code ready for: mixed model analysis and the post hoc tests nad figures with their relevant outputs. also code and results ready for heatmaps of the behavioral and dwi values correlations

code/heat_maps_correlation.py

@@ -0,0 +1,49 @@
+import os
+import pandas as pd
+import seaborn as sns
+import matplotlib.pyplot as plt
+
+# Set up the directory paths
+code_dir = os.path.dirname(os.path.abspath(__file__))
+parent_dir = os.path.dirname(code_dir)
+csv_file = os.path.join(parent_dir, 'output', "Correlation_with_behavior", 'correlation_dti_with_behavior.csv')
+output_dir = os.path.dirname(csv_file)
+
+# Read the CSV file into a DataFrame
+df = pd.read_csv(csv_file)
+
+# Get unique Qtypes
+qtypes = df["Qtype"].unique()
+
+# Iterate over unique values of 'Qtype'
+for qtype in qtypes:
+    # Filter the DataFrame for the current 'Qtype'
+    filtered_df = df[df["Qtype"] == qtype]
+    
+    # Get unique groups within the filtered DataFrame
+    groups = filtered_df["Group"].unique()
+    
+    # Set up figure for the current Qtype
+    num_groups = len(groups)
+    fig, axes = plt.subplots(num_groups, 2, figsize=(16, num_groups * 6))
+    
+    # Iterate over unique values of 'Group' within the current Qtype
+    for i, group in enumerate(groups):
+        # Filter the DataFrame for the current 'Group'
+        group_df = filtered_df[filtered_df["Group"] == group]
+        
+        # Pivot the filtered DataFrame to prepare for heatmap
+        for j, value in enumerate(['R_corr', 'Pval_corr']):
+            heatmap_df = group_df.pivot(index='mask_name', columns='merged_timepoint', values=value)
+            
+            # Plot heatmap
+            sns.heatmap(heatmap_df, ax=axes[i, j], cmap='coolwarm', annot=True, fmt=".2f", cbar=True)
+            axes[i, j].set_title(f'Group: {group}, Qtype: {qtype}, Value: {value}')
+            axes[i, j].set_xlabel('Time Point', fontsize=8)
+            axes[i, j].set_ylabel('Tract Name', fontsize=8)
+            axes[i, j].tick_params(axis='both', which='major', labelsize=8)
+    
+    plt.tight_layout()
+    save_path = os.path.join(output_dir, f'heatmap_{qtype}.png')
+    plt.savefig(save_path, dpi=300)
+    plt.show()

code/plotting_quantitative_dti_values.py

@@ -1,24 +1,62 @@
 import os
-import sys
 import pandas as pd
 import seaborn as sns
 import matplotlib.pyplot as plt
 import statsmodels.formula.api as smf
 from statsmodels.stats.multicomp import MultiComparison
+from itertools import combinations
+import statsmodels
+import scipy
 
 # Set up warning suppression for convergence
 import warnings
 warnings.simplefilter(action='ignore')
 
+# Define the PlotBoxplot function
+def PlotBoxplot(filtered_df, qq, mm, output_folder):
+    """
+    Plot boxplots for filtered dataframe and save as images.
+
+    Parameters:
+    filtered_df (DataFrame): Filtered dataframe based on "Qtype" and "mask_name".
+    qq (str): Qtype value.
+    mm (str): Mask_name value.
+    output_folder (str): Path to the output folder to save images.
+    """
+    # Set the color palette to Set2
+    sns.set_palette("Set1")
+    
+    # Create a boxplot
+    sns.boxplot(data=filtered_df, x="merged_timepoint", y="Value", hue="Group", fliersize=3 ,flierprops={"marker": "o"})
+    
+    # Set title and labels
+    plt.title(f'{mm}')
+    plt.xlabel('Timepoint')
+    plt.ylabel(qq)
+    
+    # Show legend without title and frame
+    plt.legend(title=None, frameon=False)
+    
+    # Save the plot as an image
+    output_path = os.path.join(output_folder, f'{qq}_{mm}_mixedlm_significant.png')
+    plt.savefig(output_path, dpi=100)
+    
+    # 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__))
 
 # Get the parent directory of the code directory
 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", 'Final_Quantitative_output&behavior_data.csv')
+# Create a new folder for mixed model analysis
+mixed_model_dir = os.path.join(parent_dir, 'output', "Final_Quantitative_output", 'mixed_model_analysis')
+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')
 df = pd.read_csv(input_file_path)
 
 # Filtering the dataframe based on conditions
@@ -26,11 +64,6 @@ df_f1 = df[(df["dialation_amount"] == 0) & (~df["merged_timepoint"].isin([42, 56
 
 # Create lists to store results and terminal output
 results = []
-terminal_output = []
-
-# Redirect standard output to a file
-terminal_output_file = os.path.join(parent_dir, 'output', "Final_Quantitative_output", 'terminalOutput.txt')
-sys.stdout = open(terminal_output_file, 'w')
 
 # Iterate over unique values of "Qtype" and "mask_name"
 for qq in df["Qtype"].unique():
@@ -39,57 +72,58 @@ for qq in df["Qtype"].unique():
         filtered_df = df_f1[(df_f1["Qtype"] == qq) & (df_f1["mask_name"] == mm)]
         
         # Fit the mixed-effects model
+        model_name = f"{qq}_{mm}"
         md = smf.mixedlm("Value ~ merged_timepoint", filtered_df, groups=filtered_df["Group"])
         mdf = md.fit(method=["lbfgs"])
         
-        # Print the model name
-        model_name = str(qq) + "_" + str(mm)
-        print(model_name)
-        terminal_output.append(model_name)
+        # Log file for each combination of qq and mm
+        log_file = os.path.join(mixed_model_dir, f"{model_name}_log.txt")
+       
         
-        # Print the summary
-        summary_text = str(mdf.summary())
-        print(summary_text)
-        terminal_output.append(summary_text)
+        # Check if the p-value is significant
+        if mdf.pvalues['merged_timepoint'] < 0.05:
+            with open(log_file, 'w') as log:
+                # Print model name to log file
+                log.write(f"Model Name: {model_name}\n")
+                
+                # Print the model summary to log file
+                log.write(str(mdf.summary()) + '\n')
+                # Plot and save boxplots for significant models
+                PlotBoxplot(filtered_df, qq, mm, mixed_model_dir)
+                
+                # Perform Tukey's HSD test for post hoc analysis
+                for gg in filtered_df["Group"].unique():
+                    filtered_df2 = filtered_df[filtered_df["Group"]==gg]
+                    mc = MultiComparison(filtered_df2["Value"], filtered_df2["merged_timepoint"])
+                    tukey_result = mc.tukeyhsd()
+                    
+                    # Print the summary of the test to log file
+                    log.write(f"Posthoc Analysis for {gg}:\n")
+                    log.write(str(tukey_result.summary()) + '\n')
+                
+                # Perform the Sidak multiple comparisons for the group effect
+                group_combinations = combinations(filtered_df["Group"].unique(), 2)
+                log.write("Sidak Multiple Comparisons:\n")
+                log.write("Group1\tGroup2\tTimePoint\tPValue\tSignificantDifference\n")
+                for group1, group2 in group_combinations:
+                    for time_point in filtered_df["merged_timepoint"].unique():
+                        group1_data = filtered_df[(filtered_df["Group"] == group1) & (filtered_df["merged_timepoint"] == time_point)]["Value"]
+                        group2_data = filtered_df[(filtered_df["Group"] == group2) & (filtered_df["merged_timepoint"] == time_point)]["Value"]
+                        sidak_result = statsmodels.stats.multitest.multipletests(scipy.stats.ttest_ind(group1_data, group2_data)[1], method='sidak')
+                        if sidak_result[0]:
+                            log.write(f"{group1}\t{group2}\t{time_point}\t{sidak_result[1]}\tYes\n")
+                        else:
+                            log.write(f"{group1}\t{group2}\t{time_point}\t{sidak_result[1]}\tNo\n")
         
         # Append the results to the list
         results.append({'Qtype': qq, 'mask_name': mm, 'p_value': mdf.pvalues['merged_timepoint']})
 
-        # Check if the p-value is significant
-        if mdf.pvalues['merged_timepoint'] < 0.05:
-            # Create a boxplot
-            sns.boxplot(data=filtered_df, x="merged_timepoint", y="Value", hue="Group")
-            
-            # Set title and labels
-            plt.title(f'Mask Name: {mm}')
-            plt.xlabel('Merged Timepoint')
-            plt.ylabel(qq)
-            
-            # Show plot
-            plt.legend(title=None, frameon=False)
-            plt.show()
-            
-            # Perform Tukey's HSD test for post hoc analysis
-            mc = MultiComparison(filtered_df["Value"], filtered_df["merged_timepoint"])
-            tukey_result = mc.tukeyhsd()
-            
-            # Print the summary of the test
-            tukey_summary_text = str(tukey_result.summary())
-            print(tukey_summary_text)
-            terminal_output.append(tukey_summary_text)
-
 # Create a DataFrame from results
 results_df = pd.DataFrame(results)
 
-# Print the table
-print(results_df)
-
-# Save results_df as CSV
-output_file_path = os.path.join(parent_dir, 'output', "Final_Quantitative_output", 'mixe_model_results.csv')
+# Save results_df as CSV in mixed_model_analysis folder
+output_file_path = os.path.join(mixed_model_dir, 'mixed_model_results.csv')
 results_df.to_csv(output_file_path, index=False)
 
-# Close the file
-sys.stdout.close()
-
-# Reset standard output
-sys.stdout = sys.__stdout__
+# Print the table
+print(results_df)

code/statsmodel_training.py

@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Apr  9 11:11:14 2024
+
+@author: arefks
+"""
+
+import numpy as np
+import pandas as pd
+import statsmodels.api as sm
+import statsmodels.formula.api as smf
+
+# grab the data/load data
+data = sm.datasets.get_rdataset("dietox", "geepack").data
+
+data.head()
+
+model = smf.mixedlm("Weight ~ Time",data,groups=data["Pig"])
+res = model.fit(method=["lbfgs"])
+res.summary()

code/transpose_csv.py

@@ -0,0 +1,64 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Mar 18 22:12:25 2024
+
+@author: arefk
+"""
+
+import pandas as pd
+import os
+# Get the directory where the code file is located
+code_dir = os.path.dirname(os.path.abspath(__file__))
+# Get the parent directory of the code directory
+parent_dir = os.path.dirname(code_dir)
+
+# Get the parent directory of the code directory
+parent_dir = os.path.dirname(code_dir)
+
+# Read the behavior data CSV file into a Pandas DataFrame
+input_file_path_data = os.path.join(parent_dir, 'output',
+                                        "Final_Quantitative_output",
+                                        'Quantitative_results_from_dwi_processing.csv')
+# Read the CSV file
+df0 = pd.read_csv(input_file_path_data)
+
+#filter anything?
+
+df = df0[(df0["Qtype"] == "rd") &
+         (df0["mask_name"] == "CC_MOp(dilated)_cut.tt") &
+         (df0["dialation_amount"] == 0)]
+Values = ["Value"]
+#%%
+# Create an empty DataFrame to store the transposed data
+transposed_data = pd.DataFrame()
+transpodeCloulmn = "Group"
+
+
+for vv in Values:
+    # Create an empty DataFrame to store the transposed data for this value
+    value_transposed_data = pd.DataFrame()
+
+    for group_value in df[transpodeCloulmn].unique():
+        # Filter DataFrame for current group value
+        filtered_df = df[df[transpodeCloulmn] == group_value]
+
+        # Pivot the DataFrame for current value and group
+        pivot_df = pd.pivot_table(filtered_df, values=vv, index="merged_timepoint", columns=["subjectID", transpodeCloulmn])
+
+        # Concatenate pivot_df to value_transposed_data
+        value_transposed_data = pd.concat([value_transposed_data, pivot_df], axis=1)
+
+    # Rename the index in value_transposed_data
+    value_transposed_data.index.name = vv
+
+    # Concatenate value_transposed_data with transposed_data along the first dimension
+    transposed_data = pd.concat([transposed_data, value_transposed_data, pd.DataFrame(index=[vv])])
+
+
+
+# Define the output file path
+output_file_path = os.path.join(parent_dir, 'output', "Final_Quantitative_output",'Transposed4Prism_FA_CC_MOP_dialated.csv')
+
+transposed_data.to_csv(output_file_path, index=True, header=True)
+
+print("Data restructured and saved successfully.")

output/Final_Quantitative_output/Transposed4Prism_FA_CC_MOP_dialated.csv

@@ -0,0 +1,11 @@
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+56,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1.001511355,1.11986167,0.926739451,0.793252457,,0.737758432,,0.810342421,0.841837274,,,,,,,,,,,,,,,,,,,,,,,,
+Value,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,

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

@@ -0,0 +1,67 @@
+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

@@ -0,0 +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                                              
+====================================================================
+
+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
+---------------------------------------------------
+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
+---------------------------------------------------
+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

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs_MOs_cut.tt_log.txt

@@ -0,0 +1,67 @@
+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

@@ -0,0 +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                                               
+======================================================================
+
+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
+----------------------------------------------------
+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
+----------------------------------------------------
+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

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_SSp_ul_cut.tt_log.txt

@@ -0,0 +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                                               
+======================================================================
+
+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
+----------------------------------------------------
+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
+----------------------------------------------------
+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

output/Final_Quantitative_output/mixed_model_analysis/ad_CST_links_CC_cut_log.txt

@@ -0,0 +1,67 @@
+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

@@ -0,0 +1,67 @@
+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

@@ -0,0 +1,67 @@
+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_Thalamocorticale_rechts_SSp_ll_and_ul_ROI.tt_log.txt

@@ -0,0 +1,67 @@
+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_MOs_MOs_cut.tt_log.txt

@@ -0,0 +1,67 @@
+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

@@ -0,0 +1,67 @@
+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

@@ -0,0 +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                                             
+===================================================================
+
+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
+----------------------------------------------------
+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
+---------------------------------------------------
+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

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_SSp_ll_cut.tt_log.txt

@@ -0,0 +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                                              
+====================================================================
+
+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
+----------------------------------------------------
+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
+---------------------------------------------------
+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

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_SSp_ul_cut.tt_log.txt

@@ -0,0 +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                                              
+====================================================================
+
+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
+----------------------------------------------------
+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
+---------------------------------------------------
+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

output/Final_Quantitative_output/mixed_model_analysis/fa_CST_links_CCasROA_log.txt

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

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

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

@@ -0,0 +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                                              
+====================================================================
+
+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
+---------------------------------------------------
+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
+---------------------------------------------------
+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

output/Final_Quantitative_output/mixed_model_analysis/fa_Thalamocorticale_links_SSp_ll_and_ul_ROI.tt_log.txt

@@ -0,0 +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                                              
+====================================================================
+
+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
+---------------------------------------------------
+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
+---------------------------------------------------
+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

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

@@ -0,0 +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                                              
+====================================================================
+
+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
+---------------------------------------------------
+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
+---------------------------------------------------
+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

output/Final_Quantitative_output/mixed_model_analysis/fa_Thalamocorticale_rechts_SSp_and_SSs_End_log.txt

@@ -0,0 +1,67 @@
+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

@@ -0,0 +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                                              
+====================================================================
+
+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
+---------------------------------------------------
+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
+---------------------------------------------------
+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

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

@@ -0,0 +1,67 @@
+Model Name: md_CC_MOp(dilated)_cut.tt
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   364      Method:              REML    
+No. Groups:         2        Scale:               0.0134  
+Min. group size:    158      Log-Likelihood:      258.1377
+Max. group size:    206      Converged:           Yes     
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        0.809    0.010 84.668 0.000  0.790  0.828
+merged_timepoint 0.003    0.001  5.119 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   0.0152 0.9929 -0.0618 0.0922  False
+     0      7   0.0127 0.9977 -0.0686  0.094  False
+     0     14   0.0899 0.0182  0.0097   0.17   True
+     0     21   0.1187 0.0004  0.0385 0.1989   True
+     0     28   0.1004 0.0083  0.0171 0.1836   True
+     3      7  -0.0025    1.0 -0.0781 0.0731  False
+     3     14   0.0747 0.0487  0.0003 0.1491   True
+     3     21   0.1035 0.0012  0.0291 0.1779   True
+     3     28   0.0852 0.0226  0.0075 0.1629   True
+     7     14   0.0772 0.0591 -0.0017 0.1561  False
+     7     21    0.106  0.002  0.0271 0.1849   True
+     7     28   0.0877 0.0284  0.0057 0.1697   True
+    14     21   0.0288 0.8938 -0.0489 0.1065  False
+    14     28   0.0105  0.999 -0.0704 0.0914  False
+    21     28  -0.0183 0.9868 -0.0992 0.0626  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0146 0.9976 -0.0793 0.1086  False
+     0      7    0.018  0.992 -0.0711 0.1071  False
+     0     14   0.0702 0.1745 -0.0154 0.1557  False
+     0     21   0.0187 0.9938 -0.0792 0.1166  False
+     0     28   0.0474 0.6827 -0.0455 0.1402  False
+     3      7   0.0033    1.0 -0.0921 0.0988  False
+     3     14   0.0555 0.5078 -0.0366 0.1476  False
+     3     21   0.0041    1.0 -0.0996 0.1078  False
+     3     28   0.0327 0.9314 -0.0662 0.1317  False
+     7     14   0.0522 0.5153  -0.035 0.1393  False
+     7     21   0.0008    1.0 -0.0985    0.1  False
+     7     28   0.0294 0.9463  -0.065 0.1237  False
+    14     21  -0.0514 0.6362 -0.1475 0.0447  False
+    14     28  -0.0228 0.9788 -0.1138 0.0682  False
+    21     28   0.0286 0.9664 -0.0741 0.1313  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.25217692]	No
+Stroke	Sham	14	[0.69414023]	No
+Stroke	Sham	21	[0.05766087]	No
+Stroke	Sham	28	[0.50471347]	No
+Stroke	Sham	7	[0.09801856]	No
+Stroke	Sham	0	[0.35118689]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CC_MOp_MOp_cut.tt_log.txt

@@ -0,0 +1,67 @@
+Model Name: md_CC_MOp_MOp_cut.tt
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       364          Method:                  REML  
+No. Groups:             2            Scale:                   0.0113
+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 207664.941 0.000 1.000 -407015.805 407015.805
+merged_timepoint 0.002      0.001 3.270 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    0.019 0.9701 -0.0509  0.089  False
+     0      7   0.0101 0.9988 -0.0638  0.084  False
+     0     14   0.0739 0.0448   0.001 0.1468   True
+     0     21   0.0858 0.0108   0.013 0.1587   True
+     0     28   0.0609 0.1927 -0.0148 0.1366  False
+     3      7   -0.009  0.999 -0.0777 0.0598  False
+     3     14   0.0548 0.1856 -0.0128 0.1225  False
+     3     21   0.0668  0.055 -0.0008 0.1344  False
+     3     28   0.0419   0.53 -0.0288 0.1125  False
+     7     14   0.0638 0.1121 -0.0079 0.1355  False
+     7     21   0.0758 0.0316  0.0041 0.1474   True
+     7     28   0.0508 0.3683 -0.0237 0.1253  False
+    14     21    0.012 0.9966 -0.0587 0.0826  False
+    14     28   -0.013 0.9958 -0.0865 0.0605  False
+    21     28  -0.0249 0.9249 -0.0985 0.0486  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0283 0.9373 -0.0592 0.1157  False
+     0      7    0.016 0.9935 -0.0669  0.099  False
+     0     14   0.0527 0.3984 -0.0268 0.1323  False
+     0     21   0.0047    1.0 -0.0864 0.0958  False
+     0     28   0.0298 0.9187 -0.0566 0.1162  False
+     3      7  -0.0122 0.9987  -0.101 0.0766  False
+     3     14   0.0245 0.9627 -0.0612 0.1102  False
+     3     21  -0.0236  0.981 -0.1201 0.0729  False
+     3     28   0.0015    1.0 -0.0905 0.0936  False
+     7     14   0.0367 0.7808 -0.0444 0.1178  False
+     7     21  -0.0113 0.9993 -0.1037  0.081  False
+     7     28   0.0138 0.9976  -0.074 0.1015  False
+    14     21  -0.0481 0.6318 -0.1375 0.0414  False
+    14     28  -0.0229 0.9702 -0.1076 0.0617  False
+    21     28   0.0251 0.9739 -0.0704 0.1206  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.12990659]	No
+Stroke	Sham	14	[0.65017049]	No
+Stroke	Sham	21	[0.11542356]	No
+Stroke	Sham	28	[0.90555331]	No
+Stroke	Sham	7	[0.01588272]	Yes
+Stroke	Sham	0	[0.2434252]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CC_MOs_MOs_cut.tt_log.txt

@@ -0,0 +1,67 @@
+Model Name: md_CC_MOs_MOs_cut.tt
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       364          Method:                  REML  
+No. Groups:             2            Scale:                   0.0100
+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 195087.688 0.000 1.000 -382364.842 382364.842
+merged_timepoint 0.001      0.001 2.000 0.045       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   0.0235 0.8626 -0.0357 0.0827  False
+     0      7   0.0092 0.9982 -0.0533 0.0717  False
+     0     14   0.0447 0.2972 -0.0169 0.1064  False
+     0     21   0.0629 0.0423  0.0013 0.1246   True
+     0     28   0.0364 0.5753 -0.0276 0.1004  False
+     3      7  -0.0143 0.9808 -0.0724 0.0438  False
+     3     14   0.0212 0.8933  -0.036 0.0784  False
+     3     21   0.0394 0.3553 -0.0178 0.0966  False
+     3     28   0.0129 0.9894 -0.0468 0.0726  False
+     7     14   0.0355  0.542 -0.0251 0.0962  False
+     7     21   0.0537 0.1148 -0.0069 0.1144  False
+     7     28   0.0272 0.8157 -0.0358 0.0902  False
+    14     21   0.0182 0.9518 -0.0415 0.0779  False
+    14     28  -0.0083 0.9989 -0.0705 0.0538  False
+    21     28  -0.0265 0.8226 -0.0887 0.0356  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0372 0.8527  -0.055 0.1295  False
+     0      7   0.0117 0.9989 -0.0758 0.0992  False
+     0     14   0.0218 0.9755 -0.0622 0.1058  False
+     0     21    0.014 0.9983 -0.0822 0.1101  False
+     0     28   0.0244 0.9718 -0.0668 0.1156  False
+     3      7  -0.0255 0.9694 -0.1193 0.0682  False
+     3     14  -0.0155 0.9963 -0.1059  0.075  False
+     3     21  -0.0233 0.9859 -0.1251 0.0785  False
+     3     28  -0.0129 0.9989   -0.11 0.0843  False
+     7     14   0.0101 0.9994 -0.0755 0.0956  False
+     7     21   0.0023    1.0 -0.0952 0.0998  False
+     7     28   0.0127 0.9987 -0.0799 0.1053  False
+    14     21  -0.0078 0.9999 -0.1022 0.0866  False
+    14     28   0.0026    1.0 -0.0867  0.092  False
+    21     28   0.0104 0.9997 -0.0904 0.1113  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.33787542]	No
+Stroke	Sham	14	[0.99713237]	No
+Stroke	Sham	21	[0.32555876]	No
+Stroke	Sham	28	[0.62216221]	No
+Stroke	Sham	7	[0.14567104]	No
+Stroke	Sham	0	[0.39664426]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CC_SSp_ll_cut.tt_log.txt

@@ -0,0 +1,67 @@
+Model Name: md_CC_SSp_ll_cut.tt
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM  Dependent Variable:  Value   
+No. Observations:    364      Method:              REML    
+No. Groups:          2        Scale:               0.0260  
+Min. group size:     158      Log-Likelihood:      137.6267
+Max. group size:     206      Converged:           Yes     
+Mean group size:     182.0                                 
+-----------------------------------------------------------
+                 Coef.  Std.Err.   z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept         0.750    0.023 33.000 0.000  0.706  0.795
+merged_timepoint -0.003    0.001 -3.785 0.000 -0.005 -0.002
+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   0.3175    0.0  0.2084  0.4266   True
+     0      7     -0.0    1.0 -0.1153  0.1152  False
+     0     14   0.0568 0.7043 -0.0569  0.1704  False
+     0     21    0.033 0.9603 -0.0806  0.1467  False
+     0     28   0.0078    1.0 -0.1102  0.1258  False
+     3      7  -0.3175    0.0 -0.4247 -0.2103   True
+     3     14  -0.2607    0.0 -0.3662 -0.1553   True
+     3     21  -0.2844    0.0 -0.3899  -0.179   True
+     3     28  -0.3097    0.0 -0.4198 -0.1995   True
+     7     14   0.0568 0.6888  -0.055  0.1686  False
+     7     21   0.0331 0.9573 -0.0787  0.1449  False
+     7     28   0.0078    1.0 -0.1084  0.1241  False
+    14     21  -0.0237 0.9895 -0.1339  0.0864  False
+    14     28   -0.049 0.8221 -0.1636  0.0657  False
+    21     28  -0.0253 0.9883 -0.1399  0.0894  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0919 0.0118  0.0133  0.1704   True
+     0      7   0.0114 0.9978  -0.063  0.0859  False
+     0     14   0.0033    1.0 -0.0682  0.0747  False
+     0     21   0.0218 0.9723   -0.06  0.1036  False
+     0     28  -0.0001    1.0 -0.0777  0.0774  False
+     3      7  -0.0804 0.0467 -0.1601 -0.0007   True
+     3     14  -0.0886  0.014 -0.1655 -0.0116   True
+     3     21  -0.0701 0.1866 -0.1567  0.0165  False
+     3     28   -0.092 0.0196 -0.1746 -0.0093   True
+     7     14  -0.0082 0.9995 -0.0809  0.0646  False
+     7     21   0.0103 0.9992 -0.0726  0.0933  False
+     7     28  -0.0116 0.9982 -0.0904  0.0672  False
+    14     21   0.0185 0.9854 -0.0618  0.0988  False
+    14     28  -0.0034    1.0 -0.0794  0.0726  False
+    21     28  -0.0219 0.9769 -0.1077  0.0638  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00317972]	Yes
+Stroke	Sham	14	[0.14665128]	No
+Stroke	Sham	21	[0.78060792]	No
+Stroke	Sham	28	[0.36966905]	No
+Stroke	Sham	7	[0.01478989]	Yes
+Stroke	Sham	0	[0.37370702]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CC_SSp_ul_cut.tt_log.txt

@@ -0,0 +1,67 @@
+Model Name: md_CC_SSp_ul_cut.tt
+                Mixed Linear Model Regression Results
+======================================================================
+Model:                  MixedLM       Dependent Variable:       Value 
+No. Observations:       364           Method:                   REML  
+No. Groups:             2             Scale:                    0.0234
+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 299172.909 -0.000 1.000 -586368.127 586368.127
+merged_timepoint -0.002      0.001 -2.268 0.023      -0.004     -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   0.2883    0.0  0.1808  0.3957   True
+     0      7   0.0156 0.9987 -0.0979  0.1291  False
+     0     14   0.0714 0.4447 -0.0405  0.1833  False
+     0     21   0.0615 0.6113 -0.0504  0.1734  False
+     0     28   0.0618  0.645 -0.0544   0.178  False
+     3      7  -0.2727    0.0 -0.3782 -0.1672   True
+     3     14  -0.2169    0.0 -0.3207  -0.113   True
+     3     21  -0.2268    0.0 -0.3306 -0.1229   True
+     3     28  -0.2265    0.0 -0.3349  -0.118   True
+     7     14   0.0558 0.6902 -0.0542  0.1659  False
+     7     21   0.0459  0.836 -0.0641   0.156  False
+     7     28   0.0462 0.8541 -0.0682  0.1607  False
+    14     21  -0.0099 0.9998 -0.1184  0.0986  False
+    14     28  -0.0096 0.9999 -0.1225  0.1033  False
+    21     28   0.0003    1.0 -0.1126  0.1132  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0897 0.0093  0.0146  0.1648   True
+     0      7   0.0218 0.9495 -0.0493   0.093  False
+     0     14   0.0007    1.0 -0.0677   0.069  False
+     0     21   0.0215 0.9684 -0.0567  0.0997  False
+     0     28   0.0126 0.9965 -0.0616  0.0867  False
+     3      7  -0.0679 0.1111 -0.1441  0.0083  False
+     3     14   -0.089 0.0081 -0.1626 -0.0155   True
+     3     21  -0.0682 0.1707  -0.151  0.0146  False
+     3     28  -0.0771 0.0601 -0.1562  0.0019  False
+     7     14  -0.0212 0.9512 -0.0908  0.0484  False
+     7     21  -0.0003    1.0 -0.0796  0.0789  False
+     7     28  -0.0093 0.9992 -0.0846  0.0661  False
+    14     21   0.0208   0.97 -0.0559  0.0976  False
+    14     28   0.0119  0.997 -0.0607  0.0846  False
+    21     28  -0.0089 0.9996 -0.0909  0.0731  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00290961]	Yes
+Stroke	Sham	14	[0.03183808]	Yes
+Stroke	Sham	21	[0.60369338]	No
+Stroke	Sham	28	[0.21298985]	No
+Stroke	Sham	7	[0.13060867]	No
+Stroke	Sham	0	[0.50771223]	No

output/Final_Quantitative_output/mixed_model_analysis/md_Thalamocorticale_rechts_SSp_ll_and_ul_ROI.tt_log.txt

@@ -0,0 +1,67 @@
+Model Name: md_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:                   0.0150
+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 239786.966 0.000 1.000 -469973.817 469973.817
+merged_timepoint 0.002      0.001 2.650 0.008       0.000      0.003
+Group Var        0.000                                              
+====================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0154 0.9859 -0.0515 0.0822  False
+     0      7  -0.0221 0.9459 -0.0927 0.0485  False
+     0     14   0.0061 0.9999 -0.0635 0.0757  False
+     0     21   0.0381 0.6169 -0.0315 0.1077  False
+     0     28   0.0518 0.3119 -0.0205 0.1241  False
+     3      7  -0.0375  0.572 -0.1031 0.0282  False
+     3     14  -0.0092 0.9985 -0.0738 0.0554  False
+     3     21   0.0227 0.9136 -0.0419 0.0873  False
+     3     28   0.0364 0.6299  -0.031 0.1039  False
+     7     14   0.0282 0.8433 -0.0403 0.0967  False
+     7     21   0.0602 0.1209 -0.0083 0.1286  False
+     7     28   0.0739 0.0369  0.0027 0.1451   True
+    14     21    0.032 0.7492 -0.0355 0.0994  False
+    14     28   0.0457 0.4229 -0.0246 0.1159  False
+    21     28   0.0137 0.9933 -0.0565 0.0839  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.1264 0.0244  0.0102  0.2426   True
+     0      7   0.0056    1.0 -0.1046  0.1158  False
+     0     14   0.0684 0.4273 -0.0374  0.1741  False
+     0     21    0.083 0.3597 -0.0381   0.204  False
+     0     28   0.0714  0.473 -0.0435  0.1862  False
+     3      7  -0.1208 0.0414 -0.2388 -0.0028   True
+     3     14   -0.058 0.6835 -0.1719  0.0559  False
+     3     21  -0.0434 0.9243 -0.1716  0.0848  False
+     3     28   -0.055 0.7855 -0.1774  0.0673  False
+     7     14   0.0628 0.5458  -0.045  0.1705  False
+     7     21   0.0774 0.4567 -0.0454  0.2001  False
+     7     28   0.0658 0.5818 -0.0509  0.1824  False
+    14     21   0.0146 0.9993 -0.1042  0.1334  False
+    14     28    0.003    1.0 -0.1095  0.1155  False
+    21     28  -0.0116 0.9998 -0.1385  0.1153  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.02816253]	Yes
+Stroke	Sham	14	[0.23630525]	No
+Stroke	Sham	21	[0.64988207]	No
+Stroke	Sham	28	[0.86481712]	No
+Stroke	Sham	7	[0.94461207]	No
+Stroke	Sham	0	[0.10059491]	No

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

@@ -0,0 +1,67 @@
+Model Name: rd_CC_MOp(dilated)_cut.tt
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       364          Method:                  REML  
+No. Groups:             2            Scale:                   0.0136
+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 228079.890 0.000 1.000 -447028.370 447028.370
+merged_timepoint 0.003      0.001 5.211 0.000       0.002      0.005
+Group Var        0.000                                              
+====================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0472 0.4714 -0.0285 0.1228  False
+     0      7   0.0224 0.9663 -0.0575 0.1023  False
+     0     14   0.1083 0.0015  0.0295  0.187   True
+     0     21   0.1368    0.0   0.058 0.2156   True
+     0     28   0.1154  0.001  0.0336 0.1972   True
+     3      7  -0.0248 0.9296 -0.0991 0.0495  False
+     3     14   0.0611 0.1597  -0.012 0.1342  False
+     3     21   0.0896 0.0068  0.0165 0.1627   True
+     3     28   0.0683  0.109 -0.0081 0.1446  False
+     7     14   0.0859 0.0203  0.0084 0.1634   True
+     7     21   0.1144 0.0005  0.0369 0.1919   True
+     7     28   0.0931 0.0133  0.0125 0.1737   True
+    14     21   0.0285 0.8908 -0.0478 0.1049  False
+    14     28   0.0072 0.9998 -0.0723 0.0867  False
+    21     28  -0.0214 0.9718 -0.1008 0.0581  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0203 0.9904 -0.0761 0.1166  False
+     0      7   0.0179 0.9931 -0.0734 0.1092  False
+     0     14   0.0712 0.1838 -0.0165 0.1588  False
+     0     21   0.0142 0.9985 -0.0861 0.1145  False
+     0     28    0.055 0.5557 -0.0402 0.1502  False
+     3      7  -0.0024    1.0 -0.1002 0.0955  False
+     3     14   0.0509 0.6285 -0.0435 0.1453  False
+     3     21  -0.0061    1.0 -0.1123 0.1002  False
+     3     28   0.0347 0.9212 -0.0667 0.1361  False
+     7     14   0.0533 0.5199  -0.036 0.1426  False
+     7     21  -0.0037    1.0 -0.1055 0.0981  False
+     7     28   0.0371 0.8779 -0.0596 0.1338  False
+    14     21   -0.057 0.5543 -0.1555 0.0415  False
+    14     28  -0.0162 0.9961 -0.1094 0.0771  False
+    21     28   0.0408 0.8732 -0.0645  0.146  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.51728467]	No
+Stroke	Sham	14	[0.85204373]	No
+Stroke	Sham	21	[0.02740397]	Yes
+Stroke	Sham	28	[0.62529813]	No
+Stroke	Sham	7	[0.10444998]	No
+Stroke	Sham	0	[0.17546995]	No

output/Final_Quantitative_output/mixed_model_analysis/rd_CC_MOp_MOp_cut.tt_log.txt

@@ -0,0 +1,67 @@
+Model Name: rd_CC_MOp_MOp_cut.tt
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       364          Method:                  REML  
+No. Groups:             2            Scale:                   0.0111
+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 205803.425 0.000 1.000 -403367.300 403367.300
+merged_timepoint 0.001      0.001 2.626 0.009       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   0.0654 0.0533 -0.0005 0.1313  False
+     0      7   0.0131 0.9944 -0.0566 0.0827  False
+     0     14   0.0899  0.003  0.0212 0.1585   True
+     0     21   0.0913 0.0024  0.0226   0.16   True
+     0     28   0.0678 0.0732 -0.0036 0.1391  False
+     3      7  -0.0523 0.1894 -0.1171 0.0125  False
+     3     14   0.0245 0.8792 -0.0393 0.0882  False
+     3     21   0.0259 0.8506 -0.0378 0.0897  False
+     3     28   0.0024    1.0 -0.0642 0.0689  False
+     7     14   0.0768 0.0158  0.0092 0.1444   True
+     7     21   0.0782  0.013  0.0107 0.1458   True
+     7     28   0.0547 0.2246 -0.0156 0.1249  False
+    14     21   0.0015    1.0 -0.0651  0.068  False
+    14     28  -0.0221 0.9416 -0.0914 0.0472  False
+    21     28  -0.0236 0.9244 -0.0929 0.0457  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0342 0.8805 -0.0555  0.124  False
+     0      7   0.0095 0.9995 -0.0756 0.0946  False
+     0     14   0.0426 0.6606  -0.039 0.1243  False
+     0     21  -0.0037    1.0 -0.0971 0.0898  False
+     0     28   0.0319 0.9043 -0.0568 0.1206  False
+     3      7  -0.0247 0.9702 -0.1158 0.0664  False
+     3     14   0.0084 0.9998 -0.0795 0.0964  False
+     3     21  -0.0379  0.879 -0.1369 0.0611  False
+     3     28  -0.0023    1.0 -0.0968 0.0922  False
+     7     14   0.0331   0.86 -0.0501 0.1163  False
+     7     21  -0.0132 0.9986  -0.108 0.0816  False
+     7     28   0.0224 0.9797 -0.0677 0.1124  False
+    14     21  -0.0463 0.6925  -0.138 0.0455  False
+    14     28  -0.0107 0.9992 -0.0976 0.0761  False
+    21     28   0.0355 0.9013 -0.0625 0.1336  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.55324595]	No
+Stroke	Sham	14	[0.971857]	No
+Stroke	Sham	21	[0.11891786]	No
+Stroke	Sham	28	[0.75755204]	No
+Stroke	Sham	7	[0.01949132]	Yes
+Stroke	Sham	0	[0.06342366]	No

output/Final_Quantitative_output/mixed_model_analysis/rd_CC_SSp_ll_cut.tt_log.txt

@@ -0,0 +1,67 @@
+Model Name: rd_CC_SSp_ll_cut.tt
+                Mixed Linear Model Regression Results
+======================================================================
+Model:                  MixedLM       Dependent Variable:       Value 
+No. Observations:       364           Method:                   REML  
+No. Groups:             2             Scale:                    0.0229
+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 296087.665 -0.000 1.000 -580321.160 580321.160
+merged_timepoint -0.003      0.001 -4.022 0.000      -0.005     -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   0.3076    0.0  0.2051  0.4101   True
+     0      7  -0.0017    1.0   -0.11  0.1066  False
+     0     14   0.0549 0.6785 -0.0519  0.1616  False
+     0     21   0.0309 0.9612 -0.0759  0.1377  False
+     0     28   0.0056    1.0 -0.1053  0.1165  False
+     3      7  -0.3093    0.0   -0.41 -0.2086   True
+     3     14  -0.2528    0.0 -0.3518 -0.1537   True
+     3     21  -0.2767    0.0 -0.3758 -0.1776   True
+     3     28   -0.302    0.0 -0.4055 -0.1985   True
+     7     14   0.0565 0.6331 -0.0485  0.1616  False
+     7     21   0.0326 0.9481 -0.0725  0.1376  False
+     7     28   0.0073    1.0 -0.1019  0.1165  False
+    14     21   -0.024 0.9854 -0.1275  0.0795  False
+    14     28  -0.0492 0.7763  -0.157  0.0585  False
+    21     28  -0.0253 0.9845  -0.133  0.0825  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0707 0.0475  0.0005   0.141   True
+     0      7  -0.0001    1.0 -0.0667  0.0665  False
+     0     14  -0.0042    1.0 -0.0681  0.0598  False
+     0     21   0.0032    1.0   -0.07  0.0764  False
+     0     28  -0.0076 0.9996 -0.0771  0.0618  False
+     3      7  -0.0708  0.053 -0.1422  0.0005  False
+     3     14  -0.0749 0.0245 -0.1438  -0.006   True
+     3     21  -0.0675 0.1264  -0.145    0.01  False
+     3     28  -0.0783 0.0311 -0.1523 -0.0044   True
+     7     14  -0.0041    1.0 -0.0692  0.0611  False
+     7     21   0.0033    1.0 -0.0709  0.0775  False
+     7     28  -0.0075 0.9996 -0.0781   0.063  False
+    14     21   0.0074 0.9997 -0.0645  0.0792  False
+    14     28  -0.0035    1.0 -0.0715  0.0646  False
+    21     28  -0.0108 0.9985 -0.0876  0.0659  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00137637]	Yes
+Stroke	Sham	14	[0.18053397]	No
+Stroke	Sham	21	[0.94063527]	No
+Stroke	Sham	28	[0.34285216]	No
+Stroke	Sham	7	[0.02077902]	Yes
+Stroke	Sham	0	[0.16939567]	No

output/Final_Quantitative_output/mixed_model_analysis/rd_CC_SSp_ul_cut.tt_log.txt

@@ -0,0 +1,67 @@
+Model Name: rd_CC_SSp_ul_cut.tt
+                Mixed Linear Model Regression Results
+======================================================================
+Model:                  MixedLM       Dependent Variable:       Value 
+No. Observations:       364           Method:                   REML  
+No. Groups:             2             Scale:                    0.0200
+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 276516.291 -0.000 1.000 -541961.972 541961.972
+merged_timepoint -0.002      0.001 -2.250 0.024      -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   0.2744    0.0  0.1746  0.3742   True
+     0      7    0.012 0.9995 -0.0934  0.1174  False
+     0     14   0.0695 0.3897 -0.0344  0.1735  False
+     0     21   0.0626 0.5111 -0.0413  0.1665  False
+     0     28   0.0586 0.6248 -0.0494  0.1665  False
+     3      7  -0.2624    0.0 -0.3604 -0.1644   True
+     3     14  -0.2048    0.0 -0.3013 -0.1084   True
+     3     21  -0.2118    0.0 -0.3082 -0.1153   True
+     3     28  -0.2158    0.0 -0.3166 -0.1151   True
+     7     14   0.0576 0.5861 -0.0447  0.1598  False
+     7     21   0.0507 0.7114 -0.0516  0.1529  False
+     7     28   0.0466 0.8056 -0.0597  0.1529  False
+    14     21  -0.0069    1.0 -0.1076  0.0938  False
+    14     28   -0.011 0.9997 -0.1158  0.0939  False
+    21     28  -0.0041    1.0 -0.1089  0.1008  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0762 0.0114  0.0113  0.1412   True
+     0      7   0.0136 0.9882 -0.0481  0.0752  False
+     0     14   0.0016    1.0 -0.0575  0.0608  False
+     0     21   0.0114 0.9967 -0.0563  0.0791  False
+     0     28   0.0105  0.997 -0.0537  0.0747  False
+     3      7  -0.0627  0.073 -0.1287  0.0033  False
+     3     14  -0.0746 0.0116 -0.1383 -0.0109   True
+     3     21  -0.0649 0.1006 -0.1366  0.0068  False
+     3     28  -0.0657 0.0676 -0.1341  0.0027  False
+     7     14  -0.0119 0.9927 -0.0722  0.0483  False
+     7     21  -0.0022    1.0 -0.0708  0.0665  False
+     7     28   -0.003    1.0 -0.0683  0.0622  False
+    14     21   0.0097 0.9982 -0.0567  0.0762  False
+    14     28   0.0089 0.9985  -0.054  0.0718  False
+    21     28  -0.0008    1.0 -0.0718  0.0702  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.0014257]	Yes
+Stroke	Sham	14	[0.05550986]	No
+Stroke	Sham	21	[0.4052899]	No
+Stroke	Sham	28	[0.29902061]	No
+Stroke	Sham	7	[0.1136952]	No
+Stroke	Sham	0	[0.37309884]	No

output/Final_Quantitative_output/mixed_model_analysis/rd_Rubrospinal_tract_rechts_log.txt

@@ -0,0 +1,67 @@
+Model Name: rd_Rubrospinal_tract_rechts
+               Mixed Linear Model Regression Results
+====================================================================
+Model:                  MixedLM      Dependent Variable:      Value 
+No. Observations:       364          Method:                  REML  
+No. Groups:             2            Scale:                   0.0065
+Min. group size:        158          Log-Likelihood:          inf   
+Max. group size:        206          Converged:               Yes   
+Mean group size:        182.0                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 158061.158 0.000 1.000 -309794.177 309794.177
+merged_timepoint 0.001      0.000 2.028 0.043       0.000      0.002
+Group Var        0.000                                              
+====================================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0088 0.9968  -0.044 0.0616  False
+     0      7  -0.0205 0.8975 -0.0763 0.0353  False
+     0     14   0.0278 0.6928 -0.0272 0.0828  False
+     0     21   0.0256 0.7613 -0.0294 0.0807  False
+     0     28   0.0352 0.4859 -0.0219 0.0923  False
+     3      7  -0.0293 0.5825 -0.0812 0.0226  False
+     3     14    0.019 0.8921  -0.032   0.07  False
+     3     21   0.0168  0.933 -0.0342 0.0679  False
+     3     28   0.0264 0.7129 -0.0269 0.0797  False
+     7     14   0.0483 0.1097 -0.0058 0.1024  False
+     7     21   0.0461 0.1432  -0.008 0.1003  False
+     7     28   0.0557 0.0542 -0.0006 0.1119  False
+    14     21  -0.0022    1.0 -0.0555 0.0511  False
+    14     28   0.0074 0.9989 -0.0481 0.0628  False
+    21     28   0.0095 0.9963  -0.046  0.065  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0387 0.5619 -0.0287  0.106  False
+     0      7   -0.012 0.9944 -0.0758 0.0519  False
+     0     14   0.0192 0.9453 -0.0421 0.0805  False
+     0     21   0.0249 0.9098 -0.0453  0.095  False
+     0     28   0.0061 0.9998 -0.0604 0.0727  False
+     3      7  -0.0506 0.2742  -0.119 0.0178  False
+     3     14  -0.0195 0.9569 -0.0855 0.0465  False
+     3     21  -0.0138 0.9945 -0.0881 0.0605  False
+     3     28  -0.0325 0.7713 -0.1034 0.0384  False
+     7     14   0.0311 0.7032 -0.0313 0.0936  False
+     7     21   0.0368 0.6693 -0.0344  0.108  False
+     7     28   0.0181 0.9717 -0.0495 0.0857  False
+    14     21   0.0057 0.9999 -0.0632 0.0745  False
+    14     28   -0.013 0.9924 -0.0782 0.0522  False
+    21     28  -0.0187 0.9775 -0.0923 0.0549  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.26238246]	No
+Stroke	Sham	14	[0.58043373]	No
+Stroke	Sham	21	[0.89820083]	No
+Stroke	Sham	28	[0.15789177]	No
+Stroke	Sham	7	[0.65625]	No
+Stroke	Sham	0	[0.86558798]	No

output/Final_Quantitative_output/mixed_model_analysis/rd_Thalamocorticale_rechts_SSp_ll_and_ul_ROI.tt_log.txt

@@ -0,0 +1,67 @@
+Model Name: rd_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:                   0.0124
+Min. group size:        158          Log-Likelihood:          inf   
+Max. group size:        206          Converged:               Yes   
+Mean group size:        182.0                                       
+--------------------------------------------------------------------
+                 Coef.  Std.Err.    z   P>|z|    [0.025     0.975]  
+--------------------------------------------------------------------
+Intercept        0.000 217322.035 0.000 1.000 -425943.362 425943.362
+merged_timepoint 0.001      0.001 2.393 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   0.0109 0.9966 -0.0536 0.0754  False
+     0      7  -0.0231 0.9249 -0.0913  0.045  False
+     0     14  -0.0069 0.9997 -0.0741 0.0603  False
+     0     21   0.0258 0.8781 -0.0413  0.093  False
+     0     28   0.0395 0.5817 -0.0303 0.1092  False
+     3      7   -0.034 0.6352 -0.0974 0.0293  False
+     3     14  -0.0178  0.963 -0.0802 0.0445  False
+     3     21   0.0149  0.983 -0.0474 0.0773  False
+     3     28   0.0285 0.8058 -0.0366 0.0937  False
+     7     14   0.0162 0.9811 -0.0499 0.0823  False
+     7     21    0.049 0.2752 -0.0171 0.1151  False
+     7     28   0.0626 0.0972 -0.0061 0.1313  False
+    14     21   0.0328 0.6976 -0.0324 0.0979  False
+    14     28   0.0464 0.3642 -0.0214 0.1142  False
+    21     28   0.0136 0.9924 -0.0542 0.0814  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3    0.105 0.0379  0.0036  0.2065   True
+     0      7   0.0006    1.0 -0.0956  0.0968  False
+     0     14   0.0524 0.5743 -0.0399  0.1448  False
+     0     21   0.0681 0.4305 -0.0376  0.1738  False
+     0     28   0.0653 0.4181 -0.0349  0.1656  False
+     3      7  -0.1045 0.0449 -0.2075 -0.0014   True
+     3     14  -0.0526 0.6479  -0.152  0.0469  False
+     3     21  -0.0369 0.9322 -0.1488   0.075  False
+     3     28  -0.0397 0.8915 -0.1465  0.0671  False
+     7     14   0.0519 0.6056 -0.0422  0.1459  False
+     7     21   0.0676 0.4566 -0.0396  0.1747  False
+     7     28   0.0648 0.4465 -0.0371  0.1666  False
+    14     21   0.0157  0.998 -0.0881  0.1194  False
+    14     28   0.0129  0.999 -0.0853  0.1111  False
+    21     28  -0.0028    1.0 -0.1137   0.108  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.06130315]	No
+Stroke	Sham	14	[0.25606818]	No
+Stroke	Sham	21	[0.71953533]	No
+Stroke	Sham	28	[0.93642713]	No
+Stroke	Sham	7	[0.77461475]	No
+Stroke	Sham	0	[0.06472879]	No