df["mask_name"] == mm) &  (df["dialation_amount"] == dd)]
+    
+                    # Remove rows with NaN values in 'Value' or 'averageScore' columns
+                    df_f2 = df_f2.dropna(subset=['Value', 'averageScore'])
+    
+                    if not df_f2.empty:
+                        
+                        shapiro_statValue, shapiro_pvalueQValue = shapiro(df_f2["Value"])
+                        shapiro_statScore, shapiro_pvalueBehavior = shapiro(df_f2["averageScore"])
+                        
+                        if shapiro_pvalueQValue < 0.05 or shapiro_pvalueBehavior < 0.05:
+                            correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2["averageScore"])
+                        else:
+                            correlation_coefficient, p_value = spearmanr(df_f2["Value"], df_f2["averageScore"])
+                       
+    
+                        # Store the results in a dictionary
+                        result = {'Group': ss, 'merged_timepoint': time_point, 'Qtype': qq, 'mask_name': mm, 
+                                  'Pval': p_value, 'R': correlation_coefficient,
+                                  'shapiro-wilk_pvalue_qtype': shapiro_pvalueQValue,'shapiro-wilk_pvalue_behavior': shapiro_pvalueBehavior,"dialation_amount":dd}
+    
+                        # Append the dictionary to the results list
+                        results.append(result)
+                    else:
+                        print(
+                            f"No valid data found for Group: {ss}, merged_timepoint: {time_point}, Qtype: {qq}, and mask_name: {mm}. Skipping.")
 
 # Create a DataFrame from the results list
 correlation_results_df = pd.DataFrame(results)
-
-# Apply FDR correction to p-values within each Qtype and each Group separately
-unique_qtypes = correlation_results_df['Qtype'].unique()
 unique_groups = df["Group"].unique()
 unique_masks = df["mask_name"].unique()
-
-for qtype in unique_qtypes:
-    for mask in unique_masks:
-        mask_mask = correlation_results_df['mask_name'] == mask
-        qtype_group_mask = mask_mask & (correlation_results_df['Qtype'] == qtype)
-        p_values = correlation_results_df[qtype_group_mask]['Pval_corr']
-        rejected, p_values_corrected, _, _ = multipletests(p_values, method='fdr_bh')
-
-        # Assign the corrected p-values to the DataFrame
-        correlation_results_df.loc[qtype_group_mask, 'Pval_corr_corrected'] = p_values_corrected
-        
+unique_tp = df["merged_timepoint"].unique()
+unique_dd=df["dialation_amount"].unique()
+for dd in unique_dd:
+    for tt in unique_tp:
+        for mask in unique_masks:
+            for group in unique_groups:
+                time_mask = correlation_results_df['merged_timepoint'] == tt
+                mask_mask = correlation_results_df['mask_name'] == mask
+                group_mask = correlation_results_df['Group'] == group
+                dd_mask =  correlation_results_df["dialation_amount"] == dd
+                combined_mask = time_mask & mask_mask & group_mask & dd_mask
+                
+                p_values = correlation_results_df[combined_mask]['Pval']
+                rejected, p_values_corrected, _, _ = multipletests(p_values, method='fdr_bh')
+    
+                # Assign the corrected p-values to the DataFrame
+                correlation_results_df.loc[combined_mask, 'Pval_corrected'] = p_values_corrected
 # Define the output file path
-output_file_path = os.path.join(parent_dir, 'output', "Correlation_with_behavior", 'correlation_dti_with_behavior5.csv')
+output_file_path = os.path.join(parent_dir, 'output', "Correlation_with_behavior", 'correlation_dti_with_behavior.csv')
 
 # Save the correlation results DataFrame to a CSV file
 correlation_results_df.to_csv(output_file_path, index=False)

code/correlation_between_bahavior_and_DTI_anovaSpecific.py

@@ -24,7 +24,7 @@ df_annova2 = df_annova[df_annova["p_value"]<=0.05]
 
 df_temp = pd.read_csv(input_file_path)
 # Filter df based on condition
-df_f1 = df_temp[df_temp["dialation_amount"] == 0]
+df_f1 = df_temp[df_temp["dialation_amount"] == 2]
 
 # Merge df_f1 and df_annova2 on common columns "Qtype" and "mask_name"
 merged_df = pd.merge(df_f1, df_annova2[['Qtype', 'mask_name', 'p_value']], on=['Qtype', 'mask_name'], how='left')
@@ -58,7 +58,7 @@ for ss in df["Group"].unique():
                     shapiro_statScore, shapiro_pvalueBehavior = shapiro(df_f2["averageScore"])
                     
                     if shapiro_pvalueQValue < 0.05 or shapiro_pvalueBehavior < 0.05:
-                        correlation_coefficient, p_value = spearmanr(df_f2["Value"], df_f2["averageScore"])
+                        correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2["averageScore"])
                     else:
                         correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2["averageScore"])
                    
@@ -76,24 +76,25 @@ for ss in df["Group"].unique():
 
 # Create a DataFrame from the results list
 correlation_results_df = pd.DataFrame(results)
-
-# Apply FDR correction to p-values within each Qtype and each Group separately
-unique_qtypes = correlation_results_df['Qtype'].unique()
 unique_groups = df["Group"].unique()
 unique_masks = df["mask_name"].unique()
 unique_tp = df["merged_timepoint"].unique()
-for qtype in unique_qtypes:
-    for tt in unique_tp:
-        time_mask = correlation_results_df['merged_timepoint'] == tt
-        qtype_group_mask = time_mask  & (correlation_results_df['Qtype'] == qtype)
-        p_values = correlation_results_df[qtype_group_mask]['Pval']
-        rejected, p_values_corrected, _, _ = multipletests(p_values, method='fdr_bh')
-    
-        # Assign the corrected p-values to the DataFrame
-        correlation_results_df.loc[qtype_group_mask, 'Pval_corrected'] = p_values_corrected
-        
+
+for tt in unique_tp:
+    for mask in unique_masks:
+        for group in unique_groups:
+            time_mask = correlation_results_df['merged_timepoint'] == tt
+            mask_mask = correlation_results_df['mask_name'] == mask
+            group_mask = correlation_results_df['Group'] == group
+            combined_mask = time_mask & mask_mask & group_mask
+            
+            p_values = correlation_results_df[combined_mask]['Pval']
+            rejected, p_values_corrected, _, _ = multipletests(p_values, method='fdr_bh')
+
+            # Assign the corrected p-values to the DataFrame
+            correlation_results_df.loc[combined_mask, 'Pval_corrected'] = p_values_corrected
 # Define the output file path
-output_file_path = os.path.join(parent_dir, 'output', "Correlation_with_behavior", 'correlation_dti_with_behavior6.csv')
+output_file_path = os.path.join(parent_dir, 'output', "Correlation_with_behavior", 'correlation_dti_with_behavior.csv')
 
 # Save the correlation results DataFrame to a CSV file
 correlation_results_df.to_csv(output_file_path, index=False)

code/incooparate_behavior_data.py

@@ -28,7 +28,7 @@ merged_df = pd.merge(df_q, df_b[['subjectID', 'merged_timepoint', 'paw_dragZ-sco
 
 
 # Define the output file path
-output_file_path = os.path.join(parent_dir, 'output', 'Final_Quantitative_output&behavior_data.csv')
+output_file_path = os.path.join(parent_dir, 'output', 'Final_Quantitative_output','Quantitative_results_from_dwi_processing_merged_with_behavior_data.csv')
 
 # Save the merged DataFrame as a CSV file
 merged_df.to_csv(output_file_path, index=False)

code/plotting_quantitative_dti_values.py

@@ -24,7 +24,10 @@ def PlotBoxplot(filtered_df, qq, mm, output_folder):
     output_folder (str): Path to the output folder to save images.
     """
     # Set the color palette to Set2
-    sns.set_palette("Set1")
+    sns.set_palette("Set2")
+    
+    # Set the figure size to 18 cm in width
+    plt.figure(figsize=(18/2.54, 4))  # Convert 18 cm to inches
     
     # Create a boxplot
     sns.boxplot(data=filtered_df, x="merged_timepoint", y="Value", hue="Group", fliersize=3 ,flierprops={"marker": "o"})
@@ -44,7 +47,6 @@ def PlotBoxplot(filtered_df, qq, mm, output_folder):
     # Close the plot to avoid displaying it
     plt.close()
 
-
 # Get the directory where the code file is located
 code_dir = os.path.dirname(os.path.abspath(__file__))
 
@@ -56,11 +58,23 @@ mixed_model_dir = os.path.join(parent_dir, 'output', "Final_Quantitative_output"
 os.makedirs(mixed_model_dir, exist_ok=True)
 
 # Step 4: Save the resulting dataframe to a CSV file
-input_file_path = os.path.join(parent_dir, 'output', "Final_Quantitative_output", 'Quantitative_results_from_dwi_processing_merged_with_behavior_data.csv')
+input_file_path = os.path.join(parent_dir, 'output', "Final_Quantitative_output", 'Quantitative_results_from_dwi_processing.csv')
 df = pd.read_csv(input_file_path)
+qc_csv = os.path.join(parent_dir,"input","AIDAqc_ouptut_for_data","Voting_remapped.csv")
+df_qc = pd.read_csv(qc_csv)
+df_qc_5 = df_qc[(df_qc["Voting outliers (from 5)"]>4) & (df_qc["sequence_type"]=="diff")]
+
 
 # Filtering the dataframe based on conditions
-df_f1 = df[(df["dialation_amount"] == 0) & (~df["merged_timepoint"].isin([42, 56]))]
+df_f0 = df[(df["dialation_amount"] == 2) & (~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)
+
+# Drop the entries that are present in both df_f1 and df_qc_5
+df_f1 = merged_df[merged_df["_merge"] == "left_only"].drop(columns=["_merge"])
+# Drop unnecessary columns with NaN values
+df_f1 = df_f1.dropna(axis=1, how="all")
+
 
 # Create lists to store results and terminal output
 results = []

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp(dilated)_cut.tt_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOp(dilated)_cut.tt
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       364          Method:                  REML  
-No. Groups:             2            Scale:                   0.0169
-Min. group size:        158          Log-Likelihood:          inf   
-Max. group size:        206          Converged:               Yes   
-Mean group size:        182.0                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 254318.725 0.000 1.000 -498455.542 498455.542
-merged_timepoint 0.003      0.001 4.360 0.000       0.002      0.004
-Group Var        0.000                                              
-====================================================================
-
-Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3  -0.0487 0.6093 -0.1372 0.0397  False
-     0      7  -0.0067 0.9999 -0.1001 0.0868  False
-     0     14   0.0531 0.5611  -0.039 0.1452  False
-     0     21   0.0825 0.1078 -0.0096 0.1746  False
-     0     28   0.0703 0.2845 -0.0254 0.1659  False
-     3      7   0.0421 0.7314 -0.0448 0.1289  False
-     3     14   0.1018 0.0095  0.0163 0.1873   True
-     3     21   0.1312 0.0002  0.0457 0.2167   True
-     3     28    0.119 0.0023  0.0297 0.2083   True
-     7     14   0.0597  0.407 -0.0309 0.1504  False
-     7     21   0.0892 0.0567 -0.0015 0.1798  False
-     7     28   0.0769 0.1796 -0.0173 0.1711  False
-    14     21   0.0294 0.9334 -0.0599 0.1187  False
-    14     28   0.0172 0.9948 -0.0757 0.1101  False
-    21     28  -0.0122  0.999 -0.1052 0.0807  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0034    1.0 -0.0992  0.106  False
-     0      7   0.0182 0.9944 -0.0791 0.1154  False
-     0     14   0.0682 0.2888 -0.0252 0.1615  False
-     0     21   0.0278 0.9749  -0.079 0.1347  False
-     0     28   0.0321 0.9423 -0.0692 0.1335  False
-     3      7   0.0148 0.9985 -0.0894 0.1189  False
-     3     14   0.0648 0.4312 -0.0358 0.1653  False
-     3     21   0.0244 0.9892 -0.0887 0.1376  False
-     3     28   0.0287 0.9726 -0.0793 0.1367  False
-     7     14     0.05 0.6534 -0.0451 0.1451  False
-     7     21   0.0097 0.9998 -0.0987  0.118  False
-     7     28   0.0139 0.9988  -0.089 0.1169  False
-    14     21  -0.0403 0.8765 -0.1452 0.0645  False
-    14     28  -0.0361 0.9006 -0.1354 0.0632  False
-    21     28   0.0043    1.0 -0.1078 0.1163  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.08875339]	No
-Stroke	Sham	14	[0.46650669]	No
-Stroke	Sham	21	[0.23873131]	No
-Stroke	Sham	28	[0.27736324]	No
-Stroke	Sham	7	[0.14738904]	No
-Stroke	Sham	0	[0.83188168]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp_MOp_cut.tt_log.txt

@@ -1,67 +1,67 @@
 Model Name: ad_CC_MOp_MOp_cut.tt
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       364          Method:                  REML  
-No. Groups:             2            Scale:                   0.0190
-Min. group size:        158          Log-Likelihood:          inf   
-Max. group size:        206          Converged:               Yes   
-Mean group size:        182.0                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 269751.770 0.000 1.000 -528703.754 528703.754
-merged_timepoint 0.003      0.001 3.545 0.000       0.001      0.004
-Group Var        0.000                                              
-====================================================================
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0103
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.001 2.180 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  -0.0737 0.2272 -0.1686 0.0212  False
-     0      7   0.0041    1.0 -0.0962 0.1044  False
-     0     14   0.0419 0.8265 -0.0569 0.1408  False
-     0     21   0.0749 0.2518  -0.024 0.1738  False
-     0     28   0.0472 0.7724 -0.0555 0.1498  False
-     3      7   0.0778 0.1612 -0.0155  0.171  False
-     3     14   0.1156 0.0049  0.0239 0.2074   True
-     3     21   0.1486 0.0001  0.0568 0.2403   True
-     3     28   0.1208 0.0048   0.025 0.2167   True
-     7     14   0.0378  0.873 -0.0594 0.1351  False
-     7     21   0.0708 0.2944 -0.0265 0.1681  False
-     7     28   0.0431 0.8239 -0.0581 0.1442  False
-    14     21    0.033 0.9207 -0.0629 0.1288  False
-    14     28   0.0052    1.0 -0.0945  0.105  False
-    21     28  -0.0277 0.9673 -0.1275  0.072  False
+     0      3   0.0146 0.9911 -0.0558  0.085  False
+     0      7   0.0119 0.9974 -0.0625 0.0863  False
+     0     14   0.0364 0.7101 -0.0369 0.1097  False
+     0     21   0.0541 0.2795 -0.0192 0.1274  False
+     0     28   0.0558 0.2868 -0.0203 0.1319  False
+     3      7  -0.0027    1.0 -0.0719 0.0664  False
+     3     14   0.0218 0.9409 -0.0463 0.0898  False
+     3     21   0.0395 0.5531 -0.0285 0.1075  False
+     3     28   0.0412 0.5547 -0.0299 0.1123  False
+     7     14   0.0245 0.9249 -0.0477 0.0966  False
+     7     21   0.0422 0.5442 -0.0299 0.1143  False
+     7     28   0.0439 0.5436 -0.0311 0.1189  False
+    14     21   0.0177 0.9796 -0.0533 0.0888  False
+    14     28   0.0194 0.9744 -0.0545 0.0934  False
+    21     28   0.0017    1.0 -0.0723 0.0757  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0164 0.9977 -0.0889 0.1217  False
-     0      7   0.0291 0.9594 -0.0707 0.1289  False
-     0     14    0.073 0.2445 -0.0228 0.1688  False
-     0     21   0.0214 0.9932 -0.0882  0.131  False
-     0     28   0.0256 0.9803 -0.0784 0.1297  False
-     3      7   0.0127 0.9994 -0.0942 0.1196  False
-     3     14   0.0566 0.6109 -0.0466 0.1598  False
-     3     21    0.005    1.0 -0.1111 0.1211  False
-     3     28   0.0093 0.9999 -0.1016 0.1201  False
-     7     14   0.0439 0.7854 -0.0537 0.1415  False
-     7     21  -0.0077    1.0 -0.1189 0.1035  False
-     7     28  -0.0034    1.0 -0.1091 0.1022  False
-    14     21  -0.0516  0.737 -0.1592  0.056  False
-    14     28  -0.0473 0.7617 -0.1492 0.0546  False
-    21     28   0.0042    1.0 -0.1107 0.1192  False
+     0      3   0.0286 0.9069 -0.0515 0.1087  False
+     0      7   0.0222 0.9588 -0.0538 0.0982  False
+     0     14   0.0286 0.8668 -0.0443 0.1016  False
+     0     21    0.002    1.0 -0.0814 0.0855  False
+     0     28   0.0156 0.9929 -0.0636 0.0948  False
+     3      7  -0.0064 0.9999 -0.0878 0.0749  False
+     3     14      0.0    1.0 -0.0785 0.0785  False
+     3     21  -0.0266 0.9535  -0.115 0.0618  False
+     3     28   -0.013 0.9977 -0.0974 0.0713  False
+     7     14   0.0064 0.9999 -0.0678 0.0807  False
+     7     21  -0.0202 0.9831 -0.1048 0.0645  False
+     7     28  -0.0066 0.9999  -0.087 0.0738  False
+    14     21  -0.0266 0.9362 -0.1085 0.0553  False
+    14     28  -0.0131 0.9966 -0.0906 0.0645  False
+    21     28   0.0135 0.9977  -0.074 0.1011  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.01493831]	Yes
-Stroke	Sham	14	[0.25081718]	No
-Stroke	Sham	21	[0.19163849]	No
-Stroke	Sham	28	[0.72810399]	No
-Stroke	Sham	7	[0.09183713]	No
-Stroke	Sham	0	[0.79962711]	No
+Stroke	Sham	3	[0.30854775]	No
+Stroke	Sham	14	[0.39929633]	No
+Stroke	Sham	21	[0.27388309]	No
+Stroke	Sham	28	[0.34448089]	No
+Stroke	Sham	7	[0.02614731]	Yes
+Stroke	Sham	0	[0.55196568]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs_MOs_cut.tt_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CC_MOs_MOs_cut.tt
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       364          Method:                  REML  
-No. Groups:             2            Scale:                   0.0196
-Min. group size:        158          Log-Likelihood:          inf   
-Max. group size:        206          Converged:               Yes   
-Mean group size:        182.0                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 273441.060 0.000 1.000 -535934.630 535934.630
-merged_timepoint 0.002      0.001 3.026 0.002       0.001      0.004
-Group Var        0.000                                              
-====================================================================
-
-Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3  -0.0378 0.8255 -0.1269 0.0512  False
-     0      7   0.0271 0.9619  -0.067 0.1212  False
-     0     14   0.0346 0.8917 -0.0582 0.1273  False
-     0     21     0.08 0.1343 -0.0127 0.1728  False
-     0     28   0.0474 0.7163 -0.0489 0.1438  False
-     3      7   0.0649 0.2735 -0.0226 0.1524  False
-     3     14   0.0724 0.1541 -0.0137 0.1585  False
-     3     21   0.1178 0.0016  0.0318 0.2039   True
-     3     28   0.0853 0.0739 -0.0046 0.1752  False
-     7     14   0.0075 0.9999 -0.0838 0.0987  False
-     7     21   0.0529 0.5541 -0.0383 0.1442  False
-     7     28   0.0204 0.9897 -0.0745 0.1152  False
-    14     21   0.0454 0.6937 -0.0445 0.1353  False
-    14     28   0.0129 0.9987 -0.0807 0.1064  False
-    21     28  -0.0326 0.9171 -0.1261  0.061  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0441 0.8997  -0.077 0.1652  False
-     0      7    0.032 0.9663 -0.0828 0.1469  False
-     0     14    0.051 0.7649 -0.0592 0.1613  False
-     0     21   0.0412 0.9348  -0.085 0.1673  False
-     0     28    0.044 0.8955 -0.0756 0.1637  False
-     3      7  -0.0121 0.9997 -0.1351 0.1109  False
-     3     14   0.0069    1.0 -0.1118 0.1256  False
-     3     21  -0.0029    1.0 -0.1365 0.1307  False
-     3     28  -0.0001    1.0 -0.1276 0.1275  False
-     7     14    0.019 0.9965 -0.0933 0.1313  False
-     7     21   0.0092 0.9999 -0.1188 0.1371  False
-     7     28    0.012 0.9997 -0.1095 0.1336  False
-    14     21  -0.0098 0.9999 -0.1337  0.114  False
-    14     28   -0.007    1.0 -0.1242 0.1103  False
-    21     28   0.0029    1.0 -0.1295 0.1352  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.04738631]	Yes
-Stroke	Sham	14	[0.15364267]	No
-Stroke	Sham	21	[0.65293282]	No
-Stroke	Sham	28	[0.48236813]	No
-Stroke	Sham	7	[0.22367389]	No
-Stroke	Sham	0	[0.59663061]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_SSp_ll_cut.tt_log.txt

@@ -1,67 +1,67 @@
 Model Name: ad_CC_SSp_ll_cut.tt
-                Mixed Linear Model Regression Results
-======================================================================
-Model:                  MixedLM       Dependent Variable:       Value 
-No. Observations:       364           Method:                   REML  
-No. Groups:             2             Scale:                    0.0389
-Min. group size:        158           Log-Likelihood:           inf   
-Max. group size:        206           Converged:                Yes   
-Mean group size:        182.0                                         
-----------------------------------------------------------------------
-                 Coef.   Std.Err.    z    P>|z|    [0.025     0.975]  
-----------------------------------------------------------------------
-Intercept        -0.000 385639.044 -0.000 1.000 -755838.638 755838.638
-merged_timepoint -0.003      0.001 -3.128 0.002      -0.005     -0.001
-Group Var         0.000                                               
-======================================================================
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM  Dependent Variable:  Value   
+No. Observations:    364      Method:              REML    
+No. Groups:          2        Scale:               0.0238  
+Min. group size:     158      Log-Likelihood:      154.2095
+Max. group size:     206      Converged:           Yes     
+Mean group size:     182.0                                 
+-----------------------------------------------------------
+                 Coef.  Std.Err.   z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept         0.969    0.022 43.259 0.000  0.925  1.013
+merged_timepoint -0.002    0.001 -2.572 0.010 -0.004 -0.001
+Group Var         0.001    0.007                           
+===========================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05 
 ====================================================
 group1 group2 meandiff p-adj   lower   upper  reject
 ----------------------------------------------------
-     0      3   0.3372    0.0  0.2024   0.472   True
-     0      7   0.0032    1.0 -0.1392  0.1457  False
-     0     14   0.0606 0.8162 -0.0799   0.201  False
-     0     21   0.0373  0.973 -0.1031  0.1778  False
-     0     28   0.0121 0.9999 -0.1337  0.1579  False
-     3      7   -0.334    0.0 -0.4664 -0.2015   True
-     3     14  -0.2767    0.0  -0.407 -0.1463   True
-     3     21  -0.2999    0.0 -0.4302 -0.1696   True
-     3     28  -0.3251    0.0 -0.4612  -0.189   True
-     7     14   0.0573 0.8395 -0.0808  0.1955  False
-     7     21   0.0341 0.9805  -0.104  0.1723  False
-     7     28   0.0089    1.0 -0.1348  0.1525  False
-    14     21  -0.0232 0.9965 -0.1593  0.1129  False
-    14     28  -0.0484 0.9227 -0.1901  0.0932  False
-    21     28  -0.0252 0.9957 -0.1669  0.1164  False
+     0      3   0.1872    0.0  0.0893   0.285   True
+     0      7  -0.0063    1.0 -0.1097   0.097  False
+     0     14   0.0636 0.4709 -0.0383  0.1655  False
+     0     21   0.0261 0.9771 -0.0758   0.128  False
+     0     28  -0.0063    1.0 -0.1121  0.0995  False
+     3      7  -0.1935    0.0 -0.2896 -0.0974   True
+     3     14  -0.1236  0.003 -0.2181  -0.029   True
+     3     21   -0.161    0.0 -0.2556 -0.0665   True
+     3     28  -0.1934    0.0 -0.2922 -0.0947   True
+     7     14   0.0699 0.3422 -0.0303  0.1701  False
+     7     21   0.0324 0.9381 -0.0678  0.1327  False
+     7     28      0.0    1.0 -0.1042  0.1042  False
+    14     21  -0.0375 0.8842 -0.1362  0.0613  False
+    14     28  -0.0699 0.3715 -0.1727  0.0329  False
+    21     28  -0.0324 0.9444 -0.1352  0.0704  False
 ----------------------------------------------------
 Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05 
-====================================================
-group1 group2 meandiff p-adj   lower   upper  reject
-----------------------------------------------------
-     0      3   0.1341 0.0089  0.0223  0.2459   True
-     0      7   0.0345 0.9355 -0.0715  0.1405  False
-     0     14   0.0181 0.9955 -0.0836  0.1199  False
-     0     21    0.059 0.6889 -0.0574  0.1754  False
-     0     28   0.0148 0.9988 -0.0956  0.1253  False
-     3      7  -0.0996  0.121 -0.2131  0.0139  False
-     3     14   -0.116 0.0312 -0.2255 -0.0064   True
-     3     21  -0.0751 0.4952 -0.1984  0.0481  False
-     3     28  -0.1193  0.045 -0.2369 -0.0016   True
-     7     14  -0.0164 0.9975   -0.12  0.0872  False
-     7     21   0.0245  0.991 -0.0936  0.1425  False
-     7     28  -0.0197 0.9959 -0.1318  0.0925  False
-    14     21   0.0408 0.9068 -0.0735  0.1551  False
-    14     28  -0.0033    1.0 -0.1115  0.1049  False
-    21     28  -0.0441 0.9025 -0.1662   0.078  False
-----------------------------------------------------
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.1066 0.1037 -0.0118  0.225  False
+     0      7   0.0256 0.9861 -0.0866 0.1379  False
+     0     14   0.0078 0.9999 -0.0999 0.1156  False
+     0     21   0.0236 0.9937 -0.0997  0.147  False
+     0     28   0.0079    1.0 -0.1091 0.1249  False
+     3      7   -0.081 0.3793 -0.2012 0.0392  False
+     3     14  -0.0988 0.1437 -0.2148 0.0173  False
+     3     21   -0.083 0.4474 -0.2136 0.0476  False
+     3     28  -0.0987 0.2064 -0.2233 0.0259  False
+     7     14  -0.0178 0.9972 -0.1275  0.092  False
+     7     21   -0.002    1.0  -0.127 0.1231  False
+     7     28  -0.0177 0.9981 -0.1365 0.1011  False
+    14     21   0.0158  0.999 -0.1052 0.1369  False
+    14     28   0.0001    1.0 -0.1145 0.1147  False
+    21     28  -0.0157 0.9993 -0.1451 0.1136  False
+---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.0159719]	Yes
-Stroke	Sham	14	[0.17914987]	No
-Stroke	Sham	21	[0.59998576]	No
-Stroke	Sham	28	[0.70162501]	No
-Stroke	Sham	7	[0.11978922]	No
-Stroke	Sham	0	[0.85759801]	No
+Stroke	Sham	3	[0.10576501]	No
+Stroke	Sham	14	[0.02214811]	Yes
+Stroke	Sham	21	[0.75379626]	No
+Stroke	Sham	28	[0.99747655]	No
+Stroke	Sham	7	[0.3723802]	No
+Stroke	Sham	0	[0.64144537]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_SSp_ul_cut.tt_log.txt

@@ -1,67 +1,67 @@
 Model Name: ad_CC_SSp_ul_cut.tt
-                Mixed Linear Model Regression Results
-======================================================================
-Model:                  MixedLM       Dependent Variable:       Value 
-No. Observations:       364           Method:                   REML  
-No. Groups:             2             Scale:                    0.0358
-Min. group size:        158           Log-Likelihood:           inf   
-Max. group size:        206           Converged:                Yes   
-Mean group size:        182.0                                         
-----------------------------------------------------------------------
-                 Coef.   Std.Err.    z    P>|z|    [0.025     0.975]  
-----------------------------------------------------------------------
-Intercept        -0.000 370096.668 -0.000 1.000 -725376.141 725376.141
-merged_timepoint -0.002      0.001 -2.139 0.032      -0.004     -0.000
-Group Var         0.000                                               
-======================================================================
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM   Dependent Variable:   Value 
+No. Observations:    364       Method:               REML  
+No. Groups:          2         Scale:                0.0200
+Min. group size:     158       Log-Likelihood:       inf   
+Max. group size:     206       Converged:            Yes   
+Mean group size:     182.0                                 
+-----------------------------------------------------------
+                 Coef.  Std.Err.   z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept         0.000                                    
+merged_timepoint -0.002    0.001 -2.271 0.023 -0.003 -0.000
+Group Var         0.000                                    
+===========================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05 
 ====================================================
 group1 group2 meandiff p-adj   lower   upper  reject
 ----------------------------------------------------
-     0      3   0.3161    0.0  0.1845  0.4477   True
-     0      7   0.0228 0.9971 -0.1162  0.1618  False
-     0     14   0.0752 0.6136 -0.0619  0.2123  False
-     0     21   0.0593 0.8138 -0.0777  0.1964  False
-     0     28   0.0683 0.7386  -0.074  0.2106  False
-     3      7  -0.2933    0.0 -0.4226  -0.164   True
-     3     14  -0.2409    0.0 -0.3681 -0.1137   True
-     3     21  -0.2567    0.0 -0.3839 -0.1295   True
-     3     28  -0.2478    0.0 -0.3806 -0.1149   True
-     7     14   0.0524 0.8734 -0.0824  0.1873  False
-     7     21   0.0365 0.9707 -0.0983  0.1714  False
-     7     28   0.0455 0.9373 -0.0947  0.1857  False
-    14     21  -0.0159 0.9994 -0.1487   0.117  False
-    14     28  -0.0069    1.0 -0.1452  0.1314  False
-    21     28    0.009    1.0 -0.1293  0.1472  False
+     0      3   0.1806    0.0  0.0885  0.2727   True
+     0      7   0.0033    1.0  -0.094  0.1005  False
+     0     14     0.06 0.4675 -0.0359  0.1559  False
+     0     21   0.0195 0.9919 -0.0764  0.1154  False
+     0     28   0.0039    1.0 -0.0957  0.1035  False
+     3      7  -0.1773    0.0 -0.2678 -0.0868   True
+     3     14  -0.1205 0.0018 -0.2096 -0.0315   True
+     3     21  -0.1611    0.0 -0.2501 -0.0721   True
+     3     28  -0.1767    0.0 -0.2696 -0.0837   True
+     7     14   0.0568 0.5131 -0.0376  0.1511  False
+     7     21   0.0162 0.9963 -0.0781  0.1106  False
+     7     28   0.0006    1.0 -0.0975  0.0987  False
+    14     21  -0.0405 0.8092 -0.1335  0.0524  False
+    14     28  -0.0561 0.5541 -0.1529  0.0406  False
+    21     28  -0.0156 0.9973 -0.1123  0.0812  False
 ----------------------------------------------------
 Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05 
-====================================================
-group1 group2 meandiff p-adj   lower   upper  reject
-----------------------------------------------------
-     0      3   0.1166   0.03   0.007  0.2263   True
-     0      7   0.0384 0.8942 -0.0656  0.1423  False
-     0     14  -0.0013    1.0 -0.1011  0.0985  False
-     0     21   0.0417 0.8984 -0.0725  0.1559  False
-     0     28   0.0166 0.9978 -0.0917   0.125  False
-     3      7  -0.0782 0.3314 -0.1896  0.0331  False
-     3     14  -0.1179 0.0226 -0.2253 -0.0104   True
-     3     21  -0.0749 0.4772 -0.1959  0.0461  False
-     3     28     -0.1 0.1308 -0.2154  0.0155  False
-     7     14  -0.0397 0.8699 -0.1413   0.062  False
-     7     21   0.0033    1.0 -0.1125  0.1192  False
-     7     28  -0.0217 0.9928 -0.1318  0.0883  False
-    14     21    0.043 0.8779 -0.0691  0.1551  False
-    14     28   0.0179 0.9966 -0.0882  0.1241  False
-    21     28  -0.0251 0.9906 -0.1449  0.0947  False
-----------------------------------------------------
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0917 0.1213 -0.0128 0.1963  False
+     0      7   0.0193 0.9933 -0.0799 0.1184  False
+     0     14   0.0036    1.0 -0.0915 0.0988  False
+     0     21   0.0238 0.9886 -0.0851 0.1327  False
+     0     28    0.026 0.9786 -0.0774 0.1293  False
+     3      7  -0.0724 0.3646 -0.1786 0.0337  False
+     3     14  -0.0881 0.1363 -0.1906 0.0144  False
+     3     21  -0.0679 0.5337 -0.1833 0.0474  False
+     3     28  -0.0658 0.5179 -0.1759 0.0443  False
+     7     14  -0.0156 0.9972 -0.1126 0.0813  False
+     7     21   0.0045    1.0  -0.106 0.1149  False
+     7     28   0.0067    1.0 -0.0983 0.1116  False
+    14     21   0.0201 0.9942 -0.0868  0.127  False
+    14     28   0.0223 0.9881 -0.0789 0.1235  False
+    21     28   0.0022    1.0  -0.112 0.1164  False
+---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.01169093]	Yes
-Stroke	Sham	14	[0.02251159]	Yes
-Stroke	Sham	21	[0.93207768]	No
-Stroke	Sham	28	[0.15781038]	No
-Stroke	Sham	7	[0.26892867]	No
-Stroke	Sham	0	[0.74258907]	No
+Stroke	Sham	3	[0.05053194]	No
+Stroke	Sham	14	[0.0216846]	Yes
+Stroke	Sham	21	[0.87636783]	No
+Stroke	Sham	28	[0.57832852]	No
+Stroke	Sham	7	[0.82810111]	No
+Stroke	Sham	0	[0.6645302]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CST_links_CC_cut_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CST_links_CC_cut
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       364          Method:                  REML  
-No. Groups:             2            Scale:                   0.0235
-Min. group size:        158          Log-Likelihood:          inf   
-Max. group size:        206          Converged:               Yes   
-Mean group size:        182.0                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 299465.744 0.000 1.000 -586942.073 586942.073
-merged_timepoint 0.002      0.001 2.305 0.021       0.000      0.004
-Group Var        0.000                                              
-====================================================================
-
-Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3  -0.0507 0.7226 -0.1544  0.053  False
-     0      7   0.0415 0.8849  -0.068  0.151  False
-     0     14   0.0192 0.9957 -0.0888 0.1272  False
-     0     21   0.0553  0.682 -0.0527 0.1633  False
-     0     28   0.0984 0.1221 -0.0138 0.2105  False
-     3      7   0.0922 0.1009 -0.0097 0.1941  False
-     3     14   0.0699 0.3422 -0.0303 0.1701  False
-     3     21    0.106 0.0314  0.0058 0.2062   True
-     3     28   0.1491 0.0008  0.0444 0.2538   True
-     7     14  -0.0223 0.9906 -0.1286 0.0839  False
-     7     21   0.0138  0.999 -0.0925 0.1201  False
-     7     28   0.0569 0.6765 -0.0536 0.1674  False
-    14     21   0.0361   0.92 -0.0686 0.1408  False
-    14     28   0.0792  0.296 -0.0298 0.1882  False
-    21     28   0.0431  0.865 -0.0659 0.1521  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3  -0.0266  0.988 -0.1468 0.0937  False
-     0      7   -0.065 0.5695  -0.179  0.049  False
-     0     14  -0.0196 0.9954 -0.1291 0.0898  False
-     0     21  -0.0183 0.9983 -0.1435  0.107  False
-     0     28  -0.0572  0.733  -0.176 0.0616  False
-     3      7  -0.0384 0.9437 -0.1606 0.0837  False
-     3     14   0.0069    1.0 -0.1109 0.1248  False
-     3     21   0.0083    1.0 -0.1243  0.141  False
-     3     28  -0.0307 0.9818 -0.1573 0.0959  False
-     7     14   0.0454 0.8479 -0.0661 0.1569  False
-     7     21   0.0468 0.8953 -0.0803 0.1738  False
-     7     28   0.0078    1.0 -0.1129 0.1285  False
-    14     21   0.0014    1.0 -0.1216 0.1243  False
-    14     28  -0.0376 0.9375  -0.154 0.0788  False
-    21     28   -0.039 0.9561 -0.1703 0.0924  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.05281125]	No
-Stroke	Sham	14	[0.61687328]	No
-Stroke	Sham	21	[0.71835254]	No
-Stroke	Sham	28	[0.0031792]	Yes
-Stroke	Sham	7	[0.1899025]	No
-Stroke	Sham	0	[0.18956687]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CST_links_CCasROA_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CST_links_CCasROA
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       364          Method:                  REML  
-No. Groups:             2            Scale:                   0.0248
-Min. group size:        158          Log-Likelihood:          inf   
-Max. group size:        206          Converged:               Yes   
-Mean group size:        182.0                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 308226.459 0.000 1.000 -604112.759 604112.759
-merged_timepoint 0.002      0.001 2.291 0.022       0.000      0.004
-Group Var        0.000                                              
-====================================================================
-
-Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   -0.045 0.8207   -0.15 0.0601  False
-     0      7    0.042 0.8848 -0.0689 0.1529  False
-     0     14   0.0285 0.9754 -0.0809 0.1378  False
-     0     21   0.0534 0.7248  -0.056 0.1627  False
-     0     28   0.0942 0.1659 -0.0194 0.2078  False
-     3      7    0.087 0.1522 -0.0162 0.1901  False
-     3     14   0.0734 0.3011 -0.0281 0.1749  False
-     3     21   0.0983 0.0637 -0.0032 0.1998  False
-     3     28   0.1392 0.0028  0.0331 0.2452   True
-     7     14  -0.0136 0.9992 -0.1212  0.094  False
-     7     21   0.0113 0.9997 -0.0963 0.1189  False
-     7     28   0.0522 0.7612 -0.0597  0.164  False
-    14     21   0.0249 0.9845 -0.0811 0.1309  False
-    14     28   0.0657  0.524 -0.0446 0.1761  False
-    21     28   0.0408 0.8945 -0.0695 0.1512  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3  -0.0355 0.9664  -0.163 0.0919  False
-     0      7  -0.0797 0.4042 -0.2005 0.0412  False
-     0     14  -0.0181 0.9976 -0.1341 0.0979  False
-     0     21  -0.0226 0.9964 -0.1554 0.1101  False
-     0     28  -0.0503 0.8579 -0.1763 0.0756  False
-     3      7  -0.0442 0.9221 -0.1736 0.0853  False
-     3     14   0.0174 0.9986 -0.1075 0.1423  False
-     3     21   0.0129 0.9998 -0.1277 0.1535  False
-     3     28  -0.0148 0.9996  -0.149 0.1194  False
-     7     14   0.0616  0.662 -0.0566 0.1798  False
-     7     21    0.057  0.825 -0.0776 0.1917  False
-     7     28   0.0294 0.9857 -0.0986 0.1573  False
-    14     21  -0.0045    1.0 -0.1349 0.1258  False
-    14     28  -0.0322 0.9746 -0.1556 0.0911  False
-    21     28  -0.0277 0.9926 -0.1669 0.1116  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.09448306]	No
-Stroke	Sham	14	[0.66176576]	No
-Stroke	Sham	21	[0.79018389]	No
-Stroke	Sham	28	[0.01384277]	Yes
-Stroke	Sham	7	[0.14849213]	No
-Stroke	Sham	0	[0.14058382]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CST_links_ROA_CC_fibers_cut_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_CST_links_ROA_CC_fibers_cut
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       364          Method:                  REML  
-No. Groups:             2            Scale:                   0.0228
-Min. group size:        158          Log-Likelihood:          inf   
-Max. group size:        206          Converged:               Yes   
-Mean group size:        182.0                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 295180.664 0.000 1.000 -578543.470 578543.470
-merged_timepoint 0.002      0.001 2.309 0.021       0.000      0.003
-Group Var        0.000                                              
-====================================================================
-
-Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3  -0.0504 0.7177 -0.1527  0.052  False
-     0      7   0.0431 0.8606  -0.065 0.1513  False
-     0     14   0.0139  0.999 -0.0927 0.1206  False
-     0     21   0.0563 0.6523 -0.0503  0.163  False
-     0     28   0.0968 0.1244 -0.0139 0.2076  False
-     3      7   0.0935 0.0849 -0.0071 0.1941  False
-     3     14   0.0643 0.4244 -0.0347 0.1632  False
-     3     21   0.1067 0.0264  0.0077 0.2056   True
-     3     28   0.1472 0.0009  0.0438 0.2505   True
-     7     14  -0.0292  0.967 -0.1341 0.0757  False
-     7     21   0.0132 0.9992 -0.0918 0.1181  False
-     7     28   0.0537 0.7172 -0.0554 0.1628  False
-    14     21   0.0424 0.8459  -0.061 0.1458  False
-    14     28   0.0829 0.2344 -0.0247 0.1905  False
-    21     28   0.0405 0.8874 -0.0671 0.1481  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3  -0.0257 0.9888 -0.1438 0.0924  False
-     0      7  -0.0629 0.5867 -0.1749 0.0491  False
-     0     14  -0.0192 0.9955 -0.1267 0.0883  False
-     0     21  -0.0177 0.9984 -0.1408 0.1053  False
-     0     28  -0.0554 0.7445 -0.1722 0.0613  False
-     3      7  -0.0371 0.9475 -0.1571 0.0828  False
-     3     14   0.0065    1.0 -0.1093 0.1223  False
-     3     21    0.008    1.0 -0.1224 0.1383  False
-     3     28  -0.0297 0.9829 -0.1541 0.0947  False
-     7     14   0.0437 0.8591 -0.0659 0.1532  False
-     7     21   0.0451 0.9024 -0.0797 0.1699  False
-     7     28   0.0074    1.0 -0.1111  0.126  False
-    14     21   0.0014    1.0 -0.1193 0.1222  False
-    14     28  -0.0362 0.9423 -0.1506 0.0781  False
-    21     28  -0.0377 0.9589 -0.1667 0.0914  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.04702943]	Yes
-Stroke	Sham	14	[0.52257062]	No
-Stroke	Sham	21	[0.69596103]	No
-Stroke	Sham	28	[0.00339809]	Yes
-Stroke	Sham	7	[0.16699645]	No
-Stroke	Sham	0	[0.19969503]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CST_rechts_CC_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CST_rechts_CC_cut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0179
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.002    0.001 2.205 0.027  0.000  0.003
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0336 0.8939 -0.1242  0.057  False
+     0      7   0.0244 0.9777 -0.0714 0.1201  False
+     0     14   0.0205 0.9892 -0.0739 0.1149  False
+     0     21   0.0341 0.9044 -0.0603 0.1285  False
+     0     28   0.0671 0.3629 -0.0309 0.1652  False
+     3      7    0.058 0.4216 -0.0311  0.147  False
+     3     14   0.0541 0.4836 -0.0335 0.1417  False
+     3     21   0.0677 0.2319 -0.0199 0.1553  False
+     3     28   0.1007 0.0216  0.0092 0.1922   True
+     7     14  -0.0039    1.0 -0.0968  0.089  False
+     7     21   0.0097 0.9997 -0.0832 0.1026  False
+     7     28   0.0428 0.7985 -0.0538 0.1393  False
+    14     21   0.0136 0.9982 -0.0779 0.1051  False
+    14     28   0.0467 0.7208 -0.0486 0.1419  False
+    21     28   0.0331 0.9178 -0.0622 0.1283  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0041    1.0 -0.1129 0.1048  False
+     0      7  -0.0299 0.9604 -0.1331 0.0733  False
+     0     14  -0.0003    1.0 -0.0994 0.0987  False
+     0     21   0.0012    1.0 -0.1121 0.1146  False
+     0     28  -0.0105 0.9998  -0.118  0.097  False
+     3      7  -0.0258 0.9845 -0.1363 0.0847  False
+     3     14   0.0037    1.0 -0.1029 0.1104  False
+     3     21   0.0053    1.0 -0.1148 0.1254  False
+     3     28  -0.0065    1.0  -0.121 0.1081  False
+     7     14   0.0295 0.9584 -0.0713 0.1304  False
+     7     21   0.0311 0.9703 -0.0838 0.1461  False
+     7     28   0.0194 0.9957 -0.0899 0.1286  False
+    14     21   0.0016    1.0 -0.1097 0.1129  False
+    14     28  -0.0102 0.9998 -0.1155 0.0952  False
+    21     28  -0.0118 0.9997 -0.1306 0.1071  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.10419809]	No
+Stroke	Sham	14	[0.65391119]	No
+Stroke	Sham	21	[0.98305963]	No
+Stroke	Sham	28	[0.11743124]	No
+Stroke	Sham	7	[0.44937881]	No
+Stroke	Sham	0	[0.37911857]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CST_rechts_CCasROA_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CST_rechts_CCasROA
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0174
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.002    0.001 2.375 0.018  0.000  0.003
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0312 0.9163 -0.1208 0.0583  False
+     0      7   0.0277 0.9594  -0.067 0.1223  False
+     0     14   0.0238 0.9773 -0.0694 0.1171  False
+     0     21   0.0388 0.8374 -0.0545 0.1321  False
+     0     28   0.0694 0.3124 -0.0275 0.1662  False
+     3      7   0.0589 0.3895 -0.0291 0.1469  False
+     3     14   0.0551 0.4484 -0.0315 0.1417  False
+     3     21   0.0701 0.1873 -0.0165 0.1566  False
+     3     28   0.1006 0.0195  0.0102  0.191   True
+     7     14  -0.0038    1.0 -0.0956  0.088  False
+     7     21   0.0112 0.9993 -0.0806  0.103  False
+     7     28   0.0417 0.8073 -0.0537 0.1371  False
+    14     21    0.015 0.9969 -0.0754 0.1054  False
+    14     28   0.0455 0.7318 -0.0486 0.1396  False
+    21     28   0.0305 0.9374 -0.0636 0.1246  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0013    1.0 -0.1083 0.1057  False
+     0      7  -0.0249 0.9807 -0.1264 0.0766  False
+     0     14    0.006    1.0 -0.0914 0.1034  False
+     0     21   0.0057    1.0 -0.1058 0.1172  False
+     0     28  -0.0063    1.0  -0.112 0.0995  False
+     3      7  -0.0236 0.9888 -0.1323 0.0851  False
+     3     14   0.0073    1.0 -0.0976 0.1122  False
+     3     21    0.007    1.0 -0.1111  0.125  False
+     3     28   -0.005    1.0 -0.1177 0.1077  False
+     7     14   0.0309 0.9463 -0.0683 0.1301  False
+     7     21   0.0306 0.9704 -0.0825 0.1436  False
+     7     28   0.0187 0.9961 -0.0888 0.1261  False
+    14     21  -0.0003    1.0 -0.1098 0.1091  False
+    14     28  -0.0122 0.9994 -0.1159 0.0914  False
+    21     28  -0.0119 0.9997 -0.1289  0.105  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.0975965]	No
+Stroke	Sham	14	[0.59539877]	No
+Stroke	Sham	21	[0.99718541]	No
+Stroke	Sham	28	[0.12959466]	No
+Stroke	Sham	7	[0.46672511]	No
+Stroke	Sham	0	[0.38682708]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CST_rechts_ROA_CC_fibers_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CST_rechts_ROA_CC_fibers_cut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0176
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.002    0.001 2.277 0.023  0.000  0.003
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0305 0.9251 -0.1205 0.0595  False
+     0      7   0.0278 0.9595 -0.0673 0.1229  False
+     0     14   0.0235 0.9794 -0.0703 0.1172  False
+     0     21   0.0383 0.8477 -0.0554 0.1321  False
+     0     28   0.0691 0.3229 -0.0283 0.1664  False
+     3      7   0.0583 0.4069 -0.0301 0.1467  False
+     3     14    0.054 0.4775  -0.033  0.141  False
+     3     21   0.0689 0.2083 -0.0181 0.1559  False
+     3     28   0.0996 0.0226  0.0087 0.1905   True
+     7     14  -0.0043    1.0 -0.0966 0.0879  False
+     7     21   0.0106 0.9995 -0.0817 0.1028  False
+     7     28   0.0413 0.8172 -0.0546 0.1372  False
+    14     21   0.0149 0.9971  -0.076 0.1057  False
+    14     28   0.0456 0.7345  -0.049 0.1402  False
+    21     28   0.0307  0.937 -0.0638 0.1253  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0018    1.0 -0.1092 0.1055  False
+     0      7  -0.0271 0.9726 -0.1288 0.0747  False
+     0     14   0.0036    1.0 -0.0941 0.1013  False
+     0     21   0.0008    1.0  -0.111 0.1126  False
+     0     28  -0.0083 0.9999 -0.1144 0.0978  False
+     3      7  -0.0252 0.9852 -0.1342 0.0838  False
+     3     14   0.0054    1.0 -0.0998 0.1106  False
+     3     21   0.0026    1.0 -0.1158  0.121  False
+     3     28  -0.0065    1.0 -0.1195 0.1065  False
+     7     14   0.0306 0.9487 -0.0689 0.1301  False
+     7     21   0.0278 0.9807 -0.0855 0.1412  False
+     7     28   0.0188  0.996  -0.089 0.1265  False
+    14     21  -0.0028    1.0 -0.1125 0.1069  False
+    14     28  -0.0119 0.9995 -0.1158  0.092  False
+    21     28  -0.0091 0.9999 -0.1263 0.1082  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.09308109]	No
+Stroke	Sham	14	[0.58816077]	No
+Stroke	Sham	21	[0.96320675]	No
+Stroke	Sham	28	[0.13416992]	No
+Stroke	Sham	7	[0.47103841]	No
+Stroke	Sham	0	[0.35572636]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_Retikulospinal_tract_links_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_Retikulospinal_tract_links
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0162
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.002    0.001 2.367 0.018  0.000  0.003
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3  -0.0895 0.0219 -0.1709 -0.0081   True
+     0      7   -0.024 0.9667   -0.11   0.062  False
+     0     14  -0.0379 0.7925 -0.1227  0.0469  False
+     0     21   0.0205 0.9823 -0.0643  0.1053  False
+     0     28   0.0532 0.5088 -0.0349  0.1412  False
+     3      7   0.0655 0.1765 -0.0144  0.1455  False
+     3     14   0.0516 0.4126 -0.0271  0.1303  False
+     3     21     0.11 0.0011  0.0313  0.1887   True
+     3     28   0.1427    0.0  0.0605  0.2248   True
+     7     14  -0.0139 0.9968 -0.0973  0.0695  False
+     7     21   0.0445 0.6423 -0.0389  0.1279  False
+     7     28   0.0771 0.1123 -0.0096  0.1639  False
+    14     21   0.0584 0.3211 -0.0238  0.1406  False
+    14     28    0.091 0.0296  0.0055  0.1766   True
+    21     28   0.0327 0.8815 -0.0529  0.1182  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0423 0.8477 -0.0615  0.146  False
+     0      7  -0.0505 0.6756 -0.1489 0.0478  False
+     0     14  -0.0027    1.0 -0.0971 0.0917  False
+     0     21  -0.0068    1.0 -0.1149 0.1012  False
+     0     28  -0.0182 0.9957 -0.1206 0.0843  False
+     3      7  -0.0928 0.1184 -0.1981 0.0125  False
+     3     14   -0.045 0.7973 -0.1466 0.0567  False
+     3     21  -0.0491 0.8173 -0.1635 0.0653  False
+     3     28  -0.0604  0.602 -0.1696 0.0488  False
+     7     14   0.0478 0.7054 -0.0483  0.144  False
+     7     21   0.0437  0.859 -0.0659 0.1533  False
+     7     28   0.0324 0.9466 -0.0717 0.1365  False
+    14     21  -0.0041    1.0 -0.1102 0.1019  False
+    14     28  -0.0154 0.9978 -0.1158 0.0849  False
+    21     28  -0.0113 0.9997 -0.1246  0.102  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00624797]	Yes
+Stroke	Sham	14	[0.60891739]	No
+Stroke	Sham	21	[0.1200763]	No
+Stroke	Sham	28	[0.01004425]	Yes
+Stroke	Sham	7	[0.09263455]	No
+Stroke	Sham	0	[0.52510691]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_Rubrospinal_tract_links__log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_Rubrospinal_tract_links_
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0132
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.002    0.001 2.929 0.003  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  -0.0619 0.1139 -0.1317 0.0078  False
+     0      7  -0.0352 0.7424 -0.1089 0.0385  False
+     0     14   -0.002    1.0 -0.0747 0.0706  False
+     0     21   0.0354 0.7265 -0.0373  0.108  False
+     0     28   0.0443 0.5408 -0.0312 0.1197  False
+     3      7   0.0267 0.8719 -0.0418 0.0952  False
+     3     14   0.0599 0.1134 -0.0075 0.1273  False
+     3     21   0.0973 0.0007  0.0299 0.1647   True
+     3     28   0.1062 0.0003  0.0358 0.1766   True
+     7     14   0.0332 0.7652 -0.0383 0.1046  False
+     7     21   0.0706 0.0552 -0.0009  0.142  False
+     7     28   0.0795 0.0284  0.0052 0.1538   True
+    14     21   0.0374 0.6464  -0.033 0.1078  False
+    14     28   0.0463 0.4565  -0.027 0.1196  False
+    21     28   0.0089 0.9993 -0.0644 0.0822  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0642 0.4488  -0.037 0.1655  False
+     0      7   -0.007 0.9999  -0.103 0.0889  False
+     0     14    0.022  0.983 -0.0701 0.1141  False
+     0     21   0.0185 0.9959  -0.087 0.1239  False
+     0     28   0.0187 0.9944 -0.0813 0.1188  False
+     3      7  -0.0713 0.3462 -0.1741 0.0315  False
+     3     14  -0.0422  0.822 -0.1414  0.057  False
+     3     21  -0.0458 0.8444 -0.1574 0.0659  False
+     3     28  -0.0455 0.8205 -0.1521 0.0611  False
+     7     14    0.029 0.9476 -0.0648 0.1229  False
+     7     21   0.0255  0.983 -0.0814 0.1324  False
+     7     28   0.0258 0.9776 -0.0758 0.1274  False
+    14     21  -0.0035    1.0  -0.107    0.1  False
+    14     28  -0.0033    1.0 -0.1012 0.0947  False
+    21     28   0.0003    1.0 -0.1103 0.1109  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.01670222]	Yes
+Stroke	Sham	14	[0.53637829]	No
+Stroke	Sham	21	[0.08025019]	No
+Stroke	Sham	28	[0.05119225]	No
+Stroke	Sham	7	[0.50939313]	No
+Stroke	Sham	0	[0.04539102]	Yes

output/Final_Quantitative_output/mixed_model_analysis/ad_Rubrospinal_tract_rechts_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_Rubrospinal_tract_rechts
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   364      Method:              REML    
+No. Groups:         2        Scale:               0.0204  
+Min. group size:    158      Log-Likelihood:      181.8143
+Max. group size:    206      Converged:           Yes     
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        1.043    0.019 54.640 0.000  1.005  1.080
+merged_timepoint 0.002    0.001  2.297 0.022  0.000  0.003
+Group Var        0.000    0.006                           
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0021    1.0 -0.0909 0.0952  False
+     0      7   0.0145 0.9982 -0.0838 0.1128  False
+     0     14   0.0187 0.9936 -0.0782 0.1157  False
+     0     21   0.0525 0.6276 -0.0445 0.1494  False
+     0     28   0.0485 0.7351 -0.0522 0.1492  False
+     3      7   0.0124 0.9988  -0.079 0.1038  False
+     3     14   0.0166 0.9949 -0.0733 0.1066  False
+     3     21   0.0503 0.5928 -0.0396 0.1403  False
+     3     28   0.0464 0.7146 -0.0476 0.1403  False
+     7     14   0.0042    1.0 -0.0912 0.0995  False
+     7     21   0.0379 0.8622 -0.0574 0.1333  False
+     7     28    0.034 0.9221 -0.0652 0.1331  False
+    14     21   0.0337 0.9063 -0.0602 0.1277  False
+    14     28   0.0298 0.9518  -0.068 0.1276  False
+    21     28   -0.004    1.0 -0.1017 0.0938  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0109 0.9998 -0.1335 0.1116  False
+     0      7    0.003    1.0 -0.1132 0.1192  False
+     0     14   0.0341 0.9503 -0.0775 0.1457  False
+     0     21   0.0651 0.6821 -0.0625 0.1928  False
+     0     28   0.0121 0.9997  -0.109 0.1332  False
+     3      7    0.014 0.9995 -0.1105 0.1384  False
+     3     14    0.045  0.888 -0.0751 0.1651  False
+     3     21   0.0761 0.5842 -0.0591 0.2113  False
+     3     28    0.023 0.9955  -0.106 0.1521  False
+     7     14   0.0311  0.969 -0.0826 0.1447  False
+     7     21   0.0621 0.7363 -0.0674 0.1916  False
+     7     28   0.0091 0.9999 -0.1139 0.1321  False
+    14     21    0.031 0.9799 -0.0943 0.1564  False
+    14     28   -0.022 0.9947 -0.1406 0.0967  False
+    21     28   -0.053 0.8625 -0.1869 0.0809  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.46030912]	No
+Stroke	Sham	14	[0.17391328]	No
+Stroke	Sham	21	[0.34279564]	No
+Stroke	Sham	28	[0.92242241]	No
+Stroke	Sham	7	[0.25066266]	No
+Stroke	Sham	0	[0.33678397]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_Thalamocorticale_links_SSp_ll_and_ul_ROI.tt_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_Thalamocorticale_links_SSp_ll_and_ul_ROI.tt
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0167
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.002    0.001 2.396 0.017  0.000  0.003
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0165 0.9909 -0.0955 0.0625  False
+     0      7  -0.0296 0.9108 -0.1131 0.0539  False
+     0     14   0.0489 0.5265 -0.0334 0.1312  False
+     0     21    0.014 0.9966 -0.0683 0.0963  False
+     0     28   0.0557 0.4205 -0.0298 0.1412  False
+     3      7  -0.0131 0.9966 -0.0907 0.0645  False
+     3     14   0.0654 0.1397  -0.011 0.1418  False
+     3     21   0.0305 0.8608 -0.0459 0.1068  False
+     3     28   0.0722  0.101 -0.0076  0.152  False
+     7     14   0.0785 0.0632 -0.0025 0.1595  False
+     7     21   0.0435 0.6339 -0.0374 0.1245  False
+     7     28   0.0853 0.0451  0.0011 0.1695   True
+    14     21   -0.035 0.8056 -0.1147 0.0448  False
+    14     28   0.0068 0.9999 -0.0762 0.0898  False
+    21     28   0.0417 0.6984 -0.0413 0.1248  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.1088 0.0653  -0.004 0.2216  False
+     0      7   0.0056    1.0 -0.1014 0.1125  False
+     0     14   0.0701 0.3633 -0.0325 0.1728  False
+     0     21   0.0435 0.8925 -0.0739  0.161  False
+     0     28   0.0477 0.8183 -0.0637 0.1592  False
+     3      7  -0.1033 0.1028 -0.2178 0.0112  False
+     3     14  -0.0387 0.9138 -0.1492 0.0718  False
+     3     21  -0.0653 0.6555 -0.1897 0.0591  False
+     3     28  -0.0611 0.6743 -0.1798 0.0576  False
+     7     14   0.0646 0.4799   -0.04 0.1691  False
+     7     21    0.038 0.9407 -0.0811 0.1571  False
+     7     28   0.0422 0.8903  -0.071 0.1554  False
+    14     21  -0.0266 0.9854 -0.1419 0.0887  False
+    14     28  -0.0224 0.9914 -0.1316 0.0868  False
+    21     28   0.0042    1.0  -0.119 0.1274  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.01188743]	Yes
+Stroke	Sham	14	[0.8818679]	No
+Stroke	Sham	21	[0.94380539]	No
+Stroke	Sham	28	[0.31095915]	No
+Stroke	Sham	7	[0.74129995]	No
+Stroke	Sham	0	[0.2212427]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_Thalamocorticale_links_SSp_ul_and_ll_End_0,2.tt_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_Thalamocorticale_links_SSp_ul_and_ll_End_0,2.tt
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0125
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.002    0.001 3.176 0.001  0.001  0.003
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   -0.026 0.8873  -0.095  0.043  False
+     0      7  -0.0422 0.5553 -0.1151 0.0307  False
+     0     14   0.0294  0.848 -0.0425 0.1013  False
+     0     21   0.0143 0.9926 -0.0576 0.0862  False
+     0     28    0.056 0.2628 -0.0187 0.1306  False
+     3      7  -0.0162  0.983  -0.084 0.0516  False
+     3     14   0.0554 0.1653 -0.0113 0.1221  False
+     3     21   0.0403 0.5073 -0.0264  0.107  False
+     3     28    0.082 0.0109  0.0123 0.1516   True
+     7     14   0.0716 0.0453  0.0009 0.1423   True
+     7     21   0.0566 0.1984 -0.0142 0.1273  False
+     7     28   0.0982 0.0022  0.0247 0.1717   True
+    14     21   -0.015 0.9894 -0.0847 0.0546  False
+    14     28   0.0266 0.8984 -0.0459 0.0991  False
+    21     28   0.0416 0.5653 -0.0309 0.1142  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0982 0.0447  0.0014  0.195   True
+     0      7   0.0166 0.9952 -0.0752 0.1084  False
+     0     14   0.0545 0.4791 -0.0337 0.1426  False
+     0     21   0.0474 0.7522 -0.0534 0.1482  False
+     0     28   0.0581  0.499 -0.0376 0.1538  False
+     3      7  -0.0816 0.1641 -0.1799 0.0167  False
+     3     14  -0.0437 0.7676 -0.1386 0.0511  False
+     3     21  -0.0508 0.7434 -0.1576  0.056  False
+     3     28  -0.0401 0.8659  -0.142 0.0618  False
+     7     14   0.0379 0.8276 -0.0519 0.1276  False
+     7     21   0.0308 0.9531 -0.0714 0.1331  False
+     7     28   0.0415 0.8199 -0.0557 0.1387  False
+    14     21   -0.007 0.9999  -0.106 0.0919  False
+    14     28   0.0036    1.0 -0.0901 0.0974  False
+    21     28   0.0107 0.9997 -0.0951 0.1164  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.01460186]	Yes
+Stroke	Sham	14	[0.63951078]	No
+Stroke	Sham	21	[0.8395124]	No
+Stroke	Sham	28	[0.22918191]	No
+Stroke	Sham	7	[0.33603054]	No
+Stroke	Sham	0	[0.04724567]	Yes

output/Final_Quantitative_output/mixed_model_analysis/ad_Thalamocorticale_rechts_SSp_ll_and_ul_ROI.tt_log.txt

@@ -1,67 +0,0 @@
-Model Name: ad_Thalamocorticale_rechts_SSp_ll_and_ul_ROI.tt
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       364          Method:                  REML  
-No. Groups:             2            Scale:                   0.0261
-Min. group size:        158          Log-Likelihood:          inf   
-Max. group size:        206          Converged:               Yes   
-Mean group size:        182.0                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 315899.293 0.000 1.000 -619151.236 619151.236
-merged_timepoint 0.002      0.001 2.741 0.006       0.001      0.004
-Group Var        0.000                                              
-====================================================================
-
-Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0242 0.9635 -0.0608 0.1093  False
-     0      7    -0.02 0.9876 -0.1098 0.0698  False
-     0     14   0.0322 0.9016 -0.0564 0.1208  False
-     0     21   0.0625 0.3285  -0.026 0.1511  False
-     0     28   0.0765 0.1639 -0.0155 0.1684  False
-     3      7  -0.0443 0.6482 -0.1278 0.0392  False
-     3     14    0.008 0.9998 -0.0742 0.0901  False
-     3     21   0.0383 0.7623 -0.0439 0.1204  False
-     3     28   0.0522 0.5002 -0.0336  0.138  False
-     7     14   0.0522 0.5167 -0.0349 0.1394  False
-     7     21   0.0825 0.0745 -0.0046 0.1697  False
-     7     28   0.0965 0.0294  0.0059 0.1871   True
-    14     21   0.0303 0.9121 -0.0555 0.1161  False
-    14     28   0.0443 0.7115 -0.0451 0.1336  False
-    21     28   0.0139 0.9977 -0.0754 0.1033  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.1691 0.0255  0.0129 0.3253   True
-     0      7   0.0156 0.9996 -0.1325 0.1637  False
-     0     14   0.1002 0.3277 -0.0419 0.2424  False
-     0     21   0.1126 0.3487 -0.0501 0.2753  False
-     0     28   0.0834 0.6263  -0.071 0.2378  False
-     3      7  -0.1535  0.064 -0.3121 0.0051  False
-     3     14  -0.0689 0.7854  -0.222 0.0842  False
-     3     21  -0.0565 0.9335 -0.2288 0.1158  False
-     3     28  -0.0857 0.6621 -0.2502 0.0788  False
-     7     14   0.0846 0.5428 -0.0602 0.2294  False
-     7     21    0.097 0.5364  -0.068  0.262  False
-     7     28   0.0678 0.8124  -0.089 0.2246  False
-    14     21   0.0124 0.9999 -0.1474 0.1721  False
-    14     28  -0.0168 0.9995  -0.168 0.1344  False
-    21     28  -0.0292 0.9963 -0.1998 0.1415  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.01524504]	Yes
-Stroke	Sham	14	[0.26147687]	No
-Stroke	Sham	21	[0.57217688]	No
-Stroke	Sham	28	[0.76935177]	No
-Stroke	Sham	7	[0.64909371]	No
-Stroke	Sham	0	[0.3411945]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_MOp(dilated)_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CC_MOp(dilated)
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   364      Method:              REML    
+No. Groups:         2        Scale:               0.0007  
+Min. group size:    158      Log-Likelihood:      788.0750
+Max. group size:    206      Converged:           Yes     
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        0.267    0.006 41.700 0.000  0.255  0.280
+merged_timepoint 0.000    0.000  2.713 0.007  0.000  0.001
+Group Var        0.000    0.004                           
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0027 0.9989 -0.0174 0.0227  False
+     0      7   0.0139 0.4147 -0.0073  0.035  False
+     0     14   0.0083 0.8653 -0.0126 0.0291  False
+     0     21    0.011 0.6552 -0.0099 0.0319  False
+     0     28   0.0149 0.3612 -0.0068 0.0365  False
+     3      7   0.0112 0.5746 -0.0085 0.0309  False
+     3     14   0.0056 0.9615 -0.0138  0.025  False
+     3     21   0.0083 0.8179  -0.011 0.0277  False
+     3     28   0.0122 0.5095  -0.008 0.0324  False
+     7     14  -0.0056 0.9695 -0.0262 0.0149  False
+     7     21  -0.0029 0.9986 -0.0234 0.0177  False
+     7     28    0.001    1.0 -0.0203 0.0224  False
+    14     21   0.0027 0.9988 -0.0175  0.023  False
+    14     28   0.0066 0.9451 -0.0144 0.0277  False
+    21     28   0.0039 0.9949 -0.0172 0.0249  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0045 0.9813  -0.014 0.0231  False
+     0      7   0.0046 0.9743  -0.013 0.0222  False
+     0     14   0.0081  0.739 -0.0088  0.025  False
+     0     21   0.0103 0.6415  -0.009 0.0296  False
+     0     28     0.01 0.6177 -0.0083 0.0283  False
+     3      7   0.0001    1.0 -0.0187 0.0189  False
+     3     14   0.0036 0.9931 -0.0146 0.0217  False
+     3     21   0.0058 0.9647 -0.0147 0.0262  False
+     3     28   0.0055 0.9656 -0.0141  0.025  False
+     7     14   0.0035 0.9921 -0.0137 0.0207  False
+     7     21   0.0057 0.9602 -0.0139 0.0253  False
+     7     28   0.0054 0.9606 -0.0132  0.024  False
+    14     21   0.0022 0.9994 -0.0168 0.0212  False
+    14     28   0.0019 0.9996  -0.016 0.0199  False
+    21     28  -0.0003    1.0 -0.0206   0.02  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.01624185]	Yes
+Stroke	Sham	14	[0.02976669]	Yes
+Stroke	Sham	21	[0.07522763]	No
+Stroke	Sham	28	[0.11586765]	No
+Stroke	Sham	7	[0.39596233]	No
+Stroke	Sham	0	[0.10443589]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_MOs_MOs_cut.tt_log.txt

@@ -1,67 +0,0 @@
-Model Name: fa_CC_MOs_MOs_cut.tt
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       364          Method:                  REML  
-No. Groups:             2            Scale:                   0.0051
-Min. group size:        158          Log-Likelihood:          inf   
-Max. group size:        206          Converged:               Yes   
-Mean group size:        182.0                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 138957.476 0.000 1.000 -272351.649 272351.649
-merged_timepoint 0.001      0.000 2.378 0.017       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  -0.0379    0.2 -0.0853 0.0096  False
-     0      7   0.0313 0.4693 -0.0188 0.0814  False
-     0     14  -0.0173 0.9149 -0.0667 0.0321  False
-     0     21   0.0096 0.9933 -0.0398 0.0591  False
-     0     28   0.0125 0.9814 -0.0388 0.0638  False
-     3      7   0.0692 0.0004  0.0226 0.1158   True
-     3     14   0.0206 0.7899 -0.0253 0.0664  False
-     3     21   0.0475 0.0374  0.0017 0.0934   True
-     3     28   0.0504 0.0327  0.0025 0.0983   True
-     7     14  -0.0486 0.0499 -0.0972   -0.0   True
-     7     21  -0.0217 0.7941 -0.0703 0.0269  False
-     7     28  -0.0188  0.893 -0.0693 0.0318  False
-    14     21    0.027 0.5868 -0.0209 0.0748  False
-    14     28   0.0298 0.5185   -0.02 0.0797  False
-    21     28   0.0029    1.0  -0.047 0.0527  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3  -0.0152 0.9698 -0.0712 0.0408  False
-     0      7   0.0165 0.9464 -0.0366 0.0696  False
-     0     14   0.0276 0.6257 -0.0234 0.0785  False
-     0     21   0.0138 0.9835 -0.0445 0.0722  False
-     0     28   0.0216 0.8703 -0.0338 0.0769  False
-     3      7   0.0317 0.5926 -0.0251 0.0886  False
-     3     14   0.0428 0.2217 -0.0121 0.0977  False
-     3     21    0.029 0.7525 -0.0327 0.0908  False
-     3     28   0.0368 0.4684 -0.0222 0.0957  False
-     7     14    0.011 0.9899 -0.0409  0.063  False
-     7     21  -0.0027    1.0 -0.0619 0.0565  False
-     7     28    0.005 0.9998 -0.0512 0.0613  False
-    14     21  -0.0137 0.9826  -0.071 0.0435  False
-    14     28   -0.006 0.9996 -0.0602 0.0482  False
-    21     28   0.0077 0.9991 -0.0534 0.0689  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.16755848]	No
-Stroke	Sham	14	[0.00364588]	Yes
-Stroke	Sham	21	[0.59515135]	No
-Stroke	Sham	28	[0.38602478]	No
-Stroke	Sham	7	[0.53797843]	No
-Stroke	Sham	0	[0.77553962]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_Mos_Mos.tt_log.txt

@@ -1,67 +0,0 @@
-Model Name: fa_CC_Mos_Mos.tt
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      364          Method:                  REML  
-No. Groups:            2            Scale:                   0.0018
-Min. group size:       158          Log-Likelihood:          inf   
-Max. group size:       206          Converged:               Yes   
-Mean group size:       182.0                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 83312.135 0.000 1.000 -163288.784 163288.784
-merged_timepoint 0.001     0.000 3.079 0.002       0.000      0.001
-Group Var        0.000                                             
-===================================================================
-
-Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0029 0.9998 -0.0272 0.0329  False
-     0      7   0.0204 0.4379 -0.0114 0.0521  False
-     0     14   0.0044 0.9986 -0.0269 0.0357  False
-     0     21   0.0218 0.3452 -0.0095 0.0531  False
-     0     28   0.0177 0.6221 -0.0148 0.0502  False
-     3      7   0.0175 0.5283  -0.012 0.0471  False
-     3     14   0.0015    1.0 -0.0275 0.0306  False
-     3     21   0.0189 0.4216 -0.0101  0.048  False
-     3     28   0.0148 0.7233 -0.0155 0.0452  False
-     7     14   -0.016 0.6693 -0.0468 0.0148  False
-     7     21   0.0014    1.0 -0.0294 0.0322  False
-     7     28  -0.0027 0.9999 -0.0347 0.0293  False
-    14     21   0.0174 0.5684  -0.013 0.0477  False
-    14     28   0.0133 0.8315 -0.0183 0.0449  False
-    21     28  -0.0041 0.9991 -0.0357 0.0275  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0128 0.8675 -0.0199 0.0456  False
-     0      7   0.0126 0.8486 -0.0184 0.0437  False
-     0     14   0.0127 0.8216 -0.0171 0.0425  False
-     0     21   0.0153 0.7898 -0.0189 0.0494  False
-     0     28   0.0319 0.0557 -0.0004 0.0643  False
-     3      7  -0.0002    1.0 -0.0335 0.0331  False
-     3     14  -0.0001    1.0 -0.0322  0.032  False
-     3     21   0.0024    1.0 -0.0337 0.0386  False
-     3     28   0.0191 0.6021 -0.0154 0.0536  False
-     7     14   0.0001    1.0 -0.0303 0.0304  False
-     7     21   0.0026 0.9999  -0.032 0.0372  False
-     7     28   0.0193 0.5384 -0.0136 0.0522  False
-    14     21   0.0026 0.9999 -0.0309 0.0361  False
-    14     28   0.0192 0.5017 -0.0125 0.0509  False
-    21     28   0.0167 0.7599 -0.0191 0.0525  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.02786781]	Yes
-Stroke	Sham	14	[0.02203897]	Yes
-Stroke	Sham	21	[0.30237194]	No
-Stroke	Sham	28	[0.00421593]	Yes
-Stroke	Sham	7	[0.30820014]	No
-Stroke	Sham	0	[0.19736463]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_SSp_ll.tt_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_CC_SSp_ll.tt
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      364          Method:                  REML  
-No. Groups:            2            Scale:                   0.0016
-Min. group size:       158          Log-Likelihood:          inf   
-Max. group size:       206          Converged:               Yes   
-Mean group size:       182.0                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 79027.986 0.000 1.000 -154892.006 154892.006
-merged_timepoint 0.001     0.000 2.469 0.014       0.000      0.001
-Group Var        0.000                                             
-===================================================================
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0011
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 4.546 0.000  0.000  0.001
+Group Var         0.000                                   
+==========================================================
 
 Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05 
-====================================================
-group1 group2 meandiff p-adj   lower   upper  reject
-----------------------------------------------------
-     0      3  -0.0353 0.0118 -0.0656 -0.0051   True
-     0      7   0.0073 0.9858 -0.0246  0.0393  False
-     0     14  -0.0062  0.993 -0.0377  0.0253  False
-     0     21  -0.0087  0.968 -0.0402  0.0228  False
-     0     28   0.0101  0.949 -0.0226  0.0428  False
-     3      7   0.0427 0.0007   0.013  0.0724   True
-     3     14   0.0291 0.0514 -0.0001  0.0584  False
-     3     21   0.0266  0.097 -0.0026  0.0559  False
-     3     28   0.0454 0.0004  0.0149   0.076   True
-     7     14  -0.0136  0.807 -0.0445  0.0174  False
-     7     21  -0.0161 0.6704 -0.0471  0.0149  False
-     7     28   0.0027 0.9999 -0.0295   0.035  False
-    14     21  -0.0025 0.9999  -0.033   0.028  False
-    14     28   0.0163   0.68 -0.0155  0.0481  False
-    21     28   0.0188 0.5316  -0.013  0.0506  False
-----------------------------------------------------
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0164 0.3642 -0.0404 0.0076  False
+     0      7   0.0191 0.2552 -0.0062 0.0445  False
+     0     14    0.012 0.7361  -0.013  0.037  False
+     0     21   0.0168 0.3867 -0.0082 0.0418  False
+     0     28   0.0211 0.1836 -0.0049  0.047  False
+     3      7   0.0355 0.0003   0.012 0.0591   True
+     3     14   0.0284 0.0068  0.0052 0.0516   True
+     3     21   0.0332 0.0008    0.01 0.0564   True
+     3     28   0.0375 0.0002  0.0133 0.0617   True
+     7     14  -0.0071 0.9612 -0.0317 0.0175  False
+     7     21  -0.0024 0.9998  -0.027 0.0222  False
+     7     28    0.002 0.9999 -0.0236 0.0275  False
+    14     21   0.0047 0.9932 -0.0195  0.029  False
+    14     28   0.0091 0.9057 -0.0161 0.0343  False
+    21     28   0.0043 0.9964 -0.0209 0.0295  False
+---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0103 0.8429 -0.0353 0.0148  False
-     0      7   0.0007    1.0 -0.0231 0.0244  False
-     0     14   0.0009    1.0 -0.0219 0.0237  False
-     0     21   0.0157 0.5089 -0.0104 0.0418  False
-     0     28     -0.0    1.0 -0.0248 0.0247  False
-     3      7   0.0109 0.8151 -0.0145 0.0364  False
-     3     14   0.0112 0.7763 -0.0134 0.0357  False
-     3     21    0.026 0.0779 -0.0016 0.0536  False
-     3     28   0.0102 0.8719 -0.0161 0.0366  False
-     7     14   0.0002    1.0  -0.023 0.0235  False
-     7     21   0.0151 0.5719 -0.0114 0.0415  False
-     7     28  -0.0007    1.0 -0.0258 0.0244  False
-    14     21   0.0148 0.5536 -0.0108 0.0404  False
-    14     28  -0.0009    1.0 -0.0252 0.0233  False
-    21     28  -0.0158 0.5588 -0.0431 0.0116  False
+     0      3   0.0087 0.8762 -0.0139 0.0314  False
+     0      7   0.0022 0.9997 -0.0193 0.0236  False
+     0     14   0.0041 0.9929 -0.0165 0.0247  False
+     0     21   0.0198 0.1565 -0.0038 0.0433  False
+     0     28   0.0149 0.3912 -0.0075 0.0373  False
+     3      7  -0.0065 0.9631 -0.0295 0.0164  False
+     3     14  -0.0047 0.9905 -0.0268 0.0175  False
+     3     21    0.011 0.7975 -0.0139  0.036  False
+     3     28   0.0062  0.975 -0.0176   0.03  False
+     7     14   0.0019 0.9998 -0.0191 0.0229  False
+     7     21   0.0176 0.2811 -0.0063 0.0415  False
+     7     28   0.0128 0.5869   -0.01 0.0355  False
+    14     21   0.0157 0.3721 -0.0075 0.0388  False
+    14     28   0.0109  0.709 -0.0111 0.0328  False
+    21     28  -0.0048 0.9931 -0.0296 0.0199  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[2.12353866e-06]	Yes
-Stroke	Sham	14	[0.00522986]	Yes
-Stroke	Sham	21	[0.00015387]	Yes
-Stroke	Sham	28	[0.31351208]	No
-Stroke	Sham	7	[0.15529692]	No
-Stroke	Sham	0	[0.11317703]	No
+Stroke	Sham	3	[1.1064041e-05]	Yes
+Stroke	Sham	14	[0.55077413]	No
+Stroke	Sham	21	[0.11753365]	No
+Stroke	Sham	28	[0.31709092]	No
+Stroke	Sham	7	[0.56245379]	No
+Stroke	Sham	0	[0.225287]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_SSp_ll_cut.tt_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_CC_SSp_ll_cut.tt
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       364          Method:                  REML  
-No. Groups:             2            Scale:                   0.0055
-Min. group size:        158          Log-Likelihood:          inf   
-Max. group size:        206          Converged:               Yes   
-Mean group size:        182.0                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 145410.565 0.000 1.000 -284999.471 284999.471
-merged_timepoint 0.002      0.000 3.801 0.000       0.001      0.002
-Group Var        0.000                                              
-====================================================================
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0030
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 3.445 0.001  0.000  0.002
+Group Var         0.000                                   
+==========================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05 
 ====================================================
 group1 group2 meandiff p-adj   lower   upper  reject
 ----------------------------------------------------
-     0      3  -0.1019    0.0 -0.1549 -0.0488   True
-     0      7   0.0213 0.8836 -0.0347  0.0773  False
-     0     14  -0.0079 0.9985 -0.0632  0.0474  False
-     0     21   0.0026    1.0 -0.0527  0.0578  False
-     0     28   0.0173 0.9543 -0.0401  0.0746  False
-     3      7   0.1232    0.0  0.0711  0.1753   True
-     3     14    0.094    0.0  0.0427  0.1453   True
-     3     21   0.1045    0.0  0.0532  0.1557   True
-     3     28   0.1191    0.0  0.0656  0.1727   True
-     7     14  -0.0292 0.6352 -0.0836  0.0252  False
-     7     21  -0.0187 0.9204 -0.0731  0.0356  False
-     7     28   -0.004 0.9999 -0.0606  0.0525  False
-    14     21   0.0105 0.9933 -0.0431   0.064  False
-    14     28   0.0252 0.7855 -0.0306  0.0809  False
-    21     28   0.0147 0.9741 -0.0411  0.0704  False
+     0      3  -0.0502 0.0014 -0.0865 -0.0138   True
+     0      7   0.0182  0.746 -0.0201  0.0566  False
+     0     14   0.0226 0.5189 -0.0152  0.0605  False
+     0     21   0.0177  0.758 -0.0201  0.0555  False
+     0     28   0.0076 0.9934 -0.0316  0.0469  False
+     3      7   0.0684    0.0  0.0327  0.1041   True
+     3     14   0.0728    0.0  0.0377  0.1079   True
+     3     21   0.0679    0.0  0.0328   0.103   True
+     3     28   0.0578 0.0001  0.0211  0.0945   True
+     7     14   0.0044 0.9994 -0.0328  0.0416  False
+     7     21  -0.0005    1.0 -0.0377  0.0367  False
+     7     28  -0.0106 0.9693 -0.0493  0.0281  False
+    14     21  -0.0049 0.9989 -0.0416  0.0317  False
+    14     28   -0.015  0.868 -0.0532  0.0232  False
+    21     28  -0.0101 0.9738 -0.0482  0.0281  False
 ----------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0045 0.9997 -0.0387 0.0476  False
-     0      7   0.0214 0.6568 -0.0195 0.0623  False
-     0     14   0.0183  0.758 -0.0209 0.0576  False
-     0     21   0.0322 0.3086 -0.0127 0.0771  False
-     0     28   0.0136 0.9401  -0.029 0.0562  False
-     3      7    0.017 0.8731 -0.0268 0.0607  False
-     3     14   0.0139 0.9335 -0.0284 0.0561  False
-     3     21   0.0278 0.5445 -0.0198 0.0753  False
-     3     28   0.0092  0.992 -0.0362 0.0546  False
-     7     14  -0.0031 0.9999 -0.0431 0.0369  False
-     7     21   0.0108 0.9835 -0.0348 0.0563  False
-     7     28  -0.0078 0.9953 -0.0511 0.0355  False
-    14     21   0.0139 0.9436 -0.0302  0.058  False
-    14     28  -0.0047 0.9995 -0.0464  0.037  False
-    21     28  -0.0186 0.8644 -0.0657 0.0285  False
+     0      3    0.019 0.7675 -0.0222 0.0603  False
+     0      7   0.0154 0.8654 -0.0237 0.0545  False
+     0     14   0.0141 0.8866 -0.0234 0.0517  False
+     0     21   0.0191 0.7946 -0.0239 0.0621  False
+     0     28   0.0228 0.5914  -0.018 0.0636  False
+     3      7  -0.0036 0.9999 -0.0455 0.0383  False
+     3     14  -0.0049 0.9993 -0.0453 0.0355  False
+     3     21   0.0001    1.0 -0.0455 0.0456  False
+     3     28   0.0038 0.9999 -0.0397 0.0472  False
+     7     14  -0.0013    1.0 -0.0395  0.037  False
+     7     21   0.0037 0.9999 -0.0399 0.0473  False
+     7     28   0.0074 0.9956  -0.034 0.0488  False
+    14     21    0.005 0.9994 -0.0372 0.0472  False
+    14     28   0.0087  0.989 -0.0313 0.0486  False
+    21     28   0.0037 0.9999 -0.0414 0.0488  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[3.65120556e-06]	Yes
-Stroke	Sham	14	[0.29480995]	No
-Stroke	Sham	21	[0.24413607]	No
-Stroke	Sham	28	[0.506431]	No
-Stroke	Sham	7	[0.54939184]	No
-Stroke	Sham	0	[0.63701489]	No
+Stroke	Sham	3	[0.00011701]	Yes
+Stroke	Sham	14	[0.0938913]	No
+Stroke	Sham	21	[0.47058644]	No
+Stroke	Sham	28	[0.86749777]	No
+Stroke	Sham	7	[0.18892638]	No
+Stroke	Sham	0	[0.39046146]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_SSp_ul.tt_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CC_SSp_ul.tt
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0014
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 4.180 0.000  0.000  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3  -0.0298 0.0202 -0.0567 -0.0029   True
+     0      7   0.0232 0.1776 -0.0052  0.0516  False
+     0     14   0.0173  0.481 -0.0107  0.0453  False
+     0     21   0.0121 0.8149 -0.0159  0.0401  False
+     0     28   0.0158 0.6226 -0.0133  0.0449  False
+     3      7   0.0531    0.0  0.0266  0.0795   True
+     3     14   0.0471    0.0  0.0211  0.0731   True
+     3     21   0.0419 0.0001  0.0159  0.0679   True
+     3     28   0.0456    0.0  0.0185  0.0728   True
+     7     14  -0.0059 0.9896 -0.0335  0.0216  False
+     7     21  -0.0111 0.8536 -0.0387  0.0164  False
+     7     28  -0.0074 0.9758 -0.0361  0.0212  False
+    14     21  -0.0052 0.9938 -0.0324  0.0219  False
+    14     28  -0.0015    1.0 -0.0298  0.0267  False
+    21     28   0.0037  0.999 -0.0245   0.032  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0094 0.8974 -0.0163 0.0351  False
+     0      7   0.0089 0.8983 -0.0155 0.0333  False
+     0     14   0.0066 0.9646 -0.0168   0.03  False
+     0     21   0.0169 0.4532 -0.0098 0.0437  False
+     0     28   0.0209 0.1721 -0.0045 0.0463  False
+     3      7  -0.0005    1.0 -0.0266 0.0256  False
+     3     14  -0.0028 0.9995  -0.028 0.0224  False
+     3     21   0.0075  0.973 -0.0208 0.0358  False
+     3     28   0.0115 0.8245 -0.0156 0.0385  False
+     7     14  -0.0023 0.9998 -0.0261 0.0215  False
+     7     21    0.008 0.9569 -0.0191 0.0351  False
+     7     28    0.012 0.7618 -0.0138 0.0378  False
+    14     21   0.0103 0.8663 -0.0159 0.0366  False
+    14     28   0.0143 0.5614 -0.0106 0.0392  False
+    21     28    0.004 0.9985 -0.0241  0.032  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[2.14962303e-05]	Yes
+Stroke	Sham	14	[0.52788483]	No
+Stroke	Sham	21	[0.36984103]	No
+Stroke	Sham	28	[0.22353458]	No
+Stroke	Sham	7	[0.19216749]	No
+Stroke	Sham	0	[0.66566373]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_SSp_ul_cut.tt_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_CC_SSp_ul_cut.tt
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       364          Method:                  REML  
-No. Groups:             2            Scale:                   0.0042
-Min. group size:        158          Log-Likelihood:          inf   
-Max. group size:        206          Converged:               Yes   
-Mean group size:        182.0                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 127230.612 0.000 1.000 -249367.417 249367.417
-merged_timepoint 0.001      0.000 2.172 0.030       0.000      0.001
-Group Var        0.000                                              
-====================================================================
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0019
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 3.823 0.000  0.000  0.001
+Group Var         0.000                                   
+==========================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05 
 ====================================================
 group1 group2 meandiff p-adj   lower   upper  reject
 ----------------------------------------------------
-     0      3   -0.088    0.0 -0.1341 -0.0419   True
-     0      7   0.0136 0.9661 -0.0351  0.0624  False
-     0     14  -0.0159 0.9317 -0.0639  0.0321  False
-     0     21  -0.0222  0.768 -0.0702  0.0258  False
-     0     28   0.0022    1.0 -0.0476  0.0521  False
-     3      7   0.1016    0.0  0.0563  0.1469   True
-     3     14   0.0721 0.0001  0.0275  0.1166   True
-     3     21   0.0658 0.0005  0.0212  0.1103   True
-     3     28   0.0902    0.0  0.0437  0.1368   True
-     7     14  -0.0296 0.4678 -0.0768  0.0177  False
-     7     21  -0.0358 0.2502 -0.0831  0.0114  False
-     7     28  -0.0114 0.9852 -0.0605  0.0377  False
-    14     21  -0.0063 0.9988 -0.0528  0.0403  False
-    14     28   0.0182 0.8894 -0.0303  0.0666  False
-    21     28   0.0244 0.6951  -0.024  0.0729  False
+     0      3  -0.0345 0.0135 -0.0645 -0.0046   True
+     0      7   0.0236 0.2693 -0.0081  0.0552  False
+     0     14   0.0216  0.352 -0.0096  0.0527  False
+     0     21   0.0157 0.6984 -0.0155  0.0469  False
+     0     28   0.0121   0.89 -0.0203  0.0445  False
+     3      7   0.0581    0.0  0.0287  0.0875   True
+     3     14   0.0561    0.0  0.0272   0.085   True
+     3     21   0.0502    0.0  0.0213  0.0792   True
+     3     28   0.0467 0.0002  0.0164  0.0769   True
+     7     14   -0.002    1.0 -0.0327  0.0287  False
+     7     21  -0.0079 0.9767 -0.0386  0.0228  False
+     7     28  -0.0114 0.9066 -0.0433  0.0205  False
+    14     21  -0.0059 0.9934 -0.0361  0.0243  False
+    14     28  -0.0094 0.9547 -0.0409   0.022  False
+    21     28  -0.0036 0.9995  -0.035  0.0279  False
 ----------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0131 0.9299 -0.0525 0.0263  False
-     0      7   0.0106 0.9634 -0.0267  0.048  False
-     0     14   0.0085 0.9834 -0.0274 0.0444  False
-     0     21    0.007 0.9965 -0.0341  0.048  False
-     0     28  -0.0001    1.0  -0.039 0.0389  False
-     3      7   0.0237 0.5268 -0.0163 0.0637  False
-     3     14   0.0216 0.5899  -0.017 0.0602  False
-     3     21   0.0201 0.7671 -0.0234 0.0635  False
-     3     28    0.013 0.9444 -0.0285 0.0545  False
-     7     14  -0.0021    1.0 -0.0386 0.0344  False
-     7     21  -0.0037 0.9999 -0.0453  0.038  False
-     7     28  -0.0107 0.9705 -0.0502 0.0289  False
-    14     21  -0.0016    1.0 -0.0418 0.0387  False
-    14     28  -0.0086 0.9869 -0.0467 0.0296  False
-    21     28   -0.007 0.9971 -0.0501  0.036  False
+     0      3   0.0143 0.7959 -0.0179 0.0465  False
+     0      7   0.0108 0.9099 -0.0197 0.0413  False
+     0     14   0.0101 0.9186 -0.0192 0.0394  False
+     0     21   0.0184 0.6105 -0.0151 0.0519  False
+     0     28   0.0235 0.2747 -0.0083 0.0554  False
+     3      7  -0.0035 0.9996 -0.0361 0.0292  False
+     3     14  -0.0042  0.999 -0.0357 0.0274  False
+     3     21   0.0041 0.9994 -0.0314 0.0396  False
+     3     28   0.0093  0.969 -0.0246 0.0432  False
+     7     14  -0.0007    1.0 -0.0305 0.0292  False
+     7     21   0.0076 0.9874 -0.0264 0.0416  False
+     7     28   0.0127 0.8652 -0.0196  0.045  False
+    14     21   0.0083 0.9784 -0.0246 0.0412  False
+    14     28   0.0134 0.8146 -0.0177 0.0446  False
+    21     28   0.0051 0.9983   -0.03 0.0403  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[6.87548352e-05]	Yes
-Stroke	Sham	14	[0.1152134]	No
-Stroke	Sham	21	[0.13325731]	No
-Stroke	Sham	28	[0.75654611]	No
-Stroke	Sham	7	[0.63137747]	No
-Stroke	Sham	0	[0.87870613]	No
+Stroke	Sham	3	[0.00032966]	Yes
+Stroke	Sham	14	[0.1805099]	No
+Stroke	Sham	21	[0.93858798]	No
+Stroke	Sham	28	[0.35951994]	No
+Stroke	Sham	7	[0.08368631]	No
+Stroke	Sham	0	[0.88801707]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CST_links_CCasROA_log.txt

@@ -1,67 +0,0 @@
-Model Name: fa_CST_links_CCasROA
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       364          Method:                  REML  
-No. Groups:             2            Scale:                   0.0038
-Min. group size:        158          Log-Likelihood:          inf   
-Max. group size:        206          Converged:               Yes   
-Mean group size:        182.0                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 120099.026 0.000 1.000 -235389.765 235389.765
-merged_timepoint 0.001      0.000 2.254 0.024       0.000      0.001
-Group Var        0.000                                              
-====================================================================
-
-Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3  -0.0008    1.0 -0.0425 0.0409  False
-     0      7   0.0313   0.32 -0.0127 0.0754  False
-     0     14   0.0078 0.9956 -0.0357 0.0512  False
-     0     21   0.0279 0.4392 -0.0156 0.0713  False
-     0     28   0.0337 0.2673 -0.0114 0.0788  False
-     3      7   0.0321 0.2182 -0.0089 0.0731  False
-     3     14   0.0085 0.9903 -0.0318 0.0488  False
-     3     21   0.0286 0.3219 -0.0117 0.0689  False
-     3     28   0.0344 0.1781 -0.0077 0.0765  False
-     7     14  -0.0236 0.6085 -0.0663 0.0192  False
-     7     21  -0.0035 0.9999 -0.0462 0.0393  False
-     7     28   0.0023    1.0 -0.0421 0.0468  False
-    14     21   0.0201 0.7432  -0.022 0.0622  False
-    14     28   0.0259  0.533 -0.0179 0.0697  False
-    21     28   0.0058 0.9989  -0.038 0.0496  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3  -0.0281 0.5697 -0.0773 0.0212  False
-     0      7  -0.0238 0.6805 -0.0705 0.0228  False
-     0     14    -0.01 0.9875 -0.0548 0.0348  False
-     0     21  -0.0132  0.976 -0.0645  0.038  False
-     0     28  -0.0026    1.0 -0.0512 0.0461  False
-     3      7   0.0042 0.9999 -0.0458 0.0542  False
-     3     14   0.0181  0.888 -0.0302 0.0663  False
-     3     21   0.0148 0.9691 -0.0395 0.0691  False
-     3     28   0.0255 0.7143 -0.0263 0.0773  False
-     7     14   0.0139 0.9514 -0.0318 0.0595  False
-     7     21   0.0106 0.9916 -0.0414 0.0626  False
-     7     28   0.0213 0.8141 -0.0281 0.0707  False
-    14     21  -0.0032    1.0 -0.0536 0.0471  False
-    14     28   0.0074 0.9976 -0.0402 0.0551  False
-    21     28   0.0107 0.9927 -0.0431 0.0644  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.91655122]	No
-Stroke	Sham	14	[0.59928458]	No
-Stroke	Sham	21	[0.31051704]	No
-Stroke	Sham	28	[0.42478602]	No
-Stroke	Sham	7	[0.07906389]	No
-Stroke	Sham	0	[0.14215384]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CST_rechts_CC_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CST_rechts_CC_cut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0030
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 3.238 0.001  0.000  0.002
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0033 0.9999 -0.0346 0.0413  False
+     0      7   0.0338 0.1522 -0.0063 0.0738  False
+     0     14   0.0041 0.9997 -0.0354 0.0436  False
+     0     21   0.0287 0.2975 -0.0108 0.0682  False
+     0     28   0.0376 0.0923 -0.0034 0.0786  False
+     3      7   0.0304 0.1792 -0.0068 0.0677  False
+     3     14   0.0007    1.0 -0.0359 0.0374  False
+     3     21   0.0253 0.3527 -0.0113  0.062  False
+     3     28   0.0343 0.1075  -0.004 0.0726  False
+     7     14  -0.0297 0.2427 -0.0685 0.0092  False
+     7     21  -0.0051  0.999  -0.044 0.0337  False
+     7     28   0.0039 0.9998 -0.0365 0.0443  False
+    14     21   0.0246 0.4371 -0.0137 0.0629  False
+    14     28   0.0336 0.1529 -0.0063 0.0734  False
+    21     28    0.009 0.9871 -0.0309 0.0488  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0201 0.7448 -0.0626 0.0223  False
+     0      7  -0.0123 0.9496 -0.0526 0.0279  False
+     0     14     -0.0    1.0 -0.0387 0.0386  False
+     0     21   0.0038 0.9999 -0.0404  0.048  False
+     0     28   0.0128 0.9508 -0.0291 0.0547  False
+     3      7   0.0078 0.9952 -0.0353 0.0509  False
+     3     14   0.0201 0.7299 -0.0215 0.0617  False
+     3     21   0.0239 0.6805 -0.0229 0.0707  False
+     3     28   0.0329 0.2791 -0.0118 0.0776  False
+     7     14   0.0123 0.9454  -0.027 0.0516  False
+     7     21   0.0161 0.9044 -0.0287 0.0609  False
+     7     28   0.0251 0.5326 -0.0175 0.0677  False
+    14     21   0.0038 0.9999 -0.0396 0.0472  False
+    14     28   0.0128 0.9458 -0.0283 0.0539  False
+    21     28    0.009 0.9934 -0.0374 0.0554  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.62789173]	No
+Stroke	Sham	14	[0.04115819]	Yes
+Stroke	Sham	21	[0.66504833]	No
+Stroke	Sham	28	[0.66406778]	No
+Stroke	Sham	7	[0.2279851]	No
+Stroke	Sham	0	[0.04645306]	Yes

output/Final_Quantitative_output/mixed_model_analysis/fa_CST_rechts_CCasROA_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CST_rechts_CCasROA
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0029
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 3.277 0.001  0.000  0.002
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0047 0.9992 -0.0329 0.0423  False
+     0      7   0.0351 0.1172 -0.0046 0.0748  False
+     0     14   0.0057 0.9983 -0.0334 0.0449  False
+     0     21   0.0305 0.2228 -0.0086 0.0697  False
+     0     28   0.0378 0.0843 -0.0028 0.0785  False
+     3      7   0.0303 0.1741 -0.0066 0.0673  False
+     3     14    0.001    1.0 -0.0354 0.0373  False
+     3     21   0.0258 0.3221 -0.0105 0.0621  False
+     3     28   0.0331 0.1261 -0.0048  0.071  False
+     7     14  -0.0294 0.2452 -0.0679 0.0092  False
+     7     21  -0.0045 0.9994 -0.0431  0.034  False
+     7     28   0.0028    1.0 -0.0373 0.0428  False
+    14     21   0.0248 0.4162 -0.0131 0.0628  False
+    14     28   0.0321 0.1828 -0.0074 0.0716  False
+    21     28   0.0073 0.9948 -0.0322 0.0468  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   -0.019 0.7806 -0.0609 0.0229  False
+     0      7  -0.0104 0.9749 -0.0501 0.0294  False
+     0     14    0.001    1.0 -0.0371 0.0392  False
+     0     21   0.0045 0.9997 -0.0392 0.0481  False
+     0     28   0.0133 0.9393 -0.0281 0.0547  False
+     3      7   0.0086 0.9919 -0.0339 0.0512  False
+     3     14     0.02 0.7228 -0.0211 0.0611  False
+     3     21   0.0234 0.6881 -0.0228 0.0697  False
+     3     28   0.0323 0.2873 -0.0119 0.0764  False
+     7     14   0.0114 0.9582 -0.0275 0.0503  False
+     7     21   0.0148 0.9281 -0.0295 0.0591  False
+     7     28   0.0237 0.5853 -0.0184 0.0657  False
+    14     21   0.0034 0.9999 -0.0395 0.0463  False
+    14     28   0.0123 0.9528 -0.0283 0.0528  False
+    21     28   0.0088 0.9936  -0.037 0.0546  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.62783192]	No
+Stroke	Sham	14	[0.04007984]	Yes
+Stroke	Sham	21	[0.71905275]	No
+Stroke	Sham	28	[0.64085779]	No
+Stroke	Sham	7	[0.25070437]	No
+Stroke	Sham	0	[0.04370333]	Yes

output/Final_Quantitative_output/mixed_model_analysis/fa_CST_rechts_ROA_CC_fibers_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CST_rechts_ROA_CC_fibers_cut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0030
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 3.226 0.001  0.000  0.002
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0045 0.9993 -0.0332 0.0423  False
+     0      7   0.0348 0.1262 -0.0051 0.0747  False
+     0     14   0.0049 0.9992 -0.0344 0.0443  False
+     0     21   0.0301 0.2417 -0.0092 0.0695  False
+     0     28   0.0376 0.0906 -0.0032 0.0785  False
+     3      7   0.0303 0.1809 -0.0069 0.0674  False
+     3     14   0.0004    1.0 -0.0362 0.0369  False
+     3     21   0.0256  0.338  -0.011 0.0621  False
+     3     28   0.0331 0.1305 -0.0051 0.0712  False
+     7     14  -0.0299 0.2327 -0.0686 0.0088  False
+     7     21  -0.0047 0.9993 -0.0434  0.034  False
+     7     28   0.0028    1.0 -0.0375 0.0431  False
+    14     21   0.0252 0.4051  -0.013 0.0634  False
+    14     28   0.0327  0.172  -0.007 0.0724  False
+    21     28   0.0075 0.9942 -0.0322 0.0472  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0194 0.7671 -0.0613 0.0226  False
+     0      7  -0.0112 0.9654 -0.0509 0.0286  False
+     0     14   0.0004    1.0 -0.0377 0.0386  False
+     0     21   0.0039 0.9998 -0.0398 0.0476  False
+     0     28   0.0127 0.9493 -0.0287 0.0542  False
+     3      7   0.0082 0.9936 -0.0344 0.0508  False
+     3     14   0.0198 0.7331 -0.0213 0.0609  False
+     3     21   0.0233 0.6958  -0.023 0.0696  False
+     3     28   0.0321 0.2946 -0.0121 0.0763  False
+     7     14   0.0116  0.955 -0.0273 0.0505  False
+     7     21   0.0151 0.9232 -0.0293 0.0594  False
+     7     28   0.0239  0.575 -0.0182  0.066  False
+    14     21   0.0035 0.9999 -0.0394 0.0464  False
+    14     28   0.0123 0.9523 -0.0283 0.0529  False
+    21     28   0.0088 0.9936  -0.037 0.0547  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.61963447]	No
+Stroke	Sham	14	[0.03777481]	Yes
+Stroke	Sham	21	[0.71077959]	No
+Stroke	Sham	28	[0.64291972]	No
+Stroke	Sham	7	[0.24633692]	No
+Stroke	Sham	0	[0.04285046]	Yes

output/Final_Quantitative_output/mixed_model_analysis/fa_Retikulospinal_tract_links_log.txt

@@ -1,67 +0,0 @@
-Model Name: fa_Retikulospinal_tract_links
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      364          Method:                  REML  
-No. Groups:            2            Scale:                   0.0021
-Min. group size:       158          Log-Likelihood:          inf   
-Max. group size:       206          Converged:               Yes   
-Mean group size:       182.0                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 90356.851 0.000 1.000 -177096.174 177096.174
-merged_timepoint 0.001     0.000 2.806 0.005       0.000      0.001
-Group Var        0.000                                             
-===================================================================
-
-Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0013    1.0 -0.0302 0.0328  False
-     0      7   0.0232 0.3436 -0.0101 0.0565  False
-     0     14   0.0011    1.0 -0.0317 0.0339  False
-     0     21   0.0149 0.7824 -0.0179 0.0477  False
-     0     28   0.0239  0.336 -0.0102  0.058  False
-     3      7   0.0219  0.325  -0.009 0.0529  False
-     3     14  -0.0001    1.0 -0.0306 0.0303  False
-     3     21   0.0136 0.7923 -0.0168 0.0441  False
-     3     28   0.0226 0.3196 -0.0092 0.0544  False
-     7     14  -0.0221 0.3659 -0.0543 0.0102  False
-     7     21  -0.0083 0.9767 -0.0406  0.024  False
-     7     28   0.0007    1.0 -0.0329 0.0343  False
-    14     21   0.0137 0.8147 -0.0181 0.0456  False
-    14     28   0.0228 0.3581 -0.0103 0.0559  False
-    21     28    0.009   0.97 -0.0241 0.0421  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3  -0.0104 0.9657 -0.0476 0.0268  False
-     0      7  -0.0026 0.9999 -0.0379 0.0327  False
-     0     14   0.0043 0.9991 -0.0295 0.0382  False
-     0     21   0.0048 0.9992 -0.0339 0.0436  False
-     0     28   0.0199 0.6268 -0.0169 0.0566  False
-     3      7   0.0078 0.9912   -0.03 0.0456  False
-     3     14   0.0148 0.8511 -0.0217 0.0512  False
-     3     21   0.0152 0.8921 -0.0258 0.0563  False
-     3     28   0.0303   0.23 -0.0089 0.0694  False
-     7     14    0.007 0.9921 -0.0275 0.0414  False
-     7     21   0.0074 0.9941 -0.0319 0.0467  False
-     7     28   0.0225 0.5098 -0.0149 0.0598  False
-    14     21   0.0005    1.0 -0.0376 0.0385  False
-    14     28   0.0155 0.8149 -0.0205 0.0515  False
-    21     28    0.015 0.8933 -0.0256 0.0557  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.58462121]	No
-Stroke	Sham	14	[0.51027284]	No
-Stroke	Sham	21	[0.59756994]	No
-Stroke	Sham	28	[0.97519405]	No
-Stroke	Sham	7	[0.01810124]	Yes
-Stroke	Sham	0	[0.77014563]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_Retikulospinal_tract_rechts_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_Retikulospinal_tract_rechts
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   364      Method:              REML    
+No. Groups:         2        Scale:               0.0019  
+Min. group size:    158      Log-Likelihood:      609.2950
+Max. group size:    206      Converged:           Yes     
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        0.355    0.005 75.647 0.000  0.346  0.365
+merged_timepoint 0.000    0.000  1.999 0.046  0.000  0.001
+Group Var        0.000    0.001                           
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0083 0.9732 -0.0229 0.0395  False
+     0      7   0.0282 0.1415 -0.0048 0.0612  False
+     0     14   0.0038 0.9994 -0.0287 0.0363  False
+     0     21   0.0183 0.5873 -0.0142 0.0508  False
+     0     28   0.0227 0.3833  -0.011 0.0565  False
+     3      7   0.0199 0.4255 -0.0108 0.0506  False
+     3     14  -0.0045 0.9982 -0.0346 0.0257  False
+     3     21     0.01 0.9315 -0.0202 0.0402  False
+     3     28   0.0144 0.7747 -0.0171  0.046  False
+     7     14  -0.0244 0.2466 -0.0563 0.0076  False
+     7     21  -0.0099 0.9486 -0.0419 0.0221  False
+     7     28  -0.0055  0.997 -0.0387 0.0278  False
+    14     21   0.0145 0.7733 -0.0171  0.046  False
+    14     28   0.0189 0.5616 -0.0139 0.0517  False
+    21     28   0.0044 0.9988 -0.0284 0.0372  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0178 0.6191 -0.0506 0.0149  False
+     0      7  -0.0038 0.9993 -0.0348 0.0273  False
+     0     14   -0.002    1.0 -0.0319 0.0278  False
+     0     21   0.0022    1.0 -0.0319 0.0364  False
+     0     28   0.0056 0.9961 -0.0268  0.038  False
+     3      7   0.0141 0.8258 -0.0192 0.0474  False
+     3     14   0.0158 0.7158 -0.0163 0.0479  False
+     3     21   0.0201 0.5983 -0.0161 0.0562  False
+     3     28   0.0235 0.3693 -0.0111  0.058  False
+     7     14   0.0017    1.0 -0.0287 0.0321  False
+     7     21    0.006 0.9961 -0.0286 0.0406  False
+     7     28   0.0094 0.9631 -0.0235 0.0423  False
+    14     21   0.0043 0.9991 -0.0292 0.0378  False
+    14     28   0.0077  0.982 -0.0241 0.0394  False
+    21     28   0.0034 0.9998 -0.0324 0.0392  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.81920039]	No
+Stroke	Sham	14	[0.10738794]	No
+Stroke	Sham	21	[0.50743873]	No
+Stroke	Sham	28	[0.57790969]	No
+Stroke	Sham	7	[0.30330254]	No
+Stroke	Sham	0	[0.10428096]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_Rubrospinal_tract_links__log.txt

@@ -1,67 +0,0 @@
-Model Name: fa_Rubrospinal_tract_links_
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      364          Method:                  REML  
-No. Groups:            2            Scale:                   0.0020
-Min. group size:       158          Log-Likelihood:          inf   
-Max. group size:       206          Converged:               Yes   
-Mean group size:       182.0                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 88497.070 0.000 1.000 -173451.070 173451.070
-merged_timepoint 0.001     0.000 2.711 0.007       0.000      0.001
-Group Var        0.000                                             
-===================================================================
-
-Posthoc Analysis for Stroke:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3   0.0146  0.802 -0.0185 0.0476  False
-     0      7   0.0237 0.3756 -0.0113 0.0586  False
-     0     14   0.0073 0.9901 -0.0271 0.0418  False
-     0     21   0.0199 0.5564 -0.0145 0.0544  False
-     0     28   0.0267 0.2655  -0.009 0.0625  False
-     3      7   0.0091 0.9664 -0.0234 0.0416  False
-     3     14  -0.0072 0.9867 -0.0392 0.0247  False
-     3     21   0.0054 0.9967 -0.0266 0.0373  False
-     3     28   0.0122 0.9006 -0.0212 0.0455  False
-     7     14  -0.0163 0.7347 -0.0502 0.0175  False
-     7     21  -0.0037 0.9996 -0.0376 0.0302  False
-     7     28   0.0031 0.9999 -0.0321 0.0383  False
-    14     21   0.0126 0.8862 -0.0208  0.046  False
-    14     28   0.0194 0.5942 -0.0153 0.0542  False
-    21     28   0.0068 0.9932 -0.0279 0.0416  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3  -0.0039 0.9994 -0.0366 0.0288  False
-     0      7   0.0184 0.5223 -0.0125 0.0494  False
-     0     14   0.0193 0.4211 -0.0104 0.0491  False
-     0     21   0.0169 0.7066 -0.0171 0.0509  False
-     0     28   0.0213 0.4013 -0.0109 0.0536  False
-     3      7   0.0223 0.3809 -0.0109 0.0555  False
-     3     14   0.0232 0.2968 -0.0088 0.0552  False
-     3     21   0.0208 0.5572 -0.0153 0.0568  False
-     3     28   0.0252 0.2843 -0.0092 0.0596  False
-     7     14   0.0009    1.0 -0.0294 0.0312  False
-     7     21  -0.0015    1.0  -0.036  0.033  False
-     7     28   0.0029 0.9998 -0.0299 0.0357  False
-    14     21  -0.0024 0.9999 -0.0358  0.031  False
-    14     28    0.002    1.0 -0.0296 0.0336  False
-    21     28   0.0044 0.9992 -0.0312 0.0401  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.3660286]	No
-Stroke	Sham	14	[0.07192902]	No
-Stroke	Sham	21	[0.78938304]	No
-Stroke	Sham	28	[0.93010227]	No
-Stroke	Sham	7	[0.90037559]	No
-Stroke	Sham	0	[0.6242753]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_Rubrospinal_tract_rechts_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_Rubrospinal_tract_rechts
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0016
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 2.749 0.006  0.000  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0069 0.9842 -0.0224 0.0361  False
+     0      7   0.0275 0.1116 -0.0034 0.0584  False
+     0     14   0.0109 0.9075 -0.0196 0.0414  False
+     0     21   0.0194 0.4445  -0.011 0.0499  False
+     0     28   0.0191 0.5083 -0.0125 0.0507  False
+     3      7   0.0206 0.3098 -0.0081 0.0493  False
+     3     14    0.004 0.9985 -0.0242 0.0323  False
+     3     21   0.0126 0.7964 -0.0157 0.0408  False
+     3     28   0.0122 0.8408 -0.0173 0.0417  False
+     7     14  -0.0166  0.603 -0.0466 0.0134  False
+     7     21  -0.0081 0.9716  -0.038 0.0219  False
+     7     28  -0.0084 0.9713 -0.0395 0.0227  False
+    14     21   0.0085  0.961  -0.021 0.0381  False
+    14     28   0.0082 0.9725 -0.0225 0.0389  False
+    21     28  -0.0003    1.0 -0.0311 0.0304  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0217 0.2276 -0.0497 0.0063  False
+     0      7   0.0055 0.9908  -0.021 0.0321  False
+     0     14    0.009 0.9117 -0.0165 0.0345  False
+     0     21    0.007 0.9825 -0.0222 0.0362  False
+     0     28   0.0127 0.7678 -0.0149 0.0404  False
+     3      7   0.0272  0.069 -0.0012 0.0556  False
+     3     14   0.0307 0.0189  0.0032 0.0581   True
+     3     21   0.0287 0.0849 -0.0022 0.0596  False
+     3     28   0.0344  0.012   0.005 0.0639   True
+     7     14   0.0034 0.9989 -0.0225 0.0294  False
+     7     21   0.0015    1.0 -0.0281  0.031  False
+     7     28   0.0072 0.9764 -0.0209 0.0353  False
+    14     21   -0.002    1.0 -0.0306 0.0266  False
+    14     28   0.0038 0.9986 -0.0233 0.0309  False
+    21     28   0.0057 0.9943 -0.0248 0.0363  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.31564999]	No
+Stroke	Sham	14	[0.11478738]	No
+Stroke	Sham	21	[0.63788659]	No
+Stroke	Sham	28	[0.24319435]	No
+Stroke	Sham	7	[0.54595648]	No
+Stroke	Sham	0	[0.1796509]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_Thalamocorticale_links_SSp_and_SSs_End_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_Thalamocorticale_links_SSp_and_SSs_End
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       364          Method:                  REML  
-No. Groups:             2            Scale:                   0.0028
-Min. group size:        158          Log-Likelihood:          inf   
-Max. group size:        206          Converged:               Yes   
-Mean group size:        182.0                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 103291.732 0.000 1.000 -202448.075 202448.075
-merged_timepoint 0.001      0.000 4.369 0.000       0.001      0.002
-Group Var        0.000                                              
-====================================================================
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   364      Method:              REML    
+No. Groups:         2        Scale:               0.0018  
+Min. group size:    158      Log-Likelihood:      626.9240
+Max. group size:    206      Converged:           Yes     
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        0.351    0.004 98.486 0.000  0.344  0.358
+merged_timepoint 0.001    0.000  2.382 0.017  0.000  0.001
+Group Var        0.000    0.001                           
+==========================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0006    1.0 -0.0366 0.0378  False
-     0      7   0.0364 0.0871 -0.0029 0.0757  False
-     0     14   0.0191 0.7141 -0.0196 0.0579  False
-     0     21   0.0267 0.3575 -0.0121 0.0654  False
-     0     28   0.0366 0.0976 -0.0036 0.0769  False
-     3      7   0.0358 0.0588 -0.0008 0.0724  False
-     3     14   0.0185 0.6757 -0.0174 0.0545  False
-     3     21   0.0261 0.2994 -0.0099  0.062  False
-     3     28    0.036 0.0686 -0.0016 0.0736  False
-     7     14  -0.0173 0.7836 -0.0554 0.0209  False
-     7     21  -0.0097 0.9775 -0.0479 0.0284  False
-     7     28   0.0002    1.0 -0.0394 0.0399  False
-    14     21   0.0075 0.9925   -0.03 0.0451  False
-    14     28   0.0175 0.7922 -0.0216 0.0566  False
-    21     28     0.01 0.9777 -0.0292 0.0491  False
+     0      3  -0.0153 0.6483 -0.0442 0.0136  False
+     0      7   0.0152  0.708 -0.0153 0.0457  False
+     0     14   0.0076 0.9789 -0.0225 0.0377  False
+     0     21  -0.0031 0.9997 -0.0332  0.027  False
+     0     28   0.0131 0.8353 -0.0182 0.0443  False
+     3      7   0.0305 0.0272  0.0021 0.0589   True
+     3     14   0.0229 0.1766  -0.005 0.0508  False
+     3     21   0.0122 0.8068 -0.0157 0.0401  False
+     3     28   0.0284 0.0617 -0.0008 0.0575  False
+     7     14  -0.0076 0.9766 -0.0372  0.022  False
+     7     21  -0.0183 0.4834 -0.0479 0.0113  False
+     7     28  -0.0021    1.0 -0.0329 0.0287  False
+    14     21  -0.0107 0.8996 -0.0398 0.0185  False
+    14     28   0.0055 0.9953 -0.0249 0.0359  False
+    21     28   0.0162 0.6445 -0.0142 0.0465  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0215 0.6303 -0.0614 0.0184  False
-     0      7   0.0064 0.9966 -0.0315 0.0442  False
-     0     14   0.0213 0.5405 -0.0151 0.0576  False
-     0     21   0.0253 0.4971 -0.0163 0.0668  False
-     0     28   0.0268  0.368 -0.0126 0.0663  False
-     3      7   0.0278 0.3568 -0.0127 0.0683  False
-     3     14   0.0427 0.0234  0.0036 0.0818   True
-     3     21   0.0468 0.0303  0.0027 0.0908   True
-     3     28   0.0483 0.0142  0.0063 0.0903   True
-     7     14   0.0149 0.8537 -0.0221 0.0519  False
-     7     21   0.0189 0.7869 -0.0232 0.0611  False
-     7     28   0.0205 0.6808 -0.0196 0.0605  False
-    14     21    0.004 0.9997 -0.0368 0.0448  False
-    14     28   0.0056 0.9984 -0.0331 0.0442  False
-    21     28   0.0015    1.0  -0.042 0.0451  False
+     0      3   0.0019    1.0 -0.0307 0.0344  False
+     0      7   0.0068 0.9879  -0.024 0.0377  False
+     0     14   0.0125 0.8275 -0.0171 0.0422  False
+     0     21   0.0063 0.9947 -0.0277 0.0402  False
+     0     28    0.021 0.4183 -0.0112 0.0531  False
+     3      7    0.005  0.998 -0.0281 0.0381  False
+     3     14   0.0107 0.9286 -0.0213 0.0426  False
+     3     21   0.0044 0.9993 -0.0315 0.0403  False
+     3     28   0.0191 0.5941 -0.0152 0.0534  False
+     7     14   0.0057 0.9943 -0.0245 0.0359  False
+     7     21  -0.0006    1.0  -0.035 0.0338  False
+     7     28   0.0141 0.8126 -0.0186 0.0468  False
+    14     21  -0.0062 0.9944 -0.0395 0.0271  False
+    14     28   0.0085 0.9715 -0.0231   0.04  False
+    21     28   0.0147   0.84 -0.0209 0.0503  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.33447047]	No
-Stroke	Sham	14	[0.42627266]	No
-Stroke	Sham	21	[0.69640622]	No
-Stroke	Sham	28	[0.72652921]	No
-Stroke	Sham	7	[0.03291398]	Yes
-Stroke	Sham	0	[0.74470625]	No
+Stroke	Sham	3	[0.1870792]	No
+Stroke	Sham	14	[0.82845236]	No
+Stroke	Sham	21	[0.65629644]	No
+Stroke	Sham	28	[0.60697592]	No
+Stroke	Sham	7	[0.23044934]	No
+Stroke	Sham	0	[0.79523627]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_Thalamocorticale_links_SSp_ll_and_ul_ROI.tt_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_Thalamocorticale_links_SSp_ll_and_ul_ROI.tt
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       364          Method:                  REML  
-No. Groups:             2            Scale:                   0.0038
-Min. group size:        158          Log-Likelihood:          inf   
-Max. group size:        206          Converged:               Yes   
-Mean group size:        182.0                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 119808.836 0.000 1.000 -234821.003 234821.003
-merged_timepoint 0.001      0.000 3.382 0.001       0.000      0.002
-Group Var        0.000                                              
-====================================================================
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0024
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 3.096 0.002  0.000  0.001
+Group Var         0.000                                   
+==========================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3    0.014 0.9417   -0.03 0.0581  False
-     0      7   0.0303  0.421 -0.0162 0.0768  False
-     0     14   0.0258 0.5884 -0.0201 0.0717  False
-     0     21    0.023 0.7017 -0.0229 0.0689  False
-     0     28   0.0212 0.7947 -0.0264 0.0689  False
-     3      7   0.0163 0.8882  -0.027 0.0595  False
-     3     14   0.0117 0.9684 -0.0308 0.0543  False
-     3     21   0.0089 0.9906 -0.0336 0.0515  False
-     3     28   0.0072 0.9973 -0.0373 0.0517  False
-     7     14  -0.0045 0.9997 -0.0497 0.0406  False
-     7     21  -0.0073 0.9972 -0.0525 0.0378  False
-     7     28  -0.0091 0.9936  -0.056 0.0378  False
-    14     21  -0.0028    1.0 -0.0473 0.0417  False
-    14     28  -0.0046 0.9998 -0.0508 0.0417  False
-    21     28  -0.0018    1.0 -0.0481 0.0445  False
+     0      3   0.0115  0.937  -0.024  0.047  False
+     0      7   0.0309 0.1705 -0.0066 0.0684  False
+     0     14   0.0213 0.5596 -0.0156 0.0583  False
+     0     21   0.0143 0.8757 -0.0227 0.0512  False
+     0     28   0.0349 0.0984 -0.0035 0.0732  False
+     3      7   0.0194 0.5992 -0.0155 0.0542  False
+     3     14   0.0098 0.9632 -0.0245 0.0441  False
+     3     21   0.0028 0.9999 -0.0315 0.0371  False
+     3     28   0.0233 0.4205 -0.0125 0.0592  False
+     7     14  -0.0096 0.9739  -0.046 0.0268  False
+     7     21  -0.0166 0.7759  -0.053 0.0197  False
+     7     28    0.004 0.9997 -0.0338 0.0418  False
+    14     21   -0.007 0.9931 -0.0429 0.0288  False
+    14     28   0.0135 0.9019 -0.0237 0.0508  False
+    21     28   0.0206 0.6071 -0.0167 0.0579  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0332 0.2532 -0.0771 0.0107  False
-     0      7  -0.0015    1.0 -0.0431 0.0401  False
-     0     14   0.0298 0.2657 -0.0101 0.0698  False
-     0     21   0.0399 0.1261 -0.0059 0.0856  False
-     0     28   0.0295 0.3678 -0.0139 0.0729  False
-     3      7   0.0316 0.3202 -0.0129 0.0762  False
-     3     14    0.063 0.0006    0.02  0.106   True
-     3     21    0.073 0.0004  0.0246 0.1214   True
-     3     28   0.0627 0.0019  0.0165 0.1089   True
-     7     14   0.0313 0.2335 -0.0094  0.072  False
-     7     21   0.0414 0.1098  -0.005 0.0878  False
-     7     28    0.031 0.3284  -0.013 0.0751  False
-    14     21     0.01 0.9873 -0.0349 0.0549  False
-    14     28  -0.0003    1.0 -0.0428 0.0422  False
-    21     28  -0.0103 0.9893 -0.0583 0.0376  False
+     0      3  -0.0161 0.7644  -0.051 0.0187  False
+     0      7  -0.0021    1.0 -0.0352 0.0309  False
+     0     14   0.0171 0.6293 -0.0146 0.0488  False
+     0     21    0.009 0.9794 -0.0273 0.0454  False
+     0     28   0.0178 0.6681 -0.0166 0.0523  False
+     3      7    0.014  0.863 -0.0214 0.0494  False
+     3     14   0.0332 0.0617 -0.0009 0.0674  False
+     3     21   0.0252 0.4123 -0.0133 0.0637  False
+     3     28    0.034 0.0869 -0.0027 0.0707  False
+     7     14   0.0192 0.5225 -0.0131 0.0516  False
+     7     21   0.0112 0.9517 -0.0257  0.048  False
+     7     28     0.02 0.5683  -0.015  0.055  False
+    14     21  -0.0081 0.9867 -0.0437 0.0276  False
+    14     28   0.0007    1.0  -0.033 0.0345  False
+    21     28   0.0088 0.9853 -0.0293 0.0469  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.04439733]	Yes
-Stroke	Sham	14	[0.14713536]	No
-Stroke	Sham	21	[0.08062381]	No
-Stroke	Sham	28	[0.14439825]	No
-Stroke	Sham	7	[0.22187249]	No
-Stroke	Sham	0	[0.43722154]	No
+Stroke	Sham	3	[0.31870497]	No
+Stroke	Sham	14	[0.45303153]	No
+Stroke	Sham	21	[0.48345388]	No
+Stroke	Sham	28	[0.84779007]	No
+Stroke	Sham	7	[0.15411489]	No
+Stroke	Sham	0	[0.14268119]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_Thalamocorticale_links_SSp_ul_and_ll_End_0,2.tt_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_Thalamocorticale_links_SSp_ul_and_ll_End_0,2.tt
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       364          Method:                  REML  
-No. Groups:             2            Scale:                   0.0029
-Min. group size:        158          Log-Likelihood:          inf   
-Max. group size:        206          Converged:               Yes   
-Mean group size:        182.0                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 104801.305 0.000 1.000 -205406.784 205406.784
-merged_timepoint 0.001      0.000 4.001 0.000       0.001      0.002
-Group Var        0.000                                              
-====================================================================
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0019
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 3.596 0.000  0.000  0.001
+Group Var         0.000                                   
+==========================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0007    1.0 -0.0409 0.0394  False
-     0      7   0.0225 0.6472 -0.0199 0.0649  False
-     0     14   0.0164 0.8688 -0.0254 0.0582  False
-     0     21   0.0177 0.8264 -0.0241 0.0596  False
-     0     28   0.0282 0.4244 -0.0152 0.0717  False
-     3      7   0.0232 0.5371 -0.0162 0.0627  False
-     3     14   0.0171  0.801 -0.0217  0.056  False
-     3     21   0.0185 0.7458 -0.0204 0.0573  False
-     3     28   0.0289 0.3163 -0.0116 0.0695  False
-     7     14  -0.0061 0.9982 -0.0473 0.0351  False
-     7     21  -0.0048 0.9994 -0.0459 0.0364  False
-     7     28   0.0057 0.9989 -0.0371 0.0485  False
-    14     21   0.0013    1.0 -0.0392 0.0419  False
-    14     28   0.0118 0.9664 -0.0304  0.054  False
-    21     28   0.0105 0.9801 -0.0317 0.0527  False
+     0      3   0.0009    1.0 -0.0315 0.0334  False
+     0      7   0.0178 0.6666 -0.0164 0.0521  False
+     0     14   0.0135 0.8575 -0.0202 0.0473  False
+     0     21   0.0104 0.9503 -0.0234 0.0441  False
+     0     28   0.0266 0.2511 -0.0085 0.0616  False
+     3      7   0.0169 0.6492  -0.015 0.0487  False
+     3     14   0.0126 0.8563 -0.0187 0.0439  False
+     3     21   0.0094 0.9545 -0.0219 0.0407  False
+     3     28   0.0256 0.2183 -0.0071 0.0583  False
+     7     14  -0.0043 0.9991 -0.0375  0.029  False
+     7     21  -0.0075 0.9873 -0.0407 0.0258  False
+     7     28   0.0088  0.978 -0.0258 0.0433  False
+    14     21  -0.0032 0.9998 -0.0359 0.0295  False
+    14     28    0.013 0.8807  -0.021 0.0471  False
+    21     28   0.0162 0.7446 -0.0178 0.0503  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0221 0.5101 -0.0588 0.0146  False
-     0      7   0.0025 0.9999 -0.0323 0.0373  False
-     0     14   0.0206 0.4846 -0.0129  0.054  False
-     0     21   0.0297 0.2256 -0.0086 0.0679  False
-     0     28   0.0272 0.2615 -0.0091 0.0635  False
-     3      7   0.0246 0.4039 -0.0127 0.0619  False
-     3     14   0.0426 0.0102  0.0067 0.0786   True
-     3     21   0.0518 0.0042  0.0113 0.0923   True
-     3     28   0.0493 0.0043  0.0106 0.0879   True
-     7     14   0.0181 0.6448  -0.016 0.0521  False
-     7     21   0.0272 0.3341 -0.0116  0.066  False
-     7     28   0.0247  0.386 -0.0122 0.0615  False
-    14     21   0.0091 0.9815 -0.0284 0.0467  False
-    14     28   0.0066 0.9945 -0.0289 0.0422  False
-    21     28  -0.0025    1.0 -0.0426 0.0376  False
+     0      3  -0.0089 0.9625 -0.0401 0.0223  False
+     0      7   0.0046 0.9978  -0.025 0.0341  False
+     0     14   0.0218 0.2377 -0.0066 0.0502  False
+     0     21   0.0153 0.7522 -0.0172 0.0478  False
+     0     28   0.0229 0.2713 -0.0079 0.0537  False
+     3      7   0.0135 0.8227 -0.0182 0.0451  False
+     3     14   0.0307 0.0485  0.0001 0.0613   True
+     3     21   0.0242 0.3305 -0.0102 0.0586  False
+     3     28   0.0318 0.0637  -0.001 0.0646  False
+     7     14   0.0172 0.5217 -0.0117 0.0461  False
+     7     21   0.0107 0.9356 -0.0222 0.0437  False
+     7     28   0.0183 0.5407  -0.013 0.0496  False
+    14     21  -0.0065 0.9917 -0.0384 0.0254  False
+    14     28   0.0011    1.0 -0.0291 0.0313  False
+    21     28   0.0076 0.9874 -0.0265 0.0417  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.37754957]	No
-Stroke	Sham	14	[0.2380515]	No
-Stroke	Sham	21	[0.12609133]	No
-Stroke	Sham	28	[0.45175961]	No
-Stroke	Sham	7	[0.44376951]	No
-Stroke	Sham	0	[0.58088757]	No
+Stroke	Sham	3	[0.34100387]	No
+Stroke	Sham	14	[0.59679531]	No
+Stroke	Sham	21	[0.7703945]	No
+Stroke	Sham	28	[0.61708763]	No
+Stroke	Sham	7	[0.15960852]	No
+Stroke	Sham	0	[0.88480905]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_Thalamocorticale_rechts_SSp_and_SSs_End_log.txt

@@ -1,67 +0,0 @@
-Model Name: fa_Thalamocorticale_rechts_SSp_and_SSs_End
-               Mixed Linear Model Regression Results
-===================================================================
-Model:                 MixedLM      Dependent Variable:      Value 
-No. Observations:      364          Method:                  REML  
-No. Groups:            2            Scale:                   0.0022
-Min. group size:       158          Log-Likelihood:          inf   
-Max. group size:       206          Converged:               Yes   
-Mean group size:       182.0                                       
--------------------------------------------------------------------
-                 Coef.  Std.Err.   z   P>|z|    [0.025     0.975]  
--------------------------------------------------------------------
-Intercept        0.000 90776.673 0.000 1.000 -177919.009 177919.009
-merged_timepoint 0.001     0.000 4.762 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  -0.0253 0.2404 -0.0584 0.0077  False
-     0      7   0.0075 0.9895 -0.0274 0.0425  False
-     0     14   0.0182 0.6501 -0.0162 0.0527  False
-     0     21   0.0132 0.8807 -0.0213 0.0476  False
-     0     28   0.0233  0.421 -0.0125 0.0591  False
-     3      7   0.0329 0.0457  0.0004 0.0654   True
-     3     14   0.0436 0.0017  0.0116 0.0756   True
-     3     21   0.0385 0.0084  0.0065 0.0705   True
-     3     28   0.0487 0.0006  0.0153 0.0821   True
-     7     14   0.0107 0.9439 -0.0232 0.0446  False
-     7     21   0.0057 0.9968 -0.0283 0.0396  False
-     7     28   0.0158 0.7911 -0.0195  0.051  False
-    14     21  -0.0051  0.998 -0.0385 0.0283  False
-    14     28   0.0051 0.9983 -0.0297 0.0398  False
-    21     28   0.0101   0.96 -0.0246 0.0449  False
----------------------------------------------------
-Posthoc Analysis for Sham:
-Multiple Comparison of Means - Tukey HSD, FWER=0.05
-===================================================
-group1 group2 meandiff p-adj   lower  upper  reject
----------------------------------------------------
-     0      3  -0.0077 0.9866 -0.0417 0.0263  False
-     0      7   0.0155 0.7371 -0.0168 0.0477  False
-     0     14   0.0194 0.4655 -0.0116 0.0504  False
-     0     21   0.0297 0.1562 -0.0057 0.0652  False
-     0     28   0.0223 0.3963 -0.0113  0.056  False
-     3      7   0.0232 0.3854 -0.0114 0.0577  False
-     3     14   0.0271 0.1837 -0.0063 0.0605  False
-     3     21   0.0374 0.0514 -0.0001  0.075  False
-     3     28     0.03 0.1564 -0.0058 0.0659  False
-     7     14   0.0039 0.9992 -0.0276 0.0355  False
-     7     21   0.0143 0.8621 -0.0217 0.0502  False
-     7     28   0.0069 0.9922 -0.0273  0.041  False
-    14     21   0.0103 0.9559 -0.0245 0.0452  False
-    14     28    0.003 0.9998   -0.03 0.0359  False
-    21     28  -0.0074 0.9926 -0.0446 0.0298  False
----------------------------------------------------
-Sidak Multiple Comparisons:
-Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.27079836]	No
-Stroke	Sham	14	[0.89400019]	No
-Stroke	Sham	21	[0.25369572]	No
-Stroke	Sham	28	[0.69822939]	No
-Stroke	Sham	7	[0.65828778]	No
-Stroke	Sham	0	[0.78797249]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_Thalamocorticale_rechts_SSp_ll_and_ul_ROI.tt_log.txt

@@ -1,67 +1,67 @@
 Model Name: fa_Thalamocorticale_rechts_SSp_ll_and_ul_ROI.tt
-               Mixed Linear Model Regression Results
-====================================================================
-Model:                  MixedLM      Dependent Variable:      Value 
-No. Observations:       364          Method:                  REML  
-No. Groups:             2            Scale:                   0.0033
-Min. group size:        158          Log-Likelihood:          inf   
-Max. group size:        206          Converged:               Yes   
-Mean group size:        182.0                                       
---------------------------------------------------------------------
-                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
---------------------------------------------------------------------
-Intercept        0.000 111977.028 0.000 1.000 -219470.942 219470.942
-merged_timepoint 0.001      0.000 1.968 0.049       0.000      0.001
-Group Var        0.000                                              
-====================================================================
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0022
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 2.258 0.024  0.000  0.001
+Group Var         0.000                                   
+==========================================================
 
 Posthoc Analysis for Stroke:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3   0.0008    1.0  -0.041 0.0427  False
-     0      7     0.02 0.7857 -0.0243 0.0642  False
-     0     14   0.0263 0.5104 -0.0173 0.0699  False
-     0     21   0.0277 0.4487 -0.0159 0.0714  False
-     0     28   0.0209  0.768 -0.0244 0.0662  False
-     3      7   0.0191 0.7642  -0.022 0.0602  False
-     3     14   0.0254  0.462  -0.015 0.0659  False
-     3     21   0.0269 0.3977 -0.0136 0.0674  False
-     3     28   0.0201 0.7464 -0.0222 0.0624  False
-     7     14   0.0063 0.9982 -0.0366 0.0492  False
-     7     21   0.0078 0.9953 -0.0351 0.0507  False
-     7     28    0.001    1.0 -0.0436 0.0456  False
-    14     21   0.0014    1.0 -0.0408 0.0437  False
-    14     28  -0.0054 0.9993 -0.0494 0.0386  False
-    21     28  -0.0068 0.9978 -0.0508 0.0372  False
+     0      3   0.0056 0.9973 -0.0291 0.0402  False
+     0      7   0.0246 0.3859  -0.012 0.0612  False
+     0     14   0.0193 0.6418 -0.0168 0.0553  False
+     0     21   0.0195 0.6298 -0.0166 0.0556  False
+     0     28   0.0262 0.3396 -0.0113 0.0637  False
+     3      7    0.019 0.5958  -0.015  0.053  False
+     3     14   0.0137 0.8481 -0.0198 0.0472  False
+     3     21   0.0139 0.8387 -0.0196 0.0474  False
+     3     28   0.0206 0.5361 -0.0144 0.0556  False
+     7     14  -0.0053 0.9981 -0.0408 0.0302  False
+     7     21  -0.0051 0.9985 -0.0406 0.0304  False
+     7     28   0.0016    1.0 -0.0353 0.0385  False
+    14     21   0.0002    1.0 -0.0347 0.0352  False
+    14     28   0.0069  0.994 -0.0295 0.0433  False
+    21     28   0.0067 0.9949 -0.0297 0.0431  False
 ---------------------------------------------------
 Posthoc Analysis for Sham:
 Multiple Comparison of Means - Tukey HSD, FWER=0.05
 ===================================================
 group1 group2 meandiff p-adj   lower  upper  reject
 ---------------------------------------------------
-     0      3  -0.0194  0.749 -0.0604 0.0217  False
-     0      7   0.0085 0.9885 -0.0304 0.0474  False
-     0     14   0.0118 0.9435 -0.0256 0.0491  False
-     0     21   0.0097 0.9867 -0.0331 0.0524  False
-     0     28  -0.0063 0.9976 -0.0468 0.0342  False
-     3      7   0.0279 0.3867 -0.0138 0.0695  False
-     3     14   0.0311 0.2278 -0.0091 0.0713  False
-     3     21    0.029 0.4364 -0.0162 0.0743  False
-     3     28   0.0131 0.9526 -0.0301 0.0562  False
-     7     14   0.0033 0.9999 -0.0348 0.0413  False
-     7     21   0.0011    1.0 -0.0422 0.0445  False
-     7     28  -0.0148 0.9038  -0.056 0.0263  False
-    14     21  -0.0021    1.0 -0.0441 0.0398  False
-    14     28  -0.0181 0.7766 -0.0578 0.0216  False
-    21     28   -0.016 0.9077 -0.0608 0.0288  False
+     0      3  -0.0071  0.991 -0.0413 0.0271  False
+     0      7   0.0078 0.9827 -0.0247 0.0402  False
+     0     14   0.0075 0.9826 -0.0237 0.0386  False
+     0     21   0.0021    1.0 -0.0336 0.0378  False
+     0     28   0.0091 0.9711 -0.0247 0.0429  False
+     3      7   0.0149 0.8189 -0.0199 0.0497  False
+     3     14   0.0146 0.8093  -0.019 0.0481  False
+     3     21   0.0092 0.9814 -0.0286  0.047  False
+     3     28   0.0162  0.786 -0.0198 0.0523  False
+     7     14  -0.0003    1.0  -0.032 0.0314  False
+     7     21  -0.0057 0.9976 -0.0419 0.0305  False
+     7     28   0.0013    1.0  -0.033 0.0357  False
+    14     21  -0.0054 0.9978 -0.0404 0.0296  False
+    14     28   0.0016    1.0 -0.0315 0.0348  False
+    21     28    0.007 0.9944 -0.0304 0.0444  False
 ---------------------------------------------------
 Sidak Multiple Comparisons:
 Group1	Group2	TimePoint	PValue	SignificantDifference
-Stroke	Sham	3	[0.7920296]	No
-Stroke	Sham	14	[0.49614679]	No
-Stroke	Sham	21	[0.65788077]	No
-Stroke	Sham	28	[0.86551507]	No
-Stroke	Sham	7	[0.30853113]	No
-Stroke	Sham	0	[0.07191963]	No
+Stroke	Sham	3	[0.96253076]	No
+Stroke	Sham	14	[0.97375745]	No
+Stroke	Sham	21	[0.690129]	No
+Stroke	Sham	28	[0.71647447]	No
+Stroke	Sham	7	[0.61687265]	No
+Stroke	Sham	0	[0.4375834]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_Thalamocorticale_rechts_SSp_ul_and_ll_End_0,2.tt_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_Thalamocorticale_rechts_SSp_ul_and_ll_End_0,2.tt
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0019
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 2.552 0.011  0.000  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0045 0.9988 -0.0285 0.0376  False
+     0      7   0.0251 0.3104 -0.0099   0.06  False
+     0     14   0.0155 0.7872 -0.0189 0.0499  False
+     0     21   0.0223 0.4271 -0.0121 0.0567  False
+     0     28   0.0214 0.5186 -0.0144 0.0572  False
+     3      7   0.0205 0.4555 -0.0119  0.053  False
+     3     14    0.011 0.9208  -0.021 0.0429  False
+     3     21   0.0178 0.5977 -0.0142 0.0498  False
+     3     28   0.0169 0.6924 -0.0165 0.0503  False
+     7     14  -0.0095 0.9652 -0.0434 0.0243  False
+     7     21  -0.0027 0.9999 -0.0366 0.0311  False
+     7     28  -0.0036 0.9997 -0.0389 0.0316  False
+    14     21   0.0068 0.9918 -0.0266 0.0402  False
+    14     28   0.0059 0.9965 -0.0288 0.0406  False
+    21     28  -0.0009    1.0 -0.0356 0.0338  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0088 0.9587 -0.0388 0.0213  False
+     0      7   0.0048 0.9966 -0.0237 0.0333  False
+     0     14   0.0059 0.9888 -0.0214 0.0333  False
+     0     21   0.0057 0.9953 -0.0256 0.0369  False
+     0     28   0.0119 0.8556 -0.0178 0.0416  False
+     3      7   0.0136 0.7934 -0.0169 0.0441  False
+     3     14   0.0147 0.6998 -0.0147 0.0442  False
+     3     21   0.0144 0.8076 -0.0187 0.0476  False
+     3     28   0.0207 0.4129 -0.0109 0.0523  False
+     7     14   0.0012    1.0 -0.0267  0.029  False
+     7     21   0.0009    1.0 -0.0309 0.0326  False
+     7     28   0.0071 0.9836  -0.023 0.0373  False
+    14     21  -0.0003    1.0  -0.031 0.0304  False
+    14     28    0.006 0.9914 -0.0231  0.035  False
+    21     28   0.0063 0.9939 -0.0266 0.0391  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.84386282]	No
+Stroke	Sham	14	[0.87053663]	No
+Stroke	Sham	21	[0.66612852]	No
+Stroke	Sham	28	[0.87916918]	No
+Stroke	Sham	7	[0.27276602]	No
+Stroke	Sham	0	[0.47316997]	No