new run

code/correlation_between_bahavior_and_DTI.py

@@ -42,7 +42,7 @@ for dd in df["dialation_amount"].unique():
                         if shapiro_pvalueQValue < 0.05 or shapiro_pvalueBehavior < 0.05:
                             correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2["averageScore"])
                         else:
-                            correlation_coefficient, p_value = spearmanr(df_f2["Value"], df_f2["averageScore"])
+                            correlation_coefficient, p_value = pearsonr(df_f2["Value"], df_f2["averageScore"])
                        
     
                         # Store the results in a dictionary

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_cut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0109
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.002    0.001 3.017 0.003  0.001  0.003
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0018    0.9 -0.0748 0.0712  False
+     0      7   0.0078    0.9 -0.0693 0.0849  False
+     0     14   0.0407 0.6214 -0.0354 0.1167  False
+     0     21   0.0653 0.1377 -0.0108 0.1413  False
+     0     28   0.0549 0.3463 -0.0241 0.1338  False
+     3      7   0.0096    0.9 -0.0621 0.0813  False
+     3     14   0.0425 0.5107 -0.0281  0.113  False
+     3     21   0.0671 0.0729 -0.0035 0.1377  False
+     3     28   0.0567 0.2363  -0.017 0.1304  False
+     7     14   0.0328 0.7789  -0.042 0.1077  False
+     7     21   0.0575 0.2373 -0.0173 0.1323  False
+     7     28   0.0471 0.5048 -0.0307 0.1249  False
+    14     21   0.0246    0.9 -0.0491 0.0983  False
+    14     28   0.0142    0.9 -0.0625 0.0909  False
+    21     28  -0.0104    0.9 -0.0871 0.0663  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0421 0.6409 -0.0387 0.1228  False
+     0      7   0.0265    0.9   -0.05 0.1031  False
+     0     14   0.0431 0.5332 -0.0304 0.1166  False
+     0     21   0.0243    0.9 -0.0598 0.1084  False
+     0     28   0.0278    0.9  -0.052 0.1076  False
+     3      7  -0.0156    0.9 -0.0976 0.0664  False
+     3     14    0.001    0.9 -0.0781 0.0802  False
+     3     21  -0.0178    0.9 -0.1069 0.0713  False
+     3     28  -0.0143    0.9 -0.0993 0.0707  False
+     7     14   0.0166    0.9 -0.0583 0.0914  False
+     7     21  -0.0022    0.9 -0.0875 0.0831  False
+     7     28   0.0013    0.9 -0.0798 0.0823  False
+    14     21  -0.0188    0.9 -0.1014 0.0638  False
+    14     28  -0.0153    0.9 -0.0935 0.0629  False
+    21     28   0.0035    0.9 -0.0847 0.0917  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.10020029]	No
+Stroke	Sham	14	[0.52614476]	No
+Stroke	Sham	21	[0.28312575]	No
+Stroke	Sham	28	[0.40668988]	No
+Stroke	Sham	7	[0.0491476]	Yes
+Stroke	Sham	0	[0.76293642]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOp-MOp_dilated_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOp-MOp_dilated_cut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0091
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.001 2.328 0.020  0.000  0.002
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0293 0.7524 -0.0351 0.0938  False
+     0      7  -0.0015    0.9 -0.0696 0.0666  False
+     0     14   0.0408 0.5002 -0.0263  0.108  False
+     0     21   0.0551  0.175  -0.012 0.1223  False
+     0     28   0.0465 0.3966 -0.0233 0.1162  False
+     3      7  -0.0308 0.6999 -0.0942 0.0325  False
+     3     14   0.0115    0.9 -0.0508 0.0738  False
+     3     21   0.0258  0.821 -0.0366 0.0881  False
+     3     28   0.0171    0.9  -0.048 0.0822  False
+     7     14   0.0423 0.4422 -0.0237 0.1084  False
+     7     21   0.0566 0.1393 -0.0095 0.1227  False
+     7     28    0.048 0.3412 -0.0207 0.1167  False
+    14     21   0.0143    0.9 -0.0508 0.0794  False
+    14     28   0.0056    0.9 -0.0621 0.0734  False
+    21     28  -0.0087    0.9 -0.0764 0.0591  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0486 0.4653  -0.029 0.1263  False
+     0      7   0.0268    0.9 -0.0469 0.1004  False
+     0     14   0.0395 0.5792 -0.0312 0.1102  False
+     0     21    0.029    0.9 -0.0519 0.1099  False
+     0     28   0.0307 0.8419 -0.0461 0.1074  False
+     3      7  -0.0219    0.9 -0.1007  0.057  False
+     3     14  -0.0092    0.9 -0.0853  0.067  False
+     3     21  -0.0196    0.9 -0.1053  0.066  False
+     3     28   -0.018    0.9 -0.0998 0.0638  False
+     7     14   0.0127    0.9 -0.0593 0.0847  False
+     7     21   0.0022    0.9 -0.0798 0.0843  False
+     7     28   0.0039    0.9 -0.0741 0.0819  False
+    14     21  -0.0105    0.9 -0.0899 0.0689  False
+    14     28  -0.0088    0.9  -0.084 0.0664  False
+    21     28   0.0017    0.9 -0.0832 0.0865  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.60457776]	No
+Stroke	Sham	14	[0.7799069]	No
+Stroke	Sham	21	[0.33493172]	No
+Stroke	Sham	28	[0.23426442]	No
+Stroke	Sham	7	[0.14155218]	No
+Stroke	Sham	0	[0.87953438]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_MOs-MOs_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_MOs-MOs_cut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0127
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.001 2.105 0.035  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    0.9 -0.0491 0.0962  False
+     0      7   0.0236    0.9 -0.0531 0.1004  False
+     0     14   0.0387 0.6585 -0.0369 0.1144  False
+     0     21    0.064 0.1499 -0.0117 0.1397  False
+     0     28   0.0536 0.3684  -0.025 0.1322  False
+     3      7   0.0001    0.9 -0.0713 0.0715  False
+     3     14   0.0152    0.9  -0.055 0.0854  False
+     3     21   0.0405 0.5527 -0.0298 0.1107  False
+     3     28   0.0301 0.8267 -0.0433 0.1034  False
+     7     14   0.0151    0.9 -0.0593 0.0896  False
+     7     21   0.0404 0.6089 -0.0341 0.1148  False
+     7     28     0.03 0.8643 -0.0474 0.1074  False
+    14     21   0.0252    0.9 -0.0481 0.0986  False
+    14     28   0.0149    0.9 -0.0615 0.0912  False
+    21     28  -0.0104    0.9 -0.0867  0.066  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0616 0.4465 -0.0352 0.1584  False
+     0      7   0.0246    0.9 -0.0672 0.1163  False
+     0     14   0.0324 0.8935 -0.0557 0.1205  False
+     0     21   0.0414 0.8227 -0.0594 0.1423  False
+     0     28   0.0275    0.9 -0.0681 0.1232  False
+     3      7  -0.0371 0.8787 -0.1354 0.0612  False
+     3     14  -0.0292    0.9 -0.1241 0.0657  False
+     3     21  -0.0202    0.9  -0.127 0.0866  False
+     3     28  -0.0341    0.9  -0.136 0.0678  False
+     7     14   0.0079    0.9 -0.0819 0.0976  False
+     7     21   0.0169    0.9 -0.0854 0.1191  False
+     7     28   0.0029    0.9 -0.0942 0.1001  False
+    14     21    0.009    0.9   -0.09  0.108  False
+    14     28  -0.0049    0.9 -0.0986 0.0888  False
+    21     28  -0.0139    0.9 -0.1197 0.0918  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.10156704]	No
+Stroke	Sham	14	[0.21125138]	No
+Stroke	Sham	21	[0.78360219]	No
+Stroke	Sham	28	[0.84803609]	No
+Stroke	Sham	7	[0.09043048]	No
+Stroke	Sham	0	[0.44817661]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_SSp_ll-SSp_ll_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_SSp_ll-SSp_ll_cut
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM   Dependent Variable:   Value 
+No. Observations:    364       Method:               REML  
+No. Groups:          2         Scale:                0.0237
+Min. group size:     158       Log-Likelihood:       inf   
+Max. group size:     206       Converged:            Yes   
+Mean group size:     182.0                                 
+-----------------------------------------------------------
+                 Coef.  Std.Err.   z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept         0.000                                    
+merged_timepoint -0.002    0.001 -2.440 0.015 -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   0.2293  0.001  0.1302  0.3285   True
+     0      7   0.0038    0.9 -0.1009  0.1085  False
+     0     14   0.0777 0.2593 -0.0256  0.1809  False
+     0     21   0.0243    0.9  -0.079  0.1275  False
+     0     28   0.0205    0.9 -0.0867  0.1278  False
+     3      7  -0.2255  0.001 -0.3229 -0.1281   True
+     3     14  -0.1517  0.001 -0.2475 -0.0558   True
+     3     21  -0.2051  0.001 -0.3009 -0.1092   True
+     3     28  -0.2088  0.001 -0.3089 -0.1087   True
+     7     14   0.0739 0.2957 -0.0277  0.1755  False
+     7     21   0.0205    0.9 -0.0811  0.1221  False
+     7     28   0.0167    0.9 -0.0889  0.1223  False
+    14     21  -0.0534 0.6232 -0.1535  0.0467  False
+    14     28  -0.0571 0.5983 -0.1613   0.047  False
+    21     28  -0.0038    0.9 -0.1079  0.1004  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.1192 0.0209  0.0114   0.227   True
+     0      7   0.0282    0.9  -0.074  0.1305  False
+     0     14   0.0104    0.9 -0.0877  0.1086  False
+     0     21   0.0516 0.7422 -0.0607  0.1639  False
+     0     28   0.0198    0.9 -0.0867  0.1263  False
+     3      7   -0.091 0.1635 -0.2004  0.0185  False
+     3     14  -0.1088 0.0397 -0.2144 -0.0031   True
+     3     21  -0.0676 0.5636 -0.1865  0.0514  False
+     3     28  -0.0994  0.123 -0.2129  0.0141  False
+     7     14  -0.0178    0.9 -0.1177  0.0821  False
+     7     21   0.0234    0.9 -0.0905  0.1373  False
+     7     28  -0.0084    0.9 -0.1166  0.0998  False
+    14     21   0.0412 0.8844  -0.069  0.1514  False
+    14     28   0.0094    0.9  -0.095  0.1137  False
+    21     28  -0.0318    0.9 -0.1496   0.086  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.03724911]	Yes
+Stroke	Sham	14	[0.01627602]	Yes
+Stroke	Sham	21	[0.65272506]	No
+Stroke	Sham	28	[0.81989574]	No
+Stroke	Sham	7	[0.29926624]	No
+Stroke	Sham	0	[0.8803554]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CC_SSp_ul-SSp_ul_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CC_SSp_ul-SSp_ul_cut
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM   Dependent Variable:   Value 
+No. Observations:    364       Method:               REML  
+No. Groups:          2         Scale:                0.0206
+Min. group size:     158       Log-Likelihood:       inf   
+Max. group size:     206       Converged:            Yes   
+Mean group size:     182.0                                 
+-----------------------------------------------------------
+                 Coef.  Std.Err.   z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept         0.000                                    
+merged_timepoint -0.002    0.001 -2.031 0.042 -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   0.2205  0.001  0.1289   0.312   True
+     0      7   0.0085    0.9 -0.0882  0.1052  False
+     0     14   0.0789  0.168 -0.0164  0.1743  False
+     0     21   0.0305    0.9 -0.0649  0.1258  False
+     0     28   0.0318    0.9 -0.0672  0.1309  False
+     3      7   -0.212  0.001 -0.3019  -0.122   True
+     3     14  -0.1416  0.001 -0.2301 -0.0531   True
+     3     21    -0.19  0.001 -0.2785 -0.1015   True
+     3     28  -0.1887  0.001 -0.2811 -0.0962   True
+     7     14   0.0704 0.2615 -0.0234  0.1642  False
+     7     21    0.022    0.9 -0.0719  0.1158  False
+     7     28   0.0233    0.9 -0.0742  0.1209  False
+    14     21  -0.0485 0.6382 -0.1409   0.044  False
+    14     28  -0.0471 0.6958 -0.1433  0.0491  False
+    21     28   0.0014    0.9 -0.0948  0.0976  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0971 0.0694 -0.0043 0.1985  False
+     0      7   0.0274    0.9 -0.0688 0.1236  False
+     0     14   0.0085    0.9 -0.0838 0.1008  False
+     0     21   0.0465 0.7742 -0.0591 0.1522  False
+     0     28   0.0254    0.9 -0.0749 0.1256  False
+     3      7  -0.0697 0.3752 -0.1727 0.0333  False
+     3     14  -0.0886 0.1108  -0.188 0.0108  False
+     3     21  -0.0506 0.7554 -0.1625 0.0613  False
+     3     28  -0.0717  0.384 -0.1785 0.0351  False
+     7     14  -0.0189    0.9 -0.1129 0.0752  False
+     7     21   0.0191    0.9  -0.088 0.1263  False
+     7     28   -0.002    0.9 -0.1038 0.0998  False
+    14     21    0.038 0.8962 -0.0657 0.1417  False
+    14     28   0.0168    0.9 -0.0813  0.115  False
+    21     28  -0.0212    0.9  -0.132 0.0896  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00987183]	Yes
+Stroke	Sham	14	[0.00821889]	Yes
+Stroke	Sham	21	[0.81933578]	No
+Stroke	Sham	28	[0.595381]	No
+Stroke	Sham	7	[0.35321043]	No
+Stroke	Sham	0	[0.88362996]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CReT_MOp-TRN_ipsilesional_CCcut_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CReT_MOp-TRN_ipsilesional_CCcut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0143
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.002    0.001 2.420 0.016  0.000  0.003
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3  -0.0874 0.0222  -0.167 -0.0078   True
+     0      7  -0.0236    0.9 -0.1077  0.0604  False
+     0     14  -0.0312  0.882 -0.1141  0.0517  False
+     0     21   0.0093    0.9 -0.0736  0.0923  False
+     0     28    0.038 0.7744 -0.0481  0.1241  False
+     3      7   0.0637 0.1809 -0.0145  0.1419  False
+     3     14   0.0562 0.2911 -0.0208  0.1331  False
+     3     21   0.0967  0.005  0.0198  0.1737   True
+     3     28   0.1254  0.001  0.0451  0.2058   True
+     7     14  -0.0076    0.9 -0.0891   0.074  False
+     7     21    0.033 0.8358 -0.0486  0.1146  False
+     7     28   0.0617 0.2952 -0.0231  0.1465  False
+    14     21   0.0406 0.6705 -0.0398  0.1209  False
+    14     28   0.0692 0.1675 -0.0144  0.1529  False
+    21     28   0.0287    0.9  -0.055  0.1123  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0435 0.7342 -0.0501  0.137  False
+     0      7  -0.0415 0.7287 -0.1302 0.0472  False
+     0     14   0.0184    0.9 -0.0668 0.1035  False
+     0     21   0.0158    0.9 -0.0817 0.1132  False
+     0     28  -0.0071    0.9 -0.0995 0.0853  False
+     3      7   -0.085  0.108 -0.1799   0.01  False
+     3     14  -0.0251    0.9 -0.1168 0.0666  False
+     3     21  -0.0277    0.9 -0.1309 0.0755  False
+     3     28  -0.0506 0.6533 -0.1491 0.0479  False
+     7     14   0.0599 0.3514 -0.0268 0.1466  False
+     7     21   0.0573 0.5445 -0.0415 0.1561  False
+     7     28   0.0344 0.8967 -0.0595 0.1283  False
+    14     21  -0.0026    0.9 -0.0982  0.093  False
+    14     28  -0.0255    0.9  -0.116  0.065  False
+    21     28  -0.0229    0.9 -0.1251 0.0793  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.01146425]	Yes
+Stroke	Sham	14	[0.4730427]	No
+Stroke	Sham	21	[0.48916469]	No
+Stroke	Sham	28	[0.01778081]	Yes
+Stroke	Sham	7	[0.02629392]	Yes
+Stroke	Sham	0	[0.31029197]	No

output/Final_Quantitative_output/mixed_model_analysis/ad_CRuT_MOp-RN_ipsilesional_log.txt

@@ -0,0 +1,67 @@
+Model Name: ad_CRuT_MOp-RN_ipsilesional
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0122
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.002    0.001 3.250 0.001  0.001  0.003
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0442 0.4732  -0.115 0.0267  False
+     0      7  -0.0303 0.8347 -0.1052 0.0445  False
+     0     14   0.0148    0.9  -0.059 0.0886  False
+     0     21   0.0367 0.6825 -0.0371 0.1105  False
+     0     28    0.055 0.3095 -0.0216 0.1317  False
+     3      7   0.0138    0.9 -0.0558 0.0835  False
+     3     14    0.059 0.1356 -0.0095 0.1275  False
+     3     21   0.0809 0.0105  0.0124 0.1494   True
+     3     28   0.0992 0.0013  0.0277 0.1708   True
+     7     14   0.0451 0.4767 -0.0275 0.1178  False
+     7     21   0.0671 0.0885 -0.0056 0.1397  False
+     7     28   0.0854 0.0166  0.0099 0.1609   True
+    14     21   0.0219    0.9 -0.0496 0.0935  False
+    14     28   0.0402 0.6118 -0.0342 0.1147  False
+    21     28   0.0183    0.9 -0.0562 0.0928  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0651  0.327 -0.0272 0.1573  False
+     0      7  -0.0088    0.9 -0.0963 0.0786  False
+     0     14   0.0354 0.8063 -0.0486 0.1193  False
+     0     21   0.0469 0.6962 -0.0492 0.1429  False
+     0     28   0.0132    0.9 -0.0779 0.1043  False
+     3      7  -0.0739   0.21 -0.1675 0.0198  False
+     3     14  -0.0297    0.9 -0.1201 0.0607  False
+     3     21  -0.0182    0.9 -0.1199 0.0836  False
+     3     28  -0.0518   0.62  -0.149 0.0453  False
+     7     14   0.0442 0.6486 -0.0413 0.1297  False
+     7     21   0.0557  0.558 -0.0418 0.1531  False
+     7     28    0.022    0.9 -0.0705 0.1146  False
+    14     21   0.0115    0.9 -0.0828 0.1058  False
+    14     28  -0.0221    0.9 -0.1114 0.0671  False
+    21     28  -0.0337    0.9 -0.1344 0.0671  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.01707707]	Yes
+Stroke	Sham	14	[0.84066081]	No
+Stroke	Sham	21	[0.6471467]	No
+Stroke	Sham	28	[0.01185435]	Yes
+Stroke	Sham	7	[0.74432185]	No
+Stroke	Sham	0	[0.22964982]	No

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

@@ -0,0 +1,67 @@
+Model Name: ad_CST_MOp-int-py_contralesional_CCasROA
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0203
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.002    0.001 2.219 0.026  0.000  0.003
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0395 0.8093 -0.1334 0.0544  False
+     0      7   0.0294    0.9 -0.0698 0.1286  False
+     0     14   0.0161    0.9 -0.0817 0.1139  False
+     0     21   0.0387 0.8506 -0.0591 0.1365  False
+     0     28   0.0755 0.2718 -0.0261  0.177  False
+     3      7   0.0689 0.2665 -0.0233 0.1611  False
+     3     14   0.0556 0.4928 -0.0352 0.1463  False
+     3     21   0.0782 0.1351 -0.0126 0.1689  False
+     3     28    0.115 0.0077  0.0202 0.2097   True
+     7     14  -0.0133    0.9 -0.1095 0.0829  False
+     7     21   0.0093    0.9 -0.0869 0.1055  False
+     7     28   0.0461 0.7433 -0.0539 0.1461  False
+    14     21   0.0226    0.9 -0.0722 0.1174  False
+    14     28   0.0594 0.5098 -0.0392  0.158  False
+    21     28   0.0368 0.8879 -0.0619 0.1354  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0222    0.9 -0.1401 0.0957  False
+     0      7  -0.0709  0.451 -0.1827 0.0409  False
+     0     14   -0.017    0.9 -0.1243 0.0903  False
+     0     21  -0.0147    0.9 -0.1375 0.1081  False
+     0     28  -0.0283    0.9 -0.1448 0.0882  False
+     3      7  -0.0487 0.8295 -0.1684  0.071  False
+     3     14   0.0052    0.9 -0.1104 0.1208  False
+     3     21   0.0075    0.9 -0.1226 0.1376  False
+     3     28  -0.0062    0.9 -0.1303  0.118  False
+     7     14   0.0539  0.687 -0.0554 0.1632  False
+     7     21   0.0562  0.756 -0.0683 0.1808  False
+     7     28   0.0426    0.9 -0.0758 0.1609  False
+    14     21   0.0023    0.9 -0.1182 0.1229  False
+    14     28  -0.0114    0.9 -0.1255 0.1028  False
+    21     28  -0.0137    0.9 -0.1425 0.1151  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.10489051]	No
+Stroke	Sham	14	[0.63232237]	No
+Stroke	Sham	21	[0.9124788]	No
+Stroke	Sham	28	[0.07907637]	No
+Stroke	Sham	7	[0.13149343]	No
+Stroke	Sham	0	[0.2300208]	No

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

@@ -0,0 +1,67 @@
+Model Name: ad_CST_MOp-int-py_contralesional_CCcut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   364      Method:              REML    
+No. Groups:         2        Scale:               0.0201  
+Min. group size:    158      Log-Likelihood:      185.3050
+Max. group size:    206      Converged:           No      
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        1.024    0.012 87.215 0.000  1.001  1.047
+merged_timepoint 0.002    0.001  2.124 0.034  0.000  0.003
+Group Var        0.000                                    
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0402 0.7978 -0.1344 0.0539  False
+     0      7   0.0298    0.9 -0.0697 0.1292  False
+     0     14   0.0126    0.9 -0.0855 0.1106  False
+     0     21   0.0379 0.8647 -0.0601  0.136  False
+     0     28   0.0745 0.2892 -0.0273 0.1763  False
+     3      7     0.07 0.2522 -0.0225 0.1625  False
+     3     14   0.0528 0.5454 -0.0382 0.1438  False
+     3     21   0.0782 0.1369 -0.0128 0.1692  False
+     3     28   0.1147 0.0082  0.0197 0.2097   True
+     7     14  -0.0172    0.9 -0.1137 0.0793  False
+     7     21   0.0082    0.9 -0.0883 0.1046  False
+     7     28   0.0447  0.768 -0.0556  0.145  False
+    14     21   0.0254    0.9 -0.0697 0.1204  False
+    14     28   0.0619  0.469  -0.037 0.1608  False
+    21     28   0.0365  0.894 -0.0624 0.1354  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0194    0.9 -0.1357 0.0969  False
+     0      7  -0.0652 0.5254 -0.1754 0.0451  False
+     0     14  -0.0176    0.9 -0.1235 0.0882  False
+     0     21   -0.014    0.9 -0.1351 0.1071  False
+     0     28    -0.03    0.9 -0.1449 0.0849  False
+     3      7  -0.0458 0.8616 -0.1638 0.0723  False
+     3     14   0.0018    0.9 -0.1122 0.1157  False
+     3     21   0.0054    0.9 -0.1229 0.1337  False
+     3     28  -0.0106    0.9  -0.133 0.1118  False
+     7     14   0.0475 0.7733 -0.0603 0.1553  False
+     7     21   0.0512 0.8138 -0.0717  0.174  False
+     7     28   0.0352    0.9 -0.0815 0.1519  False
+    14     21   0.0036    0.9 -0.1153 0.1225  False
+    14     28  -0.0124    0.9 -0.1249 0.1002  False
+    21     28   -0.016    0.9  -0.143  0.111  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.09518825]	No
+Stroke	Sham	14	[0.61412691]	No
+Stroke	Sham	21	[0.90032471]	No
+Stroke	Sham	28	[0.06764643]	No
+Stroke	Sham	7	[0.1502544]	No
+Stroke	Sham	0	[0.25138088]	No

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

@@ -0,0 +1,67 @@
+Model Name: ad_CST_MOp-int-py_contralesional_selfdrawnROA+CCcut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0199
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.002    0.001 2.161 0.031  0.000  0.003
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0405 0.7904 -0.1341 0.0532  False
+     0      7   0.0304    0.9 -0.0685 0.1293  False
+     0     14   0.0103    0.9 -0.0873 0.1078  False
+     0     21   0.0384 0.8536 -0.0591 0.1359  False
+     0     28   0.0741 0.2891 -0.0272 0.1754  False
+     3      7   0.0708 0.2353 -0.0212 0.1628  False
+     3     14   0.0507 0.5786 -0.0398 0.1412  False
+     3     21   0.0789 0.1265 -0.0116 0.1694  False
+     3     28   0.1145 0.0078    0.02 0.2091   True
+     7     14  -0.0201    0.9 -0.1161 0.0759  False
+     7     21    0.008    0.9 -0.0879  0.104  False
+     7     28   0.0437 0.7803 -0.0561 0.1435  False
+    14     21   0.0281    0.9 -0.0664 0.1227  False
+    14     28   0.0638  0.428 -0.0346 0.1622  False
+    21     28   0.0357    0.9 -0.0627 0.1341  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0205    0.9 -0.1361 0.0952  False
+     0      7  -0.0645 0.5299 -0.1742 0.0451  False
+     0     14  -0.0171    0.9 -0.1224 0.0881  False
+     0     21  -0.0127    0.9 -0.1331 0.1078  False
+     0     28  -0.0292    0.9 -0.1435 0.0851  False
+     3      7  -0.0441 0.8818 -0.1615 0.0734  False
+     3     14   0.0033    0.9   -0.11 0.1167  False
+     3     21   0.0078    0.9 -0.1198 0.1354  False
+     3     28  -0.0087    0.9 -0.1305  0.113  False
+     7     14   0.0474 0.7718 -0.0598 0.1546  False
+     7     21   0.0519 0.8005 -0.0703  0.174  False
+     7     28   0.0353    0.9 -0.0807 0.1514  False
+    14     21   0.0045    0.9 -0.1138 0.1227  False
+    14     28   -0.012    0.9  -0.124 0.0999  False
+    21     28  -0.0165    0.9 -0.1429 0.1098  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.09763973]	No
+Stroke	Sham	14	[0.56578297]	No
+Stroke	Sham	21	[0.90738246]	No
+Stroke	Sham	28	[0.07065484]	No
+Stroke	Sham	7	[0.13831167]	No
+Stroke	Sham	0	[0.25714921]	No

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

@@ -0,0 +1,67 @@
+Model Name: ad_TC_DORsm-SSp_ll+SSp_ul_ipsilesional_END+higherstepsize_
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0137
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.001 2.040 0.041  0.000  0.003
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0083    0.9 -0.0594 0.0761  False
+     0      7  -0.0488 0.3685 -0.1204 0.0228  False
+     0     14   0.0301 0.8009 -0.0406 0.1007  False
+     0     21   0.0163    0.9 -0.0543 0.0869  False
+     0     28    0.049 0.3917 -0.0243 0.1224  False
+     3      7  -0.0572 0.1376 -0.1238 0.0094  False
+     3     14   0.0217    0.9 -0.0438 0.0872  False
+     3     21    0.008    0.9 -0.0576 0.0735  False
+     3     28   0.0407 0.5221 -0.0277 0.1091  False
+     7     14   0.0789 0.0159  0.0094 0.1484   True
+     7     21   0.0651 0.0803 -0.0043 0.1346  False
+     7     28   0.0979 0.0018  0.0257 0.1701   True
+    14     21  -0.0138    0.9 -0.0822 0.0547  False
+    14     28    0.019    0.9 -0.0522 0.0902  False
+    21     28   0.0327 0.7447 -0.0385  0.104  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3    0.116 0.0233  0.0099  0.222   True
+     0      7   0.0326    0.9 -0.0679 0.1332  False
+     0     14   0.0563 0.5386 -0.0402 0.1528  False
+     0     21   0.0692 0.4656 -0.0413 0.1796  False
+     0     28   0.0431 0.8222 -0.0617 0.1479  False
+     3      7  -0.0833 0.2286  -0.191 0.0243  False
+     3     14  -0.0597 0.5539 -0.1636 0.0443  False
+     3     21  -0.0468 0.8412 -0.1638 0.0702  False
+     3     28  -0.0728 0.4185 -0.1845 0.0388  False
+     7     14   0.0237    0.9 -0.0746  0.122  False
+     7     21   0.0365    0.9 -0.0755 0.1486  False
+     7     28   0.0105    0.9 -0.0959 0.1169  False
+    14     21   0.0129    0.9 -0.0956 0.1213  False
+    14     28  -0.0132    0.9 -0.1158 0.0895  False
+    21     28   -0.026    0.9 -0.1419 0.0898  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.14949716]	No
+Stroke	Sham	14	[0.47365163]	No
+Stroke	Sham	21	[0.98353446]	No
+Stroke	Sham	28	[0.03497483]	Yes
+Stroke	Sham	7	[0.06881805]	No
+Stroke	Sham	0	[0.00114091]	Yes

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

@@ -0,0 +1,67 @@
+Model Name: ad_TC_DORsm-SSp_ll+SSp_ul_ipsilesional_ROI+CCcut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0175
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.002    0.001 2.290 0.022  0.000  0.003
+Group Var         0.000                                   
+==========================================================
+
+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    0.9 -0.0736 0.0723  False
+     0      7  -0.0406 0.6342 -0.1176 0.0365  False
+     0     14   0.0239    0.9 -0.0521 0.0999  False
+     0     21   0.0215    0.9 -0.0544 0.0975  False
+     0     28   0.0513 0.4243 -0.0276 0.1302  False
+     3      7  -0.0399 0.5837 -0.1116 0.0317  False
+     3     14   0.0246    0.9 -0.0459 0.0951  False
+     3     21   0.0222    0.9 -0.0483 0.0927  False
+     3     28    0.052 0.3283 -0.0217 0.1256  False
+     7     14   0.0645 0.1338 -0.0102 0.1392  False
+     7     21   0.0621 0.1641 -0.0126 0.1369  False
+     7     28   0.0919 0.0103  0.0142 0.1696   True
+    14     21  -0.0024    0.9  -0.076 0.0713  False
+    14     28   0.0274    0.9 -0.0492 0.1041  False
+    21     28   0.0298 0.8621 -0.0469 0.1064  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.1213 0.0632 -0.0038 0.2464  False
+     0      7   0.0359    0.9 -0.0828 0.1545  False
+     0     14   0.0789 0.3475  -0.035 0.1928  False
+     0     21   0.0912 0.3358 -0.0391 0.2215  False
+     0     28   0.0503 0.8304 -0.0734 0.1739  False
+     3      7  -0.0855 0.3823 -0.2125 0.0416  False
+     3     14  -0.0424    0.9  -0.165 0.0802  False
+     3     21  -0.0301    0.9 -0.1681 0.1079  False
+     3     28  -0.0711 0.6108 -0.2028 0.0607  False
+     7     14   0.0431 0.8886 -0.0729  0.159  False
+     7     21   0.0554 0.8099 -0.0768 0.1875  False
+     7     28   0.0144    0.9 -0.1112   0.14  False
+    14     21   0.0123    0.9 -0.1156 0.1402  False
+    14     28  -0.0287    0.9 -0.1498 0.0924  False
+    21     28   -0.041    0.9 -0.1776 0.0957  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.06450604]	No
+Stroke	Sham	14	[0.78805632]	No
+Stroke	Sham	21	[0.54665728]	No
+Stroke	Sham	28	[0.17759624]	No
+Stroke	Sham	7	[0.14228755]	No
+Stroke	Sham	0	[0.0083156]	Yes

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_MOp-MOp_dilated_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CC_MOp-MOp_dilated
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0007
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.000    0.000 3.365 0.001  0.000  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0068    0.9 -0.0132 0.0268  False
+     0      7   0.0137 0.4254 -0.0074 0.0348  False
+     0     14   0.0092 0.7734 -0.0116   0.03  False
+     0     21   0.0133 0.4432 -0.0075 0.0341  False
+     0     28   0.0163  0.255 -0.0053 0.0379  False
+     3      7   0.0069    0.9 -0.0127 0.0265  False
+     3     14   0.0024    0.9 -0.0169 0.0217  False
+     3     21   0.0065    0.9 -0.0128 0.0258  False
+     3     28   0.0095 0.7264 -0.0107 0.0297  False
+     7     14  -0.0045    0.9  -0.025  0.016  False
+     7     21  -0.0004    0.9 -0.0209 0.0201  False
+     7     28   0.0026    0.9 -0.0187 0.0239  False
+    14     21   0.0041    0.9 -0.0161 0.0243  False
+    14     28   0.0071    0.9 -0.0139 0.0281  False
+    21     28    0.003    0.9  -0.018  0.024  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0063    0.9 -0.0119 0.0245  False
+     0      7   0.0076 0.7717 -0.0096 0.0249  False
+     0     14   0.0116 0.3364  -0.005 0.0282  False
+     0     21   0.0165 0.1297 -0.0025 0.0354  False
+     0     28   0.0158 0.1219 -0.0022 0.0338  False
+     3      7   0.0013    0.9 -0.0172 0.0198  False
+     3     14   0.0053    0.9 -0.0126 0.0231  False
+     3     21   0.0101 0.6691   -0.01 0.0302  False
+     3     28   0.0095 0.6863 -0.0097 0.0287  False
+     7     14    0.004    0.9 -0.0129 0.0209  False
+     7     21   0.0088 0.7453 -0.0104 0.0281  False
+     7     28   0.0082 0.7655 -0.0101 0.0264  False
+    14     21   0.0048    0.9 -0.0138 0.0235  False
+    14     28   0.0042    0.9 -0.0135 0.0218  False
+    21     28  -0.0007    0.9 -0.0206 0.0192  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.06079431]	No
+Stroke	Sham	14	[0.0154583]	Yes
+Stroke	Sham	21	[0.02590135]	Yes
+Stroke	Sham	28	[0.05578221]	No
+Stroke	Sham	7	[0.26235955]	No
+Stroke	Sham	0	[0.17429923]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_MOs-MOs_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CC_MOs-MOs
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0011
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.000    0.000 2.125 0.034  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   0.0169 0.2966 -0.0064 0.0402  False
+     0      7    0.015 0.4941 -0.0095 0.0396  False
+     0     14   0.0059    0.9 -0.0184 0.0301  False
+     0     21   0.0145 0.5181 -0.0098 0.0387  False
+     0     28   0.0154 0.4949 -0.0098 0.0405  False
+     3      7  -0.0019    0.9 -0.0247  0.021  False
+     3     14   -0.011 0.6942 -0.0335 0.0115  False
+     3     21  -0.0024    0.9 -0.0249 0.0201  False
+     3     28  -0.0015    0.9  -0.025  0.022  False
+     7     14  -0.0092 0.8697  -0.033 0.0147  False
+     7     21  -0.0006    0.9 -0.0244 0.0233  False
+     7     28   0.0003    0.9 -0.0244 0.0251  False
+    14     21   0.0086 0.8994 -0.0149 0.0321  False
+    14     28   0.0095 0.8619 -0.0149  0.034  False
+    21     28   0.0009    0.9 -0.0235 0.0254  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0091    0.9 -0.0159 0.0341  False
+     0      7   0.0097 0.8252  -0.014 0.0334  False
+     0     14   0.0111 0.6991 -0.0117 0.0338  False
+     0     21   0.0154 0.5241 -0.0106 0.0415  False
+     0     28   0.0202  0.177 -0.0045 0.0449  False
+     3      7   0.0006    0.9 -0.0248  0.026  False
+     3     14    0.002    0.9 -0.0225 0.0265  False
+     3     21   0.0063    0.9 -0.0213 0.0339  False
+     3     28   0.0111 0.8037 -0.0152 0.0375  False
+     7     14   0.0014    0.9 -0.0218 0.0245  False
+     7     21   0.0057    0.9 -0.0207 0.0321  False
+     7     28   0.0105 0.8112 -0.0146 0.0356  False
+    14     21   0.0044    0.9 -0.0212 0.0299  False
+    14     28   0.0091 0.8778 -0.0151 0.0334  False
+    21     28   0.0048    0.9 -0.0225 0.0321  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.45214939]	No
+Stroke	Sham	14	[0.0148912]	Yes
+Stroke	Sham	21	[0.03561639]	Yes
+Stroke	Sham	28	[0.01320137]	Yes
+Stroke	Sham	7	[0.1541242]	No
+Stroke	Sham	0	[0.15505111]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_SSp_ll-SSp_ll_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CC_SSp_ll-SSp_ll_cut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0038
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 4.114 0.000  0.001  0.002
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3  -0.0553 0.0037 -0.0983 -0.0123   True
+     0      7   0.0225 0.6855 -0.0229  0.0679  False
+     0     14   0.0217  0.704 -0.0231  0.0665  False
+     0     21   0.0121    0.9 -0.0327  0.0569  False
+     0     28   0.0189 0.8309 -0.0276  0.0654  False
+     3      7   0.0778  0.001  0.0356    0.12   True
+     3     14    0.077  0.001  0.0354  0.1185   True
+     3     21   0.0674  0.001  0.0258  0.1089   True
+     3     28   0.0742  0.001  0.0308  0.1176   True
+     7     14  -0.0008    0.9 -0.0449  0.0432  False
+     7     21  -0.0104    0.9 -0.0545  0.0336  False
+     7     28  -0.0036    0.9 -0.0494  0.0422  False
+    14     21  -0.0096    0.9  -0.053  0.0338  False
+    14     28  -0.0027    0.9 -0.0479  0.0424  False
+    21     28   0.0069    0.9 -0.0383   0.052  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0225 0.6472  -0.021  0.066  False
+     0      7   0.0193 0.7305  -0.022 0.0605  False
+     0     14   0.0177 0.7649 -0.0219 0.0573  False
+     0     21   0.0436 0.0675 -0.0018 0.0889  False
+     0     28   0.0315 0.2865 -0.0115 0.0745  False
+     3      7  -0.0032    0.9 -0.0474 0.0409  False
+     3     14  -0.0048    0.9 -0.0475 0.0378  False
+     3     21    0.021 0.7778  -0.027  0.069  False
+     3     28    0.009    0.9 -0.0369 0.0548  False
+     7     14  -0.0016    0.9 -0.0419 0.0387  False
+     7     21   0.0243 0.6291 -0.0217 0.0702  False
+     7     28   0.0122    0.9 -0.0315 0.0559  False
+    14     21   0.0259 0.5409 -0.0186 0.0704  False
+    14     28   0.0138    0.9 -0.0283 0.0559  False
+    21     28  -0.0121    0.9 -0.0596 0.0354  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[4.12537157e-05]	Yes
+Stroke	Sham	14	[0.11488127]	No
+Stroke	Sham	21	[0.3770404]	No
+Stroke	Sham	28	[0.85265415]	No
+Stroke	Sham	7	[0.20484003]	No
+Stroke	Sham	0	[0.37406263]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_SSp_ll-SSp_ll_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CC_SSp_ll-SSp_ll
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0009
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 5.585 0.000  0.001  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0179 0.1873   -0.04 0.0042  False
+     0      7   0.0144 0.4856  -0.009 0.0377  False
+     0     14   0.0116 0.6749 -0.0115 0.0346  False
+     0     21   0.0125 0.6052 -0.0105 0.0355  False
+     0     28   0.0222 0.0848 -0.0017 0.0461  False
+     3      7   0.0323  0.001  0.0106  0.054   True
+     3     14   0.0294 0.0014  0.0081 0.0508   True
+     3     21   0.0304  0.001  0.0091 0.0518   True
+     3     28   0.0401  0.001  0.0178 0.0624   True
+     7     14  -0.0028    0.9 -0.0255 0.0198  False
+     7     21  -0.0019    0.9 -0.0245 0.0208  False
+     7     28   0.0078    0.9 -0.0157 0.0314  False
+    14     21    0.001    0.9 -0.0213 0.0233  False
+    14     28   0.0107  0.745 -0.0125 0.0339  False
+    21     28   0.0097 0.8141 -0.0135 0.0329  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0089   0.74 -0.0104 0.0281  False
+     0      7   0.0046    0.9 -0.0137 0.0228  False
+     0     14   0.0114 0.4234 -0.0061 0.0288  False
+     0     21   0.0264 0.0028  0.0064 0.0464   True
+     0     28   0.0173 0.0949 -0.0016 0.0363  False
+     3      7  -0.0043    0.9 -0.0238 0.0152  False
+     3     14   0.0025    0.9 -0.0163 0.0213  False
+     3     21   0.0175 0.1672 -0.0037 0.0387  False
+     3     28   0.0085 0.8097 -0.0118 0.0287  False
+     7     14   0.0068 0.8703  -0.011 0.0246  False
+     7     21   0.0218 0.0269  0.0015 0.0421   True
+     7     28   0.0128 0.3996 -0.0065 0.0321  False
+    14     21    0.015 0.2396 -0.0046 0.0347  False
+    14     28    0.006    0.9 -0.0126 0.0246  False
+    21     28  -0.0091 0.7889   -0.03 0.0119  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[5.9133252e-06]	Yes
+Stroke	Sham	14	[0.25567023]	No
+Stroke	Sham	21	[0.01643561]	Yes
+Stroke	Sham	28	[0.63851444]	No
+Stroke	Sham	7	[0.77161845]	No
+Stroke	Sham	0	[0.40988323]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_SSp_ul-SSp_ul_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CC_SSp_ul-SSp_ul_cut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0022
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 4.422 0.000  0.001  0.002
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3  -0.0341 0.0306 -0.0662 -0.0019   True
+     0      7   0.0229 0.3808  -0.011  0.0568  False
+     0     14   0.0236 0.3308 -0.0099   0.057  False
+     0     21   0.0126 0.8821 -0.0209  0.0461  False
+     0     28   0.0192 0.5902 -0.0155   0.054  False
+     3      7    0.057  0.001  0.0254  0.0885   True
+     3     14   0.0576  0.001  0.0266  0.0887   True
+     3     21   0.0467  0.001  0.0156  0.0777   True
+     3     28   0.0533  0.001  0.0209  0.0857   True
+     7     14   0.0007    0.9 -0.0323  0.0336  False
+     7     21  -0.0103    0.9 -0.0432  0.0226  False
+     7     28  -0.0037    0.9 -0.0379  0.0305  False
+    14     21   -0.011    0.9 -0.0434  0.0215  False
+    14     28  -0.0043    0.9 -0.0381  0.0294  False
+    21     28   0.0066    0.9 -0.0271  0.0404  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0102    0.9 -0.0237 0.0441  False
+     0      7   0.0115    0.9 -0.0206 0.0436  False
+     0     14   0.0157 0.6591 -0.0151 0.0466  False
+     0     21   0.0294 0.1604 -0.0059 0.0647  False
+     0     28   0.0262 0.2177 -0.0073 0.0597  False
+     3      7   0.0013    0.9 -0.0331 0.0357  False
+     3     14   0.0055    0.9 -0.0277 0.0387  False
+     3     21   0.0192 0.6522 -0.0181 0.0566  False
+     3     28    0.016 0.7611 -0.0197 0.0517  False
+     7     14   0.0042    0.9 -0.0272 0.0356  False
+     7     21   0.0179 0.6752 -0.0179 0.0537  False
+     7     28   0.0147 0.7886 -0.0193 0.0487  False
+    14     21   0.0137 0.8487 -0.0209 0.0483  False
+    14     28   0.0105    0.9 -0.0223 0.0433  False
+    21     28  -0.0032    0.9 -0.0402 0.0338  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.0009496]	Yes
+Stroke	Sham	14	[0.31518053]	No
+Stroke	Sham	21	[0.29987297]	No
+Stroke	Sham	28	[0.64353791]	No
+Stroke	Sham	7	[0.17292649]	No
+Stroke	Sham	0	[0.88228405]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CC_SSp_ul-SSp_ul_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CC_SSp_ul-SSp_ul
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0015
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 4.394 0.000  0.001  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   -0.033 0.0067 -0.0598 -0.0061   True
+     0      7   0.0168 0.5259 -0.0116  0.0452  False
+     0     14   0.0157 0.5795 -0.0123  0.0436  False
+     0     21   0.0063    0.9 -0.0216  0.0343  False
+     0     28   0.0131 0.7571 -0.0159  0.0422  False
+     3      7   0.0498  0.001  0.0234  0.0762   True
+     3     14   0.0486  0.001  0.0227  0.0746   True
+     3     21   0.0393  0.001  0.0134  0.0653   True
+     3     28   0.0461  0.001   0.019  0.0732   True
+     7     14  -0.0011    0.9 -0.0287  0.0264  False
+     7     21  -0.0105 0.8758  -0.038  0.0171  False
+     7     28  -0.0037    0.9 -0.0323  0.0249  False
+    14     21  -0.0093    0.9 -0.0364  0.0178  False
+    14     28  -0.0025    0.9 -0.0307  0.0257  False
+    21     28   0.0068    0.9 -0.0214   0.035  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0062    0.9 -0.0214 0.0338  False
+     0      7   0.0059    0.9 -0.0203 0.0321  False
+     0     14   0.0108 0.7918 -0.0143 0.0359  False
+     0     21    0.027 0.0797 -0.0018 0.0557  False
+     0     28   0.0208 0.2415 -0.0064 0.0481  False
+     3      7  -0.0003    0.9 -0.0283 0.0278  False
+     3     14   0.0046    0.9 -0.0224 0.0317  False
+     3     21   0.0208 0.3648 -0.0097 0.0512  False
+     3     28   0.0146 0.6693 -0.0144 0.0437  False
+     7     14   0.0049    0.9 -0.0207 0.0305  False
+     7     21   0.0211  0.301 -0.0081 0.0502  False
+     7     28   0.0149 0.6126 -0.0128 0.0426  False
+    14     21   0.0162 0.5551  -0.012 0.0444  False
+    14     28     0.01 0.8813 -0.0167 0.0368  False
+    21     28  -0.0061    0.9 -0.0363  0.024  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00017546]	Yes
+Stroke	Sham	14	[0.70248548]	No
+Stroke	Sham	21	[0.04725519]	Yes
+Stroke	Sham	28	[0.24881882]	No
+Stroke	Sham	7	[0.25775816]	No
+Stroke	Sham	0	[0.88983913]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CReT_MOp-TRN_contralesional_CCcut_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CReT_MOp-TRN_contralesional_CCcut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0016
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.000    0.000 2.024 0.043  0.000  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0157 0.5573 -0.0117  0.043  False
+     0      7   0.0217 0.2596 -0.0072 0.0506  False
+     0     14   0.0013    0.9 -0.0272 0.0297  False
+     0     21   0.0135 0.7189 -0.0149  0.042  False
+     0     28   0.0197 0.3955 -0.0099 0.0493  False
+     3      7    0.006    0.9 -0.0208 0.0329  False
+     3     14  -0.0144 0.6028 -0.0408  0.012  False
+     3     21  -0.0021    0.9 -0.0286 0.0243  False
+     3     28    0.004    0.9 -0.0236 0.0316  False
+     7     14  -0.0205 0.2908 -0.0485 0.0076  False
+     7     21  -0.0082    0.9 -0.0362 0.0198  False
+     7     28   -0.002    0.9 -0.0311 0.0271  False
+    14     21   0.0123 0.7689 -0.0153 0.0399  False
+    14     28   0.0185 0.4387 -0.0103 0.0472  False
+    21     28   0.0062    0.9 -0.0225 0.0349  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0134 0.7903 -0.0445 0.0177  False
+     0      7   0.0005    0.9 -0.0289   0.03  False
+     0     14   0.0046    0.9 -0.0237 0.0329  False
+     0     21   0.0077    0.9 -0.0246 0.0401  False
+     0     28   0.0139  0.753 -0.0168 0.0446  False
+     3      7   0.0139 0.7724 -0.0176 0.0455  False
+     3     14    0.018 0.5276 -0.0125 0.0484  False
+     3     21   0.0211 0.4833 -0.0132 0.0554  False
+     3     28   0.0273 0.1598 -0.0054   0.06  False
+     7     14    0.004    0.9 -0.0248 0.0328  False
+     7     21   0.0072    0.9 -0.0256   0.04  False
+     7     28   0.0134 0.7937 -0.0178 0.0446  False
+    14     21   0.0032    0.9 -0.0286 0.0349  False
+    14     28   0.0093    0.9 -0.0207 0.0394  False
+    21     28   0.0062    0.9 -0.0278 0.0401  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.07687143]	No
+Stroke	Sham	14	[0.2089668]	No
+Stroke	Sham	21	[0.66801243]	No
+Stroke	Sham	28	[0.72922903]	No
+Stroke	Sham	7	[0.12809899]	No
+Stroke	Sham	0	[0.52040578]	No

output/Final_Quantitative_output/mixed_model_analysis/fa_CRuT_MOp-RN_contralesional_mirrored_log.txt

@@ -0,0 +1,67 @@
+Model Name: fa_CRuT_MOp-RN_contralesional_mirrored
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0012
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.000    0.000 2.427 0.015  0.000  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0094    0.9 -0.0164 0.0352  False
+     0      7   0.0184 0.3781 -0.0088 0.0456  False
+     0     14   0.0045    0.9 -0.0224 0.0313  False
+     0     21   0.0169 0.4587 -0.0099 0.0438  False
+     0     28    0.015 0.6156 -0.0129 0.0429  False
+     3      7    0.009    0.9 -0.0163 0.0343  False
+     3     14  -0.0049    0.9 -0.0298   0.02  False
+     3     21   0.0075    0.9 -0.0174 0.0324  False
+     3     28   0.0056    0.9 -0.0204 0.0316  False
+     7     14  -0.0139 0.6329 -0.0403 0.0125  False
+     7     21  -0.0015    0.9 -0.0279 0.0249  False
+     7     28  -0.0034    0.9 -0.0309  0.024  False
+    14     21   0.0125 0.7128 -0.0135 0.0385  False
+    14     28   0.0105 0.8628 -0.0166 0.0376  False
+    21     28   -0.002    0.9  -0.029 0.0251  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0053    0.9 -0.0308 0.0201  False
+     0      7   0.0099  0.827 -0.0143  0.034  False
+     0     14   0.0137  0.528 -0.0095 0.0369  False
+     0     21   0.0148 0.5816 -0.0117 0.0413  False
+     0     28   0.0133 0.6261 -0.0118 0.0385  False
+     3      7   0.0152 0.5302 -0.0106 0.0411  False
+     3     14    0.019 0.2441 -0.0059  0.044  False
+     3     21   0.0201 0.3097  -0.008 0.0482  False
+     3     28   0.0187 0.3405 -0.0081 0.0455  False
+     7     14   0.0038    0.9 -0.0198 0.0274  False
+     7     21   0.0049    0.9  -0.022 0.0318  False
+     7     28   0.0035    0.9 -0.0221  0.029  False
+    14     21   0.0011    0.9 -0.0249 0.0272  False
+    14     28  -0.0003    0.9  -0.025 0.0243  False
+    21     28  -0.0014    0.9 -0.0293 0.0264  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.37253566]	No
+Stroke	Sham	14	[0.07325188]	No
+Stroke	Sham	21	[0.71458073]	No
+Stroke	Sham	28	[0.62133784]	No
+Stroke	Sham	7	[0.64372852]	No
+Stroke	Sham	0	[0.65223641]	No

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

@@ -0,0 +1,67 @@
+Model Name: fa_CST_MOp-int-py_contralesional_CCasROA
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0026
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 2.279 0.023  0.000  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0092    0.9 -0.0255  0.044  False
+     0      7   0.0275 0.2633 -0.0092 0.0642  False
+     0     14   0.0085    0.9 -0.0277 0.0447  False
+     0     21   0.0232 0.4414  -0.013 0.0594  False
+     0     28   0.0304 0.1891 -0.0072 0.0679  False
+     3      7   0.0183 0.6208 -0.0159 0.0524  False
+     3     14  -0.0008    0.9 -0.0344 0.0328  False
+     3     21    0.014 0.8173 -0.0196 0.0475  False
+     3     28   0.0211 0.5102  -0.014 0.0562  False
+     7     14   -0.019 0.6215 -0.0546 0.0166  False
+     7     21  -0.0043    0.9 -0.0399 0.0313  False
+     7     28   0.0029    0.9 -0.0342 0.0399  False
+    14     21   0.0147 0.8102 -0.0203 0.0498  False
+    14     28   0.0219 0.5143 -0.0146 0.0584  False
+    21     28   0.0072    0.9 -0.0294 0.0437  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0233 0.5609 -0.0643 0.0176  False
+     0      7  -0.0155 0.8431 -0.0543 0.0233  False
+     0     14  -0.0028    0.9 -0.0401 0.0345  False
+     0     21  -0.0091    0.9 -0.0518 0.0335  False
+     0     28   0.0042    0.9 -0.0363 0.0446  False
+     3      7   0.0078    0.9 -0.0337 0.0494  False
+     3     14   0.0205 0.6568 -0.0196 0.0607  False
+     3     21   0.0142    0.9  -0.031 0.0594  False
+     3     28   0.0275 0.4447 -0.0156 0.0706  False
+     7     14   0.0127    0.9 -0.0253 0.0506  False
+     7     21   0.0064    0.9 -0.0369 0.0496  False
+     7     28   0.0196 0.7121 -0.0214 0.0607  False
+    14     21  -0.0063    0.9 -0.0482 0.0355  False
+    14     28    0.007    0.9 -0.0327 0.0466  False
+    21     28   0.0133    0.9 -0.0314  0.058  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.50250857]	No
+Stroke	Sham	14	[0.38715447]	No
+Stroke	Sham	21	[0.34627014]	No
+Stroke	Sham	28	[0.73519512]	No
+Stroke	Sham	7	[0.11956435]	No
+Stroke	Sham	0	[0.14252137]	No

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

@@ -0,0 +1,67 @@
+Model Name: fa_CST_MOp-int-py_contralesional_CCcut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0026
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 2.119 0.034  0.000  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0099    0.9 -0.0247 0.0445  False
+     0      7   0.0286   0.22  -0.008 0.0652  False
+     0     14   0.0074    0.9 -0.0287 0.0435  False
+     0     21   0.0231 0.4435  -0.013 0.0591  False
+     0     28   0.0298 0.2025 -0.0076 0.0673  False
+     3      7   0.0187 0.5958 -0.0153 0.0527  False
+     3     14  -0.0025    0.9 -0.0359  0.031  False
+     3     21   0.0132 0.8528 -0.0203 0.0467  False
+     3     28   0.0199 0.5626  -0.015 0.0549  False
+     7     14  -0.0212 0.5183 -0.0567 0.0143  False
+     7     21  -0.0055    0.9  -0.041   0.03  False
+     7     28   0.0012    0.9 -0.0357 0.0381  False
+    14     21   0.0157 0.7638 -0.0193 0.0506  False
+    14     28   0.0224 0.4865  -0.014 0.0588  False
+    21     28   0.0067    0.9 -0.0296 0.0431  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0223  0.595  -0.063 0.0184  False
+     0      7  -0.0134    0.9  -0.052 0.0252  False
+     0     14  -0.0022    0.9 -0.0392 0.0348  False
+     0     21  -0.0092    0.9 -0.0516 0.0332  False
+     0     28   0.0032    0.9  -0.037 0.0434  False
+     3      7   0.0089    0.9 -0.0324 0.0503  False
+     3     14   0.0201 0.6679 -0.0197   0.06  False
+     3     21   0.0131    0.9 -0.0317  0.058  False
+     3     28   0.0256 0.5166 -0.0173 0.0684  False
+     7     14   0.0112    0.9 -0.0265 0.0489  False
+     7     21   0.0042    0.9 -0.0388 0.0472  False
+     7     28   0.0166 0.8292 -0.0242 0.0575  False
+    14     21   -0.007    0.9 -0.0486 0.0346  False
+    14     28   0.0054    0.9  -0.034 0.0448  False
+    21     28   0.0124    0.9  -0.032 0.0569  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.47885735]	No
+Stroke	Sham	14	[0.35437657]	No
+Stroke	Sham	21	[0.2993808]	No
+Stroke	Sham	28	[0.65329697]	No
+Stroke	Sham	7	[0.11287096]	No
+Stroke	Sham	0	[0.16038521]	No

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

@@ -0,0 +1,67 @@
+Model Name: fa_CST_MOp-int-py_contralesional_selfdrawnROA+CCcut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0026
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 2.134 0.033  0.000  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3     0.01    0.9 -0.0246 0.0446  False
+     0      7   0.0289 0.2077 -0.0076 0.0655  False
+     0     14   0.0066    0.9 -0.0294 0.0426  False
+     0     21   0.0234 0.4287 -0.0127 0.0594  False
+     0     28     0.03 0.1955 -0.0074 0.0674  False
+     3      7   0.0189  0.585 -0.0151 0.0529  False
+     3     14  -0.0034    0.9 -0.0368   0.03  False
+     3     21   0.0133 0.8453 -0.0201 0.0468  False
+     3     28     0.02 0.5588 -0.0149 0.0549  False
+     7     14  -0.0223 0.4621 -0.0578 0.0131  False
+     7     21  -0.0056    0.9  -0.041 0.0299  False
+     7     28   0.0011    0.9 -0.0358 0.0379  False
+    14     21   0.0167 0.7125 -0.0182 0.0517  False
+    14     28   0.0234 0.4369  -0.013 0.0597  False
+    21     28   0.0067    0.9 -0.0297  0.043  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0225 0.5836 -0.0631  0.018  False
+     0      7  -0.0132    0.9 -0.0516 0.0252  False
+     0     14  -0.0021    0.9  -0.039 0.0348  False
+     0     21  -0.0087    0.9 -0.0509 0.0335  False
+     0     28   0.0032    0.9 -0.0369 0.0432  False
+     3      7   0.0093    0.9 -0.0318 0.0505  False
+     3     14   0.0204 0.6524 -0.0193 0.0601  False
+     3     21   0.0138    0.9 -0.0309 0.0585  False
+     3     28   0.0257 0.5068  -0.017 0.0684  False
+     7     14   0.0111    0.9 -0.0265 0.0486  False
+     7     21   0.0045    0.9 -0.0383 0.0473  False
+     7     28   0.0164 0.8374 -0.0243  0.057  False
+    14     21  -0.0066    0.9  -0.048 0.0348  False
+    14     28   0.0053    0.9 -0.0339 0.0445  False
+    21     28   0.0119    0.9 -0.0324 0.0562  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.46924618]	No
+Stroke	Sham	14	[0.31570383]	No
+Stroke	Sham	21	[0.312058]	No
+Stroke	Sham	28	[0.64888988]	No
+Stroke	Sham	7	[0.10619164]	No
+Stroke	Sham	0	[0.16062947]	No

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

@@ -0,0 +1,67 @@
+Model Name: fa_CST_MOp-int-py_ipsilesional_CCasROA
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0023
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 2.016 0.044  0.000  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0206 0.5306 -0.0556 0.0144  False
+     0      7   0.0105    0.9 -0.0265 0.0475  False
+     0     14    -0.01    0.9 -0.0464 0.0265  False
+     0     21   0.0067    0.9 -0.0297 0.0432  False
+     0     28   0.0171 0.7588 -0.0208 0.0549  False
+     3      7   0.0311 0.1007 -0.0033 0.0655  False
+     3     14   0.0107    0.9 -0.0232 0.0445  False
+     3     21   0.0274 0.1878 -0.0065 0.0612  False
+     3     28   0.0377 0.0289  0.0024  0.073   True
+     7     14  -0.0204 0.5625 -0.0563 0.0154  False
+     7     21  -0.0038    0.9 -0.0396 0.0321  False
+     7     28   0.0066    0.9 -0.0307 0.0439  False
+    14     21   0.0167 0.7241 -0.0186  0.052  False
+    14     28    0.027 0.2835 -0.0097 0.0638  False
+    21     28   0.0104    0.9 -0.0264 0.0471  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0013    0.9 -0.0319 0.0345  False
+     0      7  -0.0165 0.6383  -0.048  0.015  False
+     0     14   0.0005    0.9 -0.0297 0.0307  False
+     0     21  -0.0063    0.9 -0.0409 0.0283  False
+     0     28   0.0036    0.9 -0.0292 0.0364  False
+     3      7  -0.0178 0.6317 -0.0515  0.016  False
+     3     14  -0.0008    0.9 -0.0334 0.0317  False
+     3     21  -0.0076    0.9 -0.0442 0.0291  False
+     3     28   0.0023    0.9 -0.0327 0.0372  False
+     7     14   0.0169 0.5929 -0.0138 0.0477  False
+     7     21   0.0102    0.9 -0.0249 0.0453  False
+     7     28     0.02 0.5094 -0.0133 0.0534  False
+    14     21  -0.0067    0.9 -0.0407 0.0272  False
+    14     28   0.0031    0.9 -0.0291 0.0352  False
+    21     28   0.0098    0.9 -0.0264 0.0461  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.08361214]	No
+Stroke	Sham	14	[0.24370631]	No
+Stroke	Sham	21	[0.36427526]	No
+Stroke	Sham	28	[0.37178342]	No
+Stroke	Sham	7	[0.04098195]	Yes
+Stroke	Sham	0	[0.85772539]	No

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

@@ -0,0 +1,67 @@
+Model Name: fa_CST_MOp-int-py_ipsilesional_selfdrawnROA+CCcut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0023
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 1.971 0.049  0.000  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0203 0.5486 -0.0554 0.0148  False
+     0      7   0.0105    0.9 -0.0266 0.0475  False
+     0     14  -0.0097    0.9 -0.0463 0.0268  False
+     0     21   0.0068    0.9 -0.0297 0.0433  False
+     0     28   0.0169 0.7689 -0.0211 0.0548  False
+     3      7   0.0308 0.1094 -0.0037 0.0652  False
+     3     14   0.0106    0.9 -0.0233 0.0445  False
+     3     21   0.0271 0.1986 -0.0068  0.061  False
+     3     28   0.0372 0.0334  0.0018 0.0726   True
+     7     14  -0.0202 0.5753 -0.0562 0.0157  False
+     7     21  -0.0037    0.9 -0.0396 0.0323  False
+     7     28   0.0064    0.9  -0.031 0.0438  False
+    14     21   0.0165 0.7331 -0.0189 0.0519  False
+    14     28   0.0266 0.3034 -0.0102 0.0635  False
+    21     28   0.0101    0.9 -0.0268 0.0469  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0005    0.9 -0.0328 0.0339  False
+     0      7   -0.017 0.6164 -0.0486 0.0147  False
+     0     14  -0.0002    0.9 -0.0306 0.0302  False
+     0     21  -0.0073    0.9 -0.0421 0.0274  False
+     0     28   0.0032    0.9 -0.0297 0.0362  False
+     3      7  -0.0175 0.6492 -0.0514 0.0164  False
+     3     14  -0.0007    0.9 -0.0335  0.032  False
+     3     21  -0.0079    0.9 -0.0447  0.029  False
+     3     28   0.0027    0.9 -0.0324 0.0378  False
+     7     14   0.0167 0.6078 -0.0142 0.0477  False
+     7     21   0.0096    0.9 -0.0256 0.0449  False
+     7     28   0.0202 0.5058 -0.0133 0.0537  False
+    14     21  -0.0071    0.9 -0.0412  0.027  False
+    14     28   0.0035    0.9 -0.0289 0.0358  False
+    21     28   0.0106    0.9 -0.0259  0.047  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.08812776]	No
+Stroke	Sham	14	[0.25234923]	No
+Stroke	Sham	21	[0.34659219]	No
+Stroke	Sham	28	[0.39886825]	No
+Stroke	Sham	7	[0.04498613]	Yes
+Stroke	Sham	0	[0.8152567]	No

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

@@ -0,0 +1,67 @@
+Model Name: fa_TC_DORsm-SSp+SSs_contralesional_END+CCcut
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM  Dependent Variable:  Value   
+No. Observations:    364      Method:              REML    
+No. Groups:          2        Scale:               0.0012  
+Min. group size:     158      Log-Likelihood:      688.0620
+Max. group size:     206      Converged:           Yes     
+Mean group size:     182.0                                 
+-----------------------------------------------------------
+                 Coef. Std.Err.    z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept        0.361    0.003 122.536 0.000  0.355  0.367
+merged_timepoint 0.001    0.000   4.775 0.000  0.001  0.001
+Group Var        0.000                                     
+===========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3    0.004    0.9 -0.0222 0.0303  False
+     0      7   0.0239 0.1331 -0.0038 0.0516  False
+     0     14   0.0168 0.4901 -0.0106 0.0441  False
+     0     21   0.0226 0.1668 -0.0047   0.05  False
+     0     28   0.0281 0.0536 -0.0003 0.0565  False
+     3      7   0.0199 0.2321 -0.0059 0.0457  False
+     3     14   0.0127  0.674 -0.0126 0.0381  False
+     3     21   0.0186  0.285 -0.0067  0.044  False
+     3     28   0.0241 0.0975 -0.0024 0.0506  False
+     7     14  -0.0072    0.9  -0.034 0.0197  False
+     7     21  -0.0013    0.9 -0.0282 0.0256  False
+     7     28   0.0042    0.9 -0.0238 0.0321  False
+    14     21   0.0059    0.9 -0.0206 0.0324  False
+    14     28   0.0114 0.8238 -0.0162 0.0389  False
+    21     28   0.0055    0.9 -0.0221  0.033  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   -0.013 0.6302 -0.0376 0.0116  False
+     0      7   0.0006    0.9 -0.0227 0.0239  False
+     0     14   0.0122 0.6004 -0.0102 0.0346  False
+     0     21   0.0191 0.2671 -0.0065 0.0447  False
+     0     28   0.0177 0.2946 -0.0067  0.042  False
+     3      7   0.0136  0.603 -0.0114 0.0386  False
+     3     14   0.0252 0.0348  0.0011 0.0493   True
+     3     21   0.0321 0.0105  0.0049 0.0592   True
+     3     28   0.0307 0.0104  0.0047 0.0566   True
+     7     14   0.0116 0.6609 -0.0112 0.0344  False
+     7     21   0.0185 0.3176 -0.0075 0.0445  False
+     7     28   0.0171 0.3516 -0.0076 0.0418  False
+    14     21   0.0069    0.9 -0.0183  0.032  False
+    14     28   0.0054    0.9 -0.0184 0.0293  False
+    21     28  -0.0014    0.9 -0.0283 0.0254  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.64655622]	No
+Stroke	Sham	14	[0.27043189]	No
+Stroke	Sham	21	[0.25382805]	No
+Stroke	Sham	28	[0.82376109]	No
+Stroke	Sham	7	[0.0889746]	No
+Stroke	Sham	0	[0.38469028]	No

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

@@ -0,0 +1,67 @@
+Model Name: fa_TC_DORsm-SSp+SSs_ipsilesional_END+CCcut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0013
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 3.653 0.000  0.000  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0001    0.9 -0.0259 0.0258  False
+     0      7   0.0093    0.9  -0.018 0.0366  False
+     0     14   0.0118 0.7814 -0.0152 0.0387  False
+     0     21    0.015 0.5842 -0.0119  0.042  False
+     0     28   0.0163 0.5437 -0.0117 0.0442  False
+     3      7   0.0094 0.8957 -0.0161 0.0348  False
+     3     14   0.0118 0.7217 -0.0132 0.0368  False
+     3     21   0.0151 0.5092 -0.0099 0.0401  False
+     3     28   0.0163 0.4699 -0.0098 0.0424  False
+     7     14   0.0025    0.9  -0.024  0.029  False
+     7     21   0.0057    0.9 -0.0208 0.0322  False
+     7     28    0.007    0.9 -0.0206 0.0345  False
+    14     21   0.0032    0.9 -0.0229 0.0293  False
+    14     28   0.0045    0.9 -0.0227 0.0317  False
+    21     28   0.0013    0.9 -0.0259 0.0284  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0058    0.9 -0.0228 0.0344  False
+     0      7   0.0125 0.7433 -0.0147 0.0396  False
+     0     14   0.0182 0.3366 -0.0078 0.0443  False
+     0     21   0.0273 0.0923 -0.0025 0.0572  False
+     0     28   0.0215 0.2487 -0.0068 0.0497  False
+     3      7   0.0066    0.9 -0.0224 0.0357  False
+     3     14   0.0124 0.7717 -0.0157 0.0405  False
+     3     21   0.0215  0.367 -0.0101 0.0531  False
+     3     28   0.0156 0.6452 -0.0145 0.0458  False
+     7     14   0.0058    0.9 -0.0208 0.0323  False
+     7     21   0.0149  0.689 -0.0154 0.0451  False
+     7     28    0.009    0.9 -0.0197 0.0377  False
+    14     21   0.0091    0.9 -0.0201 0.0384  False
+    14     28   0.0032    0.9 -0.0245 0.0309  False
+    21     28  -0.0059    0.9 -0.0372 0.0254  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.76412464]	No
+Stroke	Sham	14	[0.69963524]	No
+Stroke	Sham	21	[0.3055409]	No
+Stroke	Sham	28	[0.79159547]	No
+Stroke	Sham	7	[0.96725594]	No
+Stroke	Sham	0	[0.79395919]	No

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

@@ -0,0 +1,67 @@
+Model Name: fa_TC_DORsm-SSp_ll+SSp_ul_contralesional_END+higherstepsize
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0016
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 4.307 0.000  0.001  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0036    0.9  -0.027 0.0342  False
+     0      7   0.0238 0.2819 -0.0085 0.0561  False
+     0     14   0.0199 0.4688 -0.0119 0.0518  False
+     0     21   0.0216 0.3742 -0.0102 0.0535  False
+     0     28   0.0283 0.1414 -0.0048 0.0614  False
+     3      7   0.0202 0.3881 -0.0099 0.0502  False
+     3     14   0.0163 0.5933 -0.0133 0.0459  False
+     3     21    0.018 0.4992 -0.0116 0.0476  False
+     3     28   0.0246 0.2005 -0.0062 0.0555  False
+     7     14  -0.0039    0.9 -0.0352 0.0275  False
+     7     21  -0.0022    0.9 -0.0335 0.0292  False
+     7     28   0.0045    0.9 -0.0281 0.0371  False
+    14     21   0.0017    0.9 -0.0292 0.0326  False
+    14     28   0.0083    0.9 -0.0238 0.0405  False
+    21     28   0.0066    0.9 -0.0255 0.0388  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0167 0.4317 -0.0426 0.0092  False
+     0      7   0.0063    0.9 -0.0183 0.0308  False
+     0     14   0.0123 0.6389 -0.0113 0.0359  False
+     0     21   0.0232 0.1344 -0.0037 0.0502  False
+     0     28   0.0167 0.4174 -0.0089 0.0423  False
+     3      7    0.023 0.1244 -0.0033 0.0493  False
+     3     14    0.029  0.015  0.0036 0.0544   True
+     3     21   0.0399 0.0012  0.0114 0.0685   True
+     3     28   0.0334  0.007  0.0061 0.0607   True
+     7     14    0.006    0.9  -0.018 0.0301  False
+     7     21    0.017 0.4766 -0.0104 0.0443  False
+     7     28   0.0104 0.8386 -0.0156 0.0364  False
+    14     21   0.0109 0.8206 -0.0156 0.0374  False
+    14     28   0.0044    0.9 -0.0207 0.0295  False
+    21     28  -0.0065    0.9 -0.0348 0.0218  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.44512693]	No
+Stroke	Sham	14	[0.50414866]	No
+Stroke	Sham	21	[0.14702113]	No
+Stroke	Sham	28	[0.84606881]	No
+Stroke	Sham	7	[0.59836112]	No
+Stroke	Sham	0	[0.38009622]	No

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

@@ -0,0 +1,67 @@
+Model Name: fa_TC_DORsm-SSp_ll+SSp_ul_contralesional_ROI+CCcut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0023
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 3.399 0.001  0.000  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0141 0.8488 -0.0214 0.0496  False
+     0      7   0.0353 0.0793 -0.0023 0.0728  False
+     0     14   0.0303 0.1761 -0.0067 0.0674  False
+     0     21   0.0262 0.3237 -0.0108 0.0633  False
+     0     28   0.0329 0.1403 -0.0055 0.0713  False
+     3      7   0.0212 0.5029 -0.0137 0.0561  False
+     3     14   0.0162 0.7233 -0.0181 0.0506  False
+     3     21   0.0121    0.9 -0.0222 0.0465  False
+     3     28   0.0188  0.639 -0.0171 0.0547  False
+     7     14  -0.0049    0.9 -0.0414 0.0315  False
+     7     21   -0.009    0.9 -0.0455 0.0274  False
+     7     28  -0.0024    0.9 -0.0402 0.0355  False
+    14     21  -0.0041    0.9   -0.04 0.0318  False
+    14     28   0.0026    0.9 -0.0348 0.0399  False
+    21     28   0.0067    0.9 -0.0307  0.044  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0209 0.4329 -0.0532 0.0115  False
+     0      7   0.0059    0.9 -0.0248 0.0366  False
+     0     14   0.0139 0.7202 -0.0155 0.0434  False
+     0     21   0.0259 0.2365 -0.0078 0.0596  False
+     0     28   0.0111    0.9 -0.0209  0.043  False
+     3      7   0.0267 0.1817 -0.0061 0.0596  False
+     3     14   0.0348 0.0226  0.0031 0.0665   True
+     3     21   0.0467  0.003   0.011 0.0825   True
+     3     28   0.0319 0.0808 -0.0022  0.066  False
+     7     14   0.0081    0.9 -0.0219 0.0381  False
+     7     21     0.02 0.5351 -0.0142 0.0542  False
+     7     28   0.0052    0.9 -0.0273 0.0377  False
+    14     21   0.0119    0.9 -0.0212  0.045  False
+    14     28  -0.0029    0.9 -0.0342 0.0284  False
+    21     28  -0.0148  0.809 -0.0502 0.0205  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.16087028]	No
+Stroke	Sham	14	[0.76825281]	No
+Stroke	Sham	21	[0.1219538]	No
+Stroke	Sham	28	[0.87227025]	No
+Stroke	Sham	7	[0.38027585]	No
+Stroke	Sham	0	[0.2055141]	No

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

@@ -0,0 +1,67 @@
+Model Name: fa_TC_DORsm-SSp_ll+SSp_ul_ipsilesional_END+higherstepsize_
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0015
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 3.106 0.002  0.000  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3    0.006    0.9 -0.0234 0.0353  False
+     0      7   0.0106    0.9 -0.0204 0.0416  False
+     0     14   0.0136 0.7718  -0.017 0.0441  False
+     0     21   0.0138 0.7586 -0.0168 0.0444  False
+     0     28   0.0174 0.6006 -0.0144 0.0491  False
+     3      7   0.0046    0.9 -0.0242 0.0335  False
+     3     14   0.0076    0.9 -0.0208 0.0359  False
+     3     21   0.0078    0.9 -0.0205 0.0362  False
+     3     28   0.0114 0.8687 -0.0182  0.041  False
+     7     14   0.0029    0.9 -0.0271  0.033  False
+     7     21   0.0032    0.9 -0.0269 0.0333  False
+     7     28   0.0068    0.9 -0.0245  0.038  False
+    14     21   0.0002    0.9 -0.0294 0.0299  False
+    14     28   0.0038    0.9  -0.027 0.0347  False
+    21     28   0.0036    0.9 -0.0273 0.0344  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   -0.005    0.9 -0.0328 0.0228  False
+     0      7   0.0029    0.9 -0.0235 0.0292  False
+     0     14   0.0157 0.4758 -0.0096  0.041  False
+     0     21   0.0202 0.3381 -0.0087 0.0492  False
+     0     28   0.0169 0.4877 -0.0106 0.0443  False
+     3      7   0.0079    0.9 -0.0203 0.0361  False
+     3     14   0.0207 0.2466 -0.0065 0.0479  False
+     3     21   0.0252 0.1718 -0.0054 0.0559  False
+     3     28   0.0219 0.2645 -0.0074 0.0511  False
+     7     14   0.0128 0.6803  -0.013 0.0386  False
+     7     21   0.0173 0.5262  -0.012 0.0467  False
+     7     28    0.014 0.6744 -0.0139 0.0419  False
+    14     21   0.0045    0.9 -0.0239 0.0329  False
+    14     28   0.0012    0.9 -0.0257 0.0281  False
+    21     28  -0.0034    0.9 -0.0337  0.027  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.21966597]	No
+Stroke	Sham	14	[0.85182345]	No
+Stroke	Sham	21	[0.81707511]	No
+Stroke	Sham	28	[0.65633157]	No
+Stroke	Sham	7	[0.14750624]	No
+Stroke	Sham	0	[0.70899005]	No

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

@@ -0,0 +1,67 @@
+Model Name: fa_TC_DORsm-SSp_ll+SSp_ul_ipsilesional_ROI+CCcut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0018
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 3.027 0.002  0.000  0.001
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0061    0.9 -0.0248 0.0371  False
+     0      7   0.0134 0.8276 -0.0193 0.0461  False
+     0     14    0.014 0.7848 -0.0182 0.0463  False
+     0     21    0.018 0.5841 -0.0143 0.0502  False
+     0     28   0.0218 0.4242 -0.0117 0.0553  False
+     3      7   0.0073    0.9 -0.0231 0.0377  False
+     3     14   0.0079    0.9  -0.022 0.0378  False
+     3     21   0.0118 0.8504 -0.0181 0.0418  False
+     3     28   0.0157 0.6764 -0.0156 0.0469  False
+     7     14   0.0006    0.9 -0.0311 0.0324  False
+     7     21   0.0046    0.9 -0.0272 0.0363  False
+     7     28   0.0084    0.9 -0.0246 0.0414  False
+    14     21   0.0039    0.9 -0.0273 0.0352  False
+    14     28   0.0077    0.9 -0.0248 0.0403  False
+    21     28   0.0038    0.9 -0.0287 0.0364  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0101    0.9 -0.0401 0.0199  False
+     0      7   0.0063    0.9 -0.0221 0.0348  False
+     0     14   0.0192 0.3295 -0.0081 0.0465  False
+     0     21   0.0174 0.5834 -0.0139 0.0486  False
+     0     28   0.0106    0.9 -0.0191 0.0402  False
+     3      7   0.0165 0.6093  -0.014 0.0469  False
+     3     14   0.0294 0.0506    -0.0 0.0588  False
+     3     21   0.0275 0.1629 -0.0056 0.0606  False
+     3     28   0.0207 0.4113 -0.0109 0.0523  False
+     7     14   0.0129 0.7359 -0.0149 0.0407  False
+     7     21   0.0111    0.9 -0.0206 0.0428  False
+     7     28   0.0043    0.9 -0.0258 0.0344  False
+    14     21  -0.0018    0.9 -0.0325 0.0288  False
+    14     28  -0.0086    0.9 -0.0377 0.0204  False
+    21     28  -0.0068    0.9 -0.0396  0.026  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.29052541]	No
+Stroke	Sham	14	[0.4498976]	No
+Stroke	Sham	21	[0.79990313]	No
+Stroke	Sham	28	[0.51001913]	No
+Stroke	Sham	7	[0.69606152]	No
+Stroke	Sham	0	[0.73809472]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CC_MOp-MOp_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: md_CC_MOp-MOp_cut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0069
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.002    0.000 3.406 0.001  0.001  0.002
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0066    0.9 -0.0647 0.0516  False
+     0      7   0.0088    0.9 -0.0527 0.0702  False
+     0     14   0.0432 0.3175 -0.0174 0.1038  False
+     0     21   0.0631 0.0359  0.0025 0.1237   True
+     0     28    0.051 0.1862 -0.0119 0.1139  False
+     3      7   0.0153    0.9 -0.0418 0.0725  False
+     3     14   0.0497 0.1163 -0.0065  0.106  False
+     3     21   0.0697  0.006  0.0134 0.1259   True
+     3     28   0.0575 0.0586 -0.0012 0.1163  False
+     7     14   0.0344 0.5503 -0.0252 0.0941  False
+     7     21   0.0544 0.0963 -0.0053  0.114  False
+     7     28   0.0422 0.3696 -0.0197 0.1042  False
+    14     21   0.0199    0.9 -0.0388 0.0786  False
+    14     28   0.0078    0.9 -0.0533 0.0689  False
+    21     28  -0.0121    0.9 -0.0732  0.049  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0221    0.9 -0.0409  0.085  False
+     0      7    0.019    0.9 -0.0407 0.0787  False
+     0     14   0.0294 0.6542 -0.0279 0.0867  False
+     0     21   0.0035    0.9 -0.0621 0.0691  False
+     0     28   0.0154    0.9 -0.0468 0.0776  False
+     3      7  -0.0031    0.9  -0.067 0.0609  False
+     3     14   0.0074    0.9 -0.0544 0.0691  False
+     3     21  -0.0185    0.9  -0.088  0.051  False
+     3     28  -0.0066    0.9  -0.073 0.0597  False
+     7     14   0.0105    0.9 -0.0479 0.0688  False
+     7     21  -0.0154    0.9  -0.082 0.0511  False
+     7     28  -0.0036    0.9 -0.0668 0.0597  False
+    14     21  -0.0259 0.8377 -0.0903 0.0385  False
+    14     28   -0.014    0.9  -0.075  0.047  False
+    21     28   0.0119    0.9 -0.0569 0.0807  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.10739049]	No
+Stroke	Sham	14	[0.92448591]	No
+Stroke	Sham	21	[0.03377416]	Yes
+Stroke	Sham	28	[0.19452939]	No
+Stroke	Sham	7	[0.09278964]	No
+Stroke	Sham	0	[0.68348494]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CC_MOp-MOp_dilated_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: md_CC_MOp-MOp_dilated_cut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0058
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 2.846 0.004  0.000  0.002
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0177    0.9 -0.0353 0.0707  False
+     0      7  -0.0004    0.9 -0.0564 0.0557  False
+     0     14    0.038 0.3577 -0.0172 0.0933  False
+     0     21   0.0531 0.0679 -0.0022 0.1083  False
+     0     28   0.0434 0.2538  -0.014 0.1007  False
+     3      7  -0.0181    0.9 -0.0702  0.034  False
+     3     14   0.0203 0.8492 -0.0309 0.0716  False
+     3     21   0.0353 0.3555 -0.0159 0.0866  False
+     3     28   0.0257 0.7124 -0.0279 0.0792  False
+     7     14   0.0384 0.3277  -0.016 0.0927  False
+     7     21   0.0534 0.0572 -0.0009 0.1078  False
+     7     28   0.0437 0.2301 -0.0128 0.1002  False
+    14     21    0.015    0.9 -0.0385 0.0686  False
+    14     28   0.0053    0.9 -0.0504 0.0611  False
+    21     28  -0.0097    0.9 -0.0654  0.046  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3    0.023 0.8567 -0.0359 0.0818  False
+     0      7   0.0189    0.9 -0.0369 0.0746  False
+     0     14   0.0282 0.6324 -0.0254 0.0817  False
+     0     21   0.0083    0.9 -0.0529 0.0696  False
+     0     28   0.0204    0.9 -0.0377 0.0785  False
+     3      7  -0.0041    0.9 -0.0638 0.0556  False
+     3     14   0.0052    0.9 -0.0524 0.0629  False
+     3     21  -0.0147    0.9 -0.0795 0.0502  False
+     3     28  -0.0026    0.9 -0.0645 0.0594  False
+     7     14   0.0093    0.9 -0.0452 0.0638  False
+     7     21  -0.0106    0.9 -0.0727 0.0516  False
+     7     28   0.0015    0.9 -0.0575 0.0605  False
+    14     21  -0.0199    0.9   -0.08 0.0403  False
+    14     28  -0.0078    0.9 -0.0647 0.0491  False
+    21     28   0.0121    0.9 -0.0522 0.0763  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.95807378]	No
+Stroke	Sham	14	[0.39449075]	No
+Stroke	Sham	21	[0.04786402]	Yes
+Stroke	Sham	28	[0.09991819]	No
+Stroke	Sham	7	[0.2858972]	No
+Stroke	Sham	0	[0.87030108]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CC_MOs-MOs_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: md_CC_MOs-MOs_cut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   364      Method:              REML    
+No. Groups:         2        Scale:               0.0078  
+Min. group size:    158      Log-Likelihood:      356.1808
+Max. group size:    206      Converged:           Yes     
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        0.743    0.008 89.946 0.000  0.727  0.759
+merged_timepoint 0.001    0.000  2.272 0.023  0.000  0.002
+Group Var        0.000    0.001                           
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0147    0.9 -0.0422 0.0716  False
+     0      7     0.02    0.9 -0.0401 0.0801  False
+     0     14   0.0409 0.3543 -0.0184 0.1002  False
+     0     21   0.0599  0.046  0.0006 0.1192   True
+     0     28    0.047 0.2443 -0.0146 0.1085  False
+     3      7   0.0053    0.9 -0.0506 0.0612  False
+     3     14   0.0262 0.7173 -0.0288 0.0812  False
+     3     21   0.0452 0.1742 -0.0098 0.1002  False
+     3     28   0.0322 0.5772 -0.0252 0.0897  False
+     7     14   0.0209    0.9 -0.0374 0.0792  False
+     7     21   0.0399 0.3642 -0.0184 0.0982  False
+     7     28    0.027 0.7692 -0.0336 0.0876  False
+    14     21    0.019    0.9 -0.0385 0.0764  False
+    14     28    0.006    0.9 -0.0537 0.0658  False
+    21     28  -0.0129    0.9 -0.0727 0.0468  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0379 0.6752 -0.0378 0.1136  False
+     0      7   0.0137    0.9 -0.0581 0.0855  False
+     0     14   0.0178    0.9 -0.0511 0.0867  False
+     0     21   0.0152    0.9 -0.0637 0.0941  False
+     0     28   0.0129    0.9 -0.0619 0.0877  False
+     3      7  -0.0242    0.9 -0.1011 0.0527  False
+     3     14  -0.0201    0.9 -0.0943 0.0541  False
+     3     21  -0.0227    0.9 -0.1062 0.0608  False
+     3     28   -0.025    0.9 -0.1047 0.0548  False
+     7     14   0.0041    0.9 -0.0661 0.0743  False
+     7     21   0.0015    0.9 -0.0785 0.0815  False
+     7     28  -0.0008    0.9 -0.0768 0.0752  False
+    14     21  -0.0026    0.9   -0.08 0.0748  False
+    14     28  -0.0049    0.9 -0.0781 0.0684  False
+    21     28  -0.0023    0.9  -0.085 0.0804  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.11665273]	No
+Stroke	Sham	14	[0.82991033]	No
+Stroke	Sham	21	[0.41614924]	No
+Stroke	Sham	28	[0.69183004]	No
+Stroke	Sham	7	[0.16127883]	No
+Stroke	Sham	0	[0.37905712]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CC_SSp_ll-SSp_ll_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: md_CC_SSp_ll-SSp_ll_cut
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM   Dependent Variable:   Value 
+No. Observations:    364       Method:               REML  
+No. Groups:          2         Scale:                0.0139
+Min. group size:     158       Log-Likelihood:       inf   
+Max. group size:     206       Converged:            Yes   
+Mean group size:     182.0                                 
+-----------------------------------------------------------
+                 Coef.  Std.Err.   z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept         0.000                                    
+merged_timepoint -0.002    0.001 -3.863 0.000 -0.004 -0.001
+Group Var         0.000                                    
+===========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.2256  0.001  0.1488  0.3024   True
+     0      7  -0.0024    0.9 -0.0835  0.0787  False
+     0     14   0.0505 0.4601 -0.0295  0.1305  False
+     0     21    0.017    0.9  -0.063   0.097  False
+     0     28   0.0104    0.9 -0.0727  0.0935  False
+     3      7   -0.228  0.001 -0.3035 -0.1526   True
+     3     14  -0.1752  0.001 -0.2494 -0.1009   True
+     3     21  -0.2086  0.001 -0.2829 -0.1344   True
+     3     28  -0.2152  0.001 -0.2927 -0.1376   True
+     7     14   0.0529 0.3866 -0.0258  0.1316  False
+     7     21   0.0194    0.9 -0.0593  0.0981  False
+     7     28   0.0128    0.9  -0.069  0.0947  False
+    14     21  -0.0335 0.7905  -0.111   0.044  False
+    14     28    -0.04 0.6848 -0.1207  0.0407  False
+    21     28  -0.0065    0.9 -0.0872  0.0742  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0728 0.0244  0.0059  0.1397   True
+     0      7   0.0108    0.9 -0.0527  0.0742  False
+     0     14  -0.0032    0.9 -0.0641  0.0577  False
+     0     21   0.0093    0.9 -0.0604   0.079  False
+     0     28  -0.0048    0.9 -0.0709  0.0613  False
+     3      7   -0.062 0.0951   -0.13  0.0059  False
+     3     14   -0.076  0.013 -0.1416 -0.0104   True
+     3     21  -0.0635 0.1354 -0.1374  0.0103  False
+     3     28  -0.0776 0.0217 -0.1481 -0.0071   True
+     7     14   -0.014    0.9  -0.076  0.0481  False
+     7     21  -0.0015    0.9 -0.0722  0.0692  False
+     7     28  -0.0156    0.9 -0.0827  0.0516  False
+    14     21   0.0125    0.9 -0.0559  0.0809  False
+    14     28  -0.0016    0.9 -0.0664  0.0632  False
+    21     28  -0.0141    0.9 -0.0872   0.059  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00243782]	Yes
+Stroke	Sham	14	[0.05485291]	No
+Stroke	Sham	21	[0.79370546]	No
+Stroke	Sham	28	[0.93348063]	No
+Stroke	Sham	7	[0.00715317]	Yes
+Stroke	Sham	0	[0.4498344]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CC_SSp_ul-SSp_ul_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: md_CC_SSp_ul-SSp_ul_cut
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM   Dependent Variable:   Value 
+No. Observations:    364       Method:               REML  
+No. Groups:          2         Scale:                0.0124
+Min. group size:     158       Log-Likelihood:       inf   
+Max. group size:     206       Converged:            Yes   
+Mean group size:     182.0                                 
+-----------------------------------------------------------
+                 Coef.  Std.Err.   z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept         0.000                                    
+merged_timepoint -0.002    0.001 -3.076 0.002 -0.003 -0.001
+Group Var         0.000                                    
+===========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.2005  0.001  0.1267  0.2742   True
+     0      7   0.0005    0.9 -0.0774  0.0784  False
+     0     14   0.0515 0.3899 -0.0254  0.1283  False
+     0     21   0.0221    0.9 -0.0547   0.099  False
+     0     28   0.0213    0.9 -0.0585  0.1011  False
+     3      7     -0.2  0.001 -0.2725 -0.1275   True
+     3     14   -0.149  0.001 -0.2203 -0.0777   True
+     3     21  -0.1783  0.001 -0.2496  -0.107   True
+     3     28  -0.1792  0.001 -0.2537 -0.1047   True
+     7     14    0.051 0.3817 -0.0246  0.1266  False
+     7     21   0.0216    0.9  -0.054  0.0972  False
+     7     28   0.0208    0.9 -0.0578  0.0994  False
+    14     21  -0.0294  0.853 -0.1038  0.0451  False
+    14     28  -0.0302 0.8606 -0.1077  0.0473  False
+    21     28  -0.0008    0.9 -0.0784  0.0767  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0646 0.0561  -0.001  0.1302  False
+     0      7   0.0159    0.9 -0.0463  0.0781  False
+     0     14  -0.0026    0.9 -0.0623  0.0571  False
+     0     21   0.0158    0.9 -0.0525  0.0841  False
+     0     28   0.0024    0.9 -0.0624  0.0672  False
+     3      7  -0.0487 0.2867 -0.1153  0.0179  False
+     3     14  -0.0672 0.0347 -0.1315 -0.0029   True
+     3     21  -0.0488 0.3783 -0.1212  0.0235  False
+     3     28  -0.0622 0.1036 -0.1313  0.0069  False
+     7     14  -0.0185    0.9 -0.0793  0.0423  False
+     7     21  -0.0001    0.9 -0.0694  0.0692  False
+     7     28  -0.0135    0.9 -0.0793  0.0524  False
+    14     21   0.0184    0.9 -0.0487  0.0855  False
+    14     28    0.005    0.9 -0.0585  0.0685  False
+    21     28  -0.0134    0.9  -0.085  0.0583  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00129595]	Yes
+Stroke	Sham	14	[0.0112815]	Yes
+Stroke	Sham	21	[0.98830089]	No
+Stroke	Sham	28	[0.4237445]	No
+Stroke	Sham	7	[0.08532639]	No
+Stroke	Sham	0	[0.79223814]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CReT_MOp-TRN_ipsilesional_CCcut_log.txt

@@ -0,0 +1,67 @@
+Model Name: md_CReT_MOp-TRN_ipsilesional_CCcut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0075
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 2.424 0.015  0.000  0.002
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3  -0.0578 0.0455  -0.115 -0.0007   True
+     0      7  -0.0085    0.9 -0.0689  0.0518  False
+     0     14  -0.0132    0.9 -0.0727  0.0463  False
+     0     21   0.0178    0.9 -0.0417  0.0773  False
+     0     28   0.0302 0.6975 -0.0316   0.092  False
+     3      7   0.0493 0.1218 -0.0069  0.1054  False
+     3     14   0.0446 0.1882 -0.0106  0.0999  False
+     3     21   0.0756 0.0016  0.0204  0.1308   True
+     3     28    0.088  0.001  0.0303  0.1457   True
+     7     14  -0.0046    0.9 -0.0632  0.0539  False
+     7     21   0.0263 0.7611 -0.0322  0.0849  False
+     7     28   0.0387 0.4503 -0.0221  0.0996  False
+    14     21    0.031 0.6177 -0.0267  0.0886  False
+    14     28   0.0434 0.3032 -0.0167  0.1034  False
+    21     28   0.0124    0.9 -0.0476  0.0724  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0321 0.7262 -0.0363 0.1005  False
+     0      7  -0.0283 0.7813 -0.0931 0.0365  False
+     0     14   0.0115    0.9 -0.0507 0.0737  False
+     0     21   0.0065    0.9 -0.0647 0.0777  False
+     0     28  -0.0072    0.9 -0.0748 0.0603  False
+     3      7  -0.0604 0.1272 -0.1298  0.009  False
+     3     14  -0.0206    0.9 -0.0876 0.0464  False
+     3     21  -0.0256    0.9  -0.101 0.0498  False
+     3     28  -0.0393 0.5991 -0.1113 0.0326  False
+     7     14   0.0398 0.4635 -0.0236 0.1031  False
+     7     21   0.0348 0.7066 -0.0374  0.107  False
+     7     28    0.021    0.9 -0.0476 0.0896  False
+    14     21   -0.005    0.9 -0.0749 0.0649  False
+    14     28  -0.0187    0.9 -0.0849 0.0474  False
+    21     28  -0.0137    0.9 -0.0884 0.0609  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00613323]	Yes
+Stroke	Sham	14	[0.46404731]	No
+Stroke	Sham	21	[0.38436043]	No
+Stroke	Sham	28	[0.03722408]	Yes
+Stroke	Sham	7	[0.06255234]	No
+Stroke	Sham	0	[0.6302699]	No

output/Final_Quantitative_output/mixed_model_analysis/md_CRuT_MOp-RN_ipsilesional_log.txt

@@ -0,0 +1,67 @@
+Model Name: md_CRuT_MOp-RN_ipsilesional
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0065
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.002    0.000 3.454 0.001  0.001  0.002
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0393 0.2401 -0.0906  0.012  False
+     0      7   -0.023 0.8017 -0.0773 0.0312  False
+     0     14   0.0125    0.9  -0.041 0.0659  False
+     0     21   0.0286   0.62 -0.0248 0.0821  False
+     0     28   0.0419 0.2546 -0.0136 0.0974  False
+     3      7   0.0163    0.9 -0.0341 0.0667  False
+     3     14   0.0518  0.035  0.0022 0.1014   True
+     3     21   0.0679 0.0016  0.0183 0.1175   True
+     3     28   0.0812  0.001  0.0294  0.133   True
+     7     14   0.0355 0.3792  -0.017 0.0881  False
+     7     21   0.0517 0.0573 -0.0009 0.1042  False
+     7     28    0.065 0.0097  0.0103 0.1196   True
+    14     21   0.0161    0.9 -0.0357 0.0679  False
+    14     28   0.0294 0.6026 -0.0245 0.0834  False
+    21     28   0.0133    0.9 -0.0406 0.0672  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3    0.042 0.4683 -0.0253 0.1093  False
+     0      7  -0.0101    0.9 -0.0739 0.0538  False
+     0     14   0.0237 0.8628 -0.0376  0.085  False
+     0     21   0.0282 0.8365 -0.0419 0.0983  False
+     0     28   0.0058    0.9 -0.0607 0.0723  False
+     3      7  -0.0521 0.2435 -0.1204 0.0162  False
+     3     14  -0.0183    0.9 -0.0843 0.0476  False
+     3     21  -0.0138    0.9 -0.0881 0.0604  False
+     3     28  -0.0362 0.6571 -0.1071 0.0346  False
+     7     14   0.0338 0.6083 -0.0286 0.0961  False
+     7     21   0.0383 0.6123 -0.0328 0.1094  False
+     7     28   0.0159    0.9 -0.0517 0.0834  False
+    14     21   0.0045    0.9 -0.0643 0.0734  False
+    14     28  -0.0179    0.9  -0.083 0.0473  False
+    21     28  -0.0224    0.9  -0.096 0.0511  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00834269]	Yes
+Stroke	Sham	14	[0.85802399]	No
+Stroke	Sham	21	[0.55258977]	No
+Stroke	Sham	28	[0.01460692]	Yes
+Stroke	Sham	7	[0.8687555]	No
+Stroke	Sham	0	[0.34620705]	No

output/Final_Quantitative_output/mixed_model_analysis/mixed_model_results.csv

@@ -1,109 +1,109 @@
 Qtype,mask_name,p_value
-fa,CC_Mos_Mos.tt,0.11405214912172654
-fa,CC_MOp(dilated)_cut.tt,0.15903786737122472
-fa,CC_MOp(dilated),0.006670396399963432
-fa,CC_MOp_MOp.tt,0.21512368385177072
-fa,CC_MOp_MOp_cut.tt,0.5414687648586081
-fa,CC_MOs_MOs_cut.tt,0.47298232372188287
-fa,CC_SSp_ll.tt,5.4673285960942385e-06
-fa,CC_SSp_ll_cut.tt,0.0005709315196353194
-fa,CC_SSp_ul.tt,2.9094415342612618e-05
-fa,CC_SSp_ul_cut.tt,0.00013173228113114822
-fa,CST_links_CC_cut,0.5931046523000734
-fa,CST_links_CCasROA,0.7357868781481716
-fa,CST_links_ROA_CC_fibers_cut,0.577246960697954
-fa,CST_rechts_CC_cut,0.0012030410116490697
-fa,CST_rechts_CCasROA,0.0010507895147579627
-fa,CST_rechts_ROA_CC_fibers_cut,0.0012557208839304233
-fa,Optic_tract_final.tt,0.21462542119417183
-fa,Retikulospinal_tract_links,0.6652387814920518
-fa,Retikulospinal_tract_rechts,0.04556023474320183
-fa,Rubrospinal_tract_links_,0.6270128659828369
-fa,Rubrospinal_tract_rechts,0.00597546921548271
-fa,Thalamocorticale_links_SSp_and_SSs_End,0.017197889240495954
-fa,Thalamocorticale_links_SSp_ll_and_ul_ROI.tt,0.001958682329016975
-fa,"Thalamocorticale_links_SSp_ul_and_ll_End_0,2.tt",0.0003227909492062389
-fa,Thalamocorticale_rechts_SSp_and_SSs_End,0.14882622542919066
-fa,Thalamocorticale_rechts_SSp_ll_and_ul_ROI.tt,0.023931389352584844
-fa,"Thalamocorticale_rechts_SSp_ul_and_ll_End_0,2.tt",0.010716712632648487
-md,CC_Mos_Mos.tt,0.2810773947574957
-md,CC_MOp(dilated)_cut.tt,0.020741139250529995
-md,CC_MOp(dilated),0.8455270380222699
-md,CC_MOp_MOp.tt,0.7702318945259404
-md,CC_MOp_MOp_cut.tt,0.013622939865193662
-md,CC_MOs_MOs_cut.tt,0.1712958412152905
-md,CC_SSp_ll.tt,0.11566197265968883
-md,CC_SSp_ll_cut.tt,0.0003283308584018542
-md,CC_SSp_ul.tt,0.26534370883445224
-md,CC_SSp_ul_cut.tt,0.002057530726443143
-md,CST_links_CC_cut,0.03808032137728866
-md,CST_links_CCasROA,0.04244601620146803
-md,CST_links_ROA_CC_fibers_cut,0.0376948944972773
-md,CST_rechts_CC_cut,0.18627967975350634
-md,CST_rechts_CCasROA,0.13243565841611873
-md,CST_rechts_ROA_CC_fibers_cut,0.16099987087958534
-md,Optic_tract_final.tt,0.7781364487851996
-md,Retikulospinal_tract_links,0.007752829046917006
-md,Retikulospinal_tract_rechts,0.1344632206709199
-md,Rubrospinal_tract_links_,0.0005209526342981915
-md,Rubrospinal_tract_rechts,0.056521045618384336
-md,Thalamocorticale_links_SSp_and_SSs_End,0.6885081504822086
-md,Thalamocorticale_links_SSp_ll_and_ul_ROI.tt,0.19013370935925045
-md,"Thalamocorticale_links_SSp_ul_and_ll_End_0,2.tt",0.05370373562994426
-md,Thalamocorticale_rechts_SSp_and_SSs_End,0.3808628417456945
-md,Thalamocorticale_rechts_SSp_ll_and_ul_ROI.tt,0.36638483082873596
-md,"Thalamocorticale_rechts_SSp_ul_and_ll_End_0,2.tt",0.32400319263260824
-ad,CC_Mos_Mos.tt,0.5663168521323727
-ad,CC_MOp(dilated)_cut.tt,0.05282253286651552
-ad,CC_MOp(dilated),0.7515641603036611
-ad,CC_MOp_MOp.tt,0.9393287550358754
-ad,CC_MOp_MOp_cut.tt,0.02928115434247787
-ad,CC_MOs_MOs_cut.tt,0.19648532532657637
-ad,CC_SSp_ll.tt,0.5947534750141559
-ad,CC_SSp_ll_cut.tt,0.010105521944443386
-ad,CC_SSp_ul.tt,0.6651477256976095
-ad,CC_SSp_ul_cut.tt,0.023161772827873482
-ad,CST_links_CC_cut,0.08707362469708704
-ad,CST_links_CCasROA,0.08404103352866099
-ad,CST_links_ROA_CC_fibers_cut,0.08642229017531676
-ad,CST_rechts_CC_cut,0.02743580924187836
-ad,CST_rechts_CCasROA,0.01753718197105403
-ad,CST_rechts_ROA_CC_fibers_cut,0.022804104043713344
-ad,Optic_tract_final.tt,0.798252024050848
-ad,Retikulospinal_tract_links,0.017950938497175824
-ad,Retikulospinal_tract_rechts,0.07535893732209828
-ad,Rubrospinal_tract_links_,0.003401720829936756
-ad,Rubrospinal_tract_rechts,0.02162925060155537
-ad,Thalamocorticale_links_SSp_and_SSs_End,0.15347997982463274
-ad,Thalamocorticale_links_SSp_ll_and_ul_ROI.tt,0.01657160142163488
-ad,"Thalamocorticale_links_SSp_ul_and_ll_End_0,2.tt",0.001492192150693168
-ad,Thalamocorticale_rechts_SSp_and_SSs_End,0.3394856608079473
-ad,Thalamocorticale_rechts_SSp_ll_and_ul_ROI.tt,0.14454468979121052
-ad,"Thalamocorticale_rechts_SSp_ul_and_ll_End_0,2.tt",0.14138061556712037
-rd,CC_Mos_Mos.tt,0.16191251550364238
-rd,CC_MOp(dilated)_cut.tt,0.014314437591452511
-rd,CC_MOp(dilated),0.5877551931092652
-rd,CC_MOp_MOp.tt,0.6720556190979161
-rd,CC_MOp_MOp_cut.tt,0.010836051870955526
-rd,CC_MOs_MOs_cut.tt,0.1725984805165659
-rd,CC_SSp_ll.tt,0.02274310992844807
-rd,CC_SSp_ll_cut.tt,4.360831746039448e-05
-rd,CC_SSp_ul.tt,0.12041678715580113
-rd,CC_SSp_ul_cut.tt,0.000436232469614191
-rd,CST_links_CC_cut,0.02329915184657115
-rd,CST_links_CCasROA,0.029179316955986596
-rd,CST_links_ROA_CC_fibers_cut,0.023204502334925145
-rd,CST_rechts_CC_cut,0.6079913567749387
-rd,CST_rechts_CCasROA,0.4890982902826765
-rd,CST_rechts_ROA_CC_fibers_cut,0.5535406687444262
-rd,Optic_tract_final.tt,0.7710758903354286
-rd,Retikulospinal_tract_links,0.005482057522692925
-rd,Retikulospinal_tract_rechts,0.2370532787289491
-rd,Rubrospinal_tract_links_,0.00023857119190363567
-rd,Rubrospinal_tract_rechts,0.12787271250862955
-rd,Thalamocorticale_links_SSp_and_SSs_End,0.6908244765990648
-rd,Thalamocorticale_links_SSp_ll_and_ul_ROI.tt,0.70197539124608
-rd,"Thalamocorticale_links_SSp_ul_and_ll_End_0,2.tt",0.38515855188381376
-rd,Thalamocorticale_rechts_SSp_and_SSs_End,0.4413861816111867
-rd,Thalamocorticale_rechts_SSp_ll_and_ul_ROI.tt,0.6950630953434636
-rd,"Thalamocorticale_rechts_SSp_ul_and_ll_End_0,2.tt",0.5910678952945977
+fa,CC_MOp-MOp_dilated,0.000764702252832505
+fa,CC_MOp-MOp_dilated_cut,0.14969369072806923
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+fa,CC_MOs-MOs,0.03357907070806808
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+fa,CC_SSp_ll-SSp_ll,2.3420247004382942e-08
+fa,CC_SSp_ll-SSp_ll_cut,3.895450833514923e-05
+fa,CC_SSp_ul-SSp_ul,1.1102891499223901e-05
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+fa,TC_DORsm-SSp_ll+SSp_ul_contralesional_END+higherstepsize,1.6521308752117927e-05
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+fa,CST_MOp-int-py_ipsilesional_selfdrawnROA+CCcut,0.04872279567350309
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+fa,TC_DORsm-SSp_ll+SSp_ul_ipsilesional_END+higherstepsize_,0.0018961082226590703
+md,CC_MOp-MOp_dilated,0.9636283250141883
+md,CC_MOp-MOp_dilated_cut,0.0044321287502354974
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+md,CC_SSp_ul-SSp_ul_cut,0.00209897547029832
+md,OT_och-lgn_lgncut,0.4859229434344938
+md,CRuT_MOp-RN_contralesional_mirrored,0.2681831018414498
+md,TC_DORsm-SSp+SSs_contralesional_END+CCcut,0.9479194144552905
+md,TC_DORsm-SSp_ll+SSp_ul_contralesional_ROI+CCcut,0.807716916416026
+md,TC_DORsm-SSp_ll+SSp_ul_contralesional_END+higherstepsize,0.8049864597483745
+md,CC_MOp-MOp,0.7881203649980624
+md,CST_MOp-int-py_contralesional_CCcut,0.10903670338348209
+md,CST_MOp-int-py_contralesional_CCasROA,0.09463613493924175
+md,CST_MOp-int-py_contralesional_selfdrawnROA+CCcut,0.10523683914291054
+md,CST_MOp-int-py_ipsilesional_CCcut,0.572869411571136
+md,CST_MOp-int-py_ipsilesional_CCasROA,0.4863863121121865
+md,CST_MOp-int-py_ipsilesional_selfdrawnROA+CCcut,0.5187886425559998
+md,CReT_MOp-TRN_contralesional_CCcut,0.40014152185687957
+md,CReT_MOp-TRN_ipsilesional_CCcut,0.015352203209589714
+md,CRuT_MOp-RN_ipsilesional,0.0005513725158134129
+md,TC_DORsm-SSp_ll+SSp_ul_ipsilesional_ROI+CCcut,0.11703965363731128
+md,TC_DORsm-SSp+SSs_ipsilesional_END+CCcut,0.5511713168651224
+md,TC_DORsm-SSp_ll+SSp_ul_ipsilesional_END+higherstepsize_,0.2252152553826955
+ad,CC_MOp-MOp_dilated,0.5035527768069832
+ad,CC_MOp-MOp_dilated_cut,0.019888203311090865
+ad,CC_MOp-MOp_cut,0.002553935165370371
+ad,CC_MOs-MOs,0.7035185164066022
+ad,CC_MOs-MOs_cut,0.035262822009781446
+ad,CC_SSp_ll-SSp_ll,0.657501745170847
+ad,CC_SSp_ll-SSp_ll_cut,0.014681991500147753
+ad,CC_SSp_ul-SSp_ul,0.25803131213525643
+ad,CC_SSp_ul-SSp_ul_cut,0.04229772359990703
+ad,OT_och-lgn_lgncut,0.6032633924247919
+ad,CRuT_MOp-RN_contralesional_mirrored,0.11847929581436505
+ad,TC_DORsm-SSp+SSs_contralesional_END+CCcut,0.3208906519674166
+ad,TC_DORsm-SSp_ll+SSp_ul_contralesional_ROI+CCcut,0.4278186382610758
+ad,TC_DORsm-SSp_ll+SSp_ul_contralesional_END+higherstepsize,0.21365790599697898
+ad,CC_MOp-MOp,0.9235770992366283
+ad,CST_MOp-int-py_contralesional_CCcut,0.033637626364474316
+ad,CST_MOp-int-py_contralesional_CCasROA,0.026452817251350815
+ad,CST_MOp-int-py_contralesional_selfdrawnROA+CCcut,0.03072549006592736
+ad,CST_MOp-int-py_ipsilesional_CCcut,0.26926514457723194
+ad,CST_MOp-int-py_ipsilesional_CCasROA,0.21082349737538264
+ad,CST_MOp-int-py_ipsilesional_selfdrawnROA+CCcut,0.22856005510184274
+ad,CReT_MOp-TRN_contralesional_CCcut,0.16231373936396853
+ad,CReT_MOp-TRN_ipsilesional_CCcut,0.015538197244647596
+ad,CRuT_MOp-RN_ipsilesional,0.0011529266923220479
+ad,TC_DORsm-SSp_ll+SSp_ul_ipsilesional_ROI+CCcut,0.021993840222511597
+ad,TC_DORsm-SSp+SSs_ipsilesional_END+CCcut,0.12050220796207556
+ad,TC_DORsm-SSp_ll+SSp_ul_ipsilesional_END+higherstepsize_,0.04133446884277687
+rd,CC_MOp-MOp_dilated,0.7009037502266402
+rd,CC_MOp-MOp_dilated_cut,0.0020427344062894535
+rd,CC_MOp-MOp_cut,0.00040884837633998615
+rd,CC_MOs-MOs,0.5993823749023859
+rd,CC_MOs-MOs_cut,0.02060438223570422
+rd,CC_SSp_ll-SSp_ll,0.018898060961979588
+rd,CC_SSp_ll-SSp_ll_cut,6.024320970285604e-06
+rd,CC_SSp_ul-SSp_ul,0.01798663531654731
+rd,CC_SSp_ul-SSp_ul_cut,0.0002694326989084794
+rd,OT_och-lgn_lgncut,0.4023624934085368
+rd,CRuT_MOp-RN_contralesional_mirrored,0.4859182032711996
+rd,TC_DORsm-SSp+SSs_contralesional_END+CCcut,0.3821111109896743
+rd,TC_DORsm-SSp_ll+SSp_ul_contralesional_ROI+CCcut,0.3188948221252429
+rd,TC_DORsm-SSp_ll+SSp_ul_contralesional_END+higherstepsize,0.5949448564197659
+rd,CC_MOp-MOp,0.6230549228787323
+rd,CST_MOp-int-py_contralesional_CCcut,0.2803920439276959
+rd,CST_MOp-int-py_contralesional_CCasROA,0.2590061274423675
+rd,CST_MOp-int-py_contralesional_selfdrawnROA+CCcut,0.2783870436418653
+rd,CST_MOp-int-py_ipsilesional_CCcut,0.939526107056537
+rd,CST_MOp-int-py_ipsilesional_CCasROA,0.8519037826851101
+rd,CST_MOp-int-py_ipsilesional_selfdrawnROA+CCcut,0.8891824914166516
+rd,CReT_MOp-TRN_contralesional_CCcut,0.726175158988331
+rd,CReT_MOp-TRN_ipsilesional_CCcut,0.0201313806135242
+rd,CRuT_MOp-RN_ipsilesional,0.0006269646036643398
+rd,TC_DORsm-SSp_ll+SSp_ul_ipsilesional_ROI+CCcut,0.36634358836557956
+rd,TC_DORsm-SSp+SSs_ipsilesional_END+CCcut,0.8413260348562701
+rd,TC_DORsm-SSp_ll+SSp_ul_ipsilesional_END+higherstepsize_,0.6239315382281756

output/Final_Quantitative_output/mixed_model_analysis/rd_CC_MOp-MOp_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: rd_CC_MOp-MOp_cut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0057
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 3.534 0.000  0.001  0.002
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3  -0.0089    0.9 -0.0613 0.0434  False
+     0      7   0.0092    0.9  -0.046 0.0645  False
+     0     14   0.0445   0.18   -0.01  0.099  False
+     0     21    0.062 0.0156  0.0075 0.1165   True
+     0     28    0.049 0.1305 -0.0075 0.1056  False
+     3      7   0.0182    0.9 -0.0332 0.0696  False
+     3     14   0.0534 0.0318  0.0028  0.104   True
+     3     21   0.0709 0.0011  0.0204 0.1215   True
+     3     28    0.058 0.0223  0.0052 0.1108   True
+     7     14   0.0352 0.4125 -0.0184 0.0889  False
+     7     21   0.0528 0.0565 -0.0008 0.1064  False
+     7     28   0.0398 0.3151 -0.0159 0.0956  False
+    14     21   0.0175    0.9 -0.0353 0.0704  False
+    14     28   0.0046    0.9 -0.0504 0.0596  False
+    21     28   -0.013    0.9 -0.0679  0.042  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3    0.012    0.9 -0.0453 0.0694  False
+     0      7   0.0152    0.9 -0.0392 0.0696  False
+     0     14   0.0226 0.7878 -0.0297 0.0748  False
+     0     21  -0.0069    0.9 -0.0666 0.0529  False
+     0     28   0.0092    0.9 -0.0475 0.0659  False
+     3      7   0.0031    0.9 -0.0551 0.0614  False
+     3     14   0.0105    0.9 -0.0457 0.0668  False
+     3     21  -0.0189    0.9 -0.0822 0.0444  False
+     3     28  -0.0028    0.9 -0.0632 0.0576  False
+     7     14   0.0074    0.9 -0.0458 0.0606  False
+     7     21   -0.022    0.9 -0.0826 0.0386  False
+     7     28   -0.006    0.9 -0.0636 0.0516  False
+    14     21  -0.0294 0.6733 -0.0881 0.0292  False
+    14     28  -0.0134    0.9 -0.0689 0.0422  False
+    21     28   0.0161    0.9 -0.0466 0.0787  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.12941951]	No
+Stroke	Sham	14	[0.55234752]	No
+Stroke	Sham	21	[0.0062876]	Yes
+Stroke	Sham	28	[0.13925467]	No
+Stroke	Sham	7	[0.16464719]	No
+Stroke	Sham	0	[0.62976298]	No

output/Final_Quantitative_output/mixed_model_analysis/rd_CC_MOp-MOp_dilated_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: rd_CC_MOp-MOp_dilated_cut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0048
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 3.084 0.002  0.000  0.002
+Group Var         0.000                                   
+==========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0119    0.9 -0.0368 0.0606  False
+     0      7   0.0002    0.9 -0.0512 0.0516  False
+     0     14   0.0366  0.303 -0.0141 0.0873  False
+     0     21    0.052 0.0407  0.0013 0.1027   True
+     0     28   0.0418 0.2046 -0.0108 0.0945  False
+     3      7  -0.0117    0.9 -0.0595 0.0361  False
+     3     14   0.0247 0.6359 -0.0223 0.0718  False
+     3     21   0.0401 0.1427 -0.0069 0.0872  False
+     3     28   0.0299 0.4979 -0.0192 0.0791  False
+     7     14   0.0364 0.2915 -0.0135 0.0863  False
+     7     21   0.0518 0.0367  0.0019 0.1017   True
+     7     28   0.0416 0.1951 -0.0102 0.0935  False
+    14     21   0.0154    0.9 -0.0337 0.0645  False
+    14     28   0.0052    0.9 -0.0459 0.0564  False
+    21     28  -0.0102    0.9 -0.0613 0.0409  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0101    0.9 -0.0423 0.0626  False
+     0      7   0.0149    0.9 -0.0348 0.0647  False
+     0     14   0.0225 0.7222 -0.0252 0.0703  False
+     0     21   -0.002    0.9 -0.0566 0.0526  False
+     0     28   0.0153    0.9 -0.0366 0.0671  False
+     3      7   0.0048    0.9 -0.0484  0.058  False
+     3     14   0.0124    0.9  -0.039 0.0638  False
+     3     21  -0.0122    0.9   -0.07 0.0457  False
+     3     28   0.0051    0.9 -0.0501 0.0603  False
+     7     14   0.0076    0.9  -0.041 0.0562  False
+     7     21   -0.017    0.9 -0.0724 0.0384  False
+     7     28   0.0003    0.9 -0.0523  0.053  False
+    14     21  -0.0246 0.7454 -0.0782 0.0291  False
+    14     28  -0.0073    0.9  -0.058 0.0435  False
+    21     28   0.0173    0.9   -0.04 0.0746  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.75541552]	No
+Stroke	Sham	14	[0.22260056]	No
+Stroke	Sham	21	[0.00830744]	Yes
+Stroke	Sham	28	[0.06821765]	No
+Stroke	Sham	7	[0.43206535]	No
+Stroke	Sham	0	[0.86553924]	No

output/Final_Quantitative_output/mixed_model_analysis/rd_CC_MOs-MOs_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: rd_CC_MOs-MOs_cut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0063
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 2.315 0.021  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   0.0103    0.9 -0.0406 0.0612  False
+     0      7   0.0182    0.9 -0.0356 0.0719  False
+     0     14    0.042 0.2069  -0.011  0.095  False
+     0     21   0.0578 0.0234  0.0049 0.1108   True
+     0     28   0.0436 0.2063 -0.0114 0.0986  False
+     3      7   0.0079    0.9 -0.0421 0.0578  False
+     3     14   0.0317 0.4354 -0.0175 0.0808  False
+     3     21   0.0475 0.0645 -0.0016 0.0967  False
+     3     28   0.0333 0.4273  -0.018 0.0847  False
+     7     14   0.0238 0.7491 -0.0283 0.0759  False
+     7     21   0.0397 0.2464 -0.0124 0.0918  False
+     7     28   0.0255  0.728 -0.0287 0.0797  False
+    14     21   0.0159    0.9 -0.0355 0.0672  False
+    14     28   0.0016    0.9 -0.0518 0.0551  False
+    21     28  -0.0142    0.9 -0.0677 0.0392  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3    0.026 0.8733 -0.0424 0.0944  False
+     0      7   0.0083    0.9 -0.0566 0.0731  False
+     0     14   0.0105    0.9 -0.0518 0.0727  False
+     0     21   0.0021    0.9 -0.0691 0.0733  False
+     0     28   0.0056    0.9 -0.0619 0.0732  False
+     3      7  -0.0177    0.9 -0.0872 0.0517  False
+     3     14  -0.0156    0.9 -0.0826 0.0515  False
+     3     21  -0.0239    0.9 -0.0994 0.0515  False
+     3     28  -0.0204    0.9 -0.0924 0.0516  False
+     7     14   0.0022    0.9 -0.0612 0.0656  False
+     7     21  -0.0062    0.9 -0.0784  0.066  False
+     7     28  -0.0026    0.9 -0.0713  0.066  False
+    14     21  -0.0084    0.9 -0.0783 0.0615  False
+    14     28  -0.0048    0.9  -0.071 0.0614  False
+    21     28   0.0036    0.9 -0.0711 0.0783  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.14244451]	No
+Stroke	Sham	14	[0.65704366]	No
+Stroke	Sham	21	[0.13120273]	No
+Stroke	Sham	28	[0.48162848]	No
+Stroke	Sham	7	[0.27228604]	No
+Stroke	Sham	0	[0.33825439]	No

output/Final_Quantitative_output/mixed_model_analysis/rd_CC_SSp_ll-SSp_ll_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: rd_CC_SSp_ll-SSp_ll_cut
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM   Dependent Variable:   Value 
+No. Observations:    364       Method:               REML  
+No. Groups:          2         Scale:                0.0120
+Min. group size:     158       Log-Likelihood:       inf   
+Max. group size:     206       Converged:            Yes   
+Mean group size:     182.0                                 
+-----------------------------------------------------------
+                 Coef.  Std.Err.   z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept         0.000                                    
+merged_timepoint -0.003    0.001 -4.526 0.000 -0.004 -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   0.2237  0.001  0.1513  0.2961   True
+     0      7  -0.0055    0.9  -0.082   0.071  False
+     0     14   0.0369  0.697 -0.0386  0.1123  False
+     0     21   0.0133    0.9 -0.0621  0.0887  False
+     0     28   0.0054    0.9 -0.0729  0.0837  False
+     3      7  -0.2293  0.001 -0.3004 -0.1581   True
+     3     14  -0.1869  0.001 -0.2569 -0.1169   True
+     3     21  -0.2104  0.001 -0.2804 -0.1405   True
+     3     28  -0.2184  0.001 -0.2915 -0.1453   True
+     7     14   0.0424  0.561 -0.0318  0.1166  False
+     7     21   0.0188    0.9 -0.0554   0.093  False
+     7     28   0.0109    0.9 -0.0662   0.088  False
+    14     21  -0.0235    0.9 -0.0966  0.0495  False
+    14     28  -0.0315 0.8205 -0.1076  0.0446  False
+    21     28  -0.0079    0.9  -0.084  0.0681  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0496 0.0935 -0.0046  0.1038  False
+     0      7    0.002    0.9 -0.0494  0.0534  False
+     0     14    -0.01    0.9 -0.0594  0.0393  False
+     0     21  -0.0119    0.9 -0.0683  0.0446  False
+     0     28  -0.0171    0.9 -0.0707  0.0364  False
+     3      7  -0.0476 0.1316 -0.1026  0.0075  False
+     3     14  -0.0596  0.018 -0.1128 -0.0065   True
+     3     21  -0.0615 0.0399 -0.1213 -0.0017   True
+     3     28  -0.0667 0.0118 -0.1238 -0.0097   True
+     7     14  -0.0121    0.9 -0.0623  0.0382  False
+     7     21  -0.0139    0.9 -0.0712  0.0433  False
+     7     28  -0.0191    0.9 -0.0735  0.0353  False
+    14     21  -0.0019    0.9 -0.0573  0.0536  False
+    14     28  -0.0071    0.9 -0.0595  0.0454  False
+    21     28  -0.0052    0.9 -0.0644   0.054  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00041003]	Yes
+Stroke	Sham	14	[0.24353423]	No
+Stroke	Sham	21	[0.94390422]	No
+Stroke	Sham	28	[0.77187453]	No
+Stroke	Sham	7	[0.00488268]	Yes
+Stroke	Sham	0	[0.16862804]	No

output/Final_Quantitative_output/mixed_model_analysis/rd_CC_SSp_ll-SSp_ll_log.txt

@@ -0,0 +1,67 @@
+Model Name: rd_CC_SSp_ll-SSp_ll
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM   Dependent Variable:   Value 
+No. Observations:    364       Method:               REML  
+No. Groups:          2         Scale:                0.0046
+Min. group size:     158       Log-Likelihood:       inf   
+Max. group size:     206       Converged:            Yes   
+Mean group size:     182.0                                 
+-----------------------------------------------------------
+                 Coef.  Std.Err.   z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept         0.000                                    
+merged_timepoint -0.001    0.000 -2.348 0.019 -0.002 -0.000
+Group Var         0.000                                    
+===========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.1105  0.001  0.0667  0.1542   True
+     0      7   0.0039    0.9 -0.0422  0.0501  False
+     0     14   0.0325 0.3147  -0.013  0.0781  False
+     0     21   0.0236 0.6474 -0.0219  0.0691  False
+     0     28   0.0244 0.6514 -0.0229  0.0717  False
+     3      7  -0.1065  0.001 -0.1495 -0.0636   True
+     3     14  -0.0779  0.001 -0.1202 -0.0357   True
+     3     21  -0.0868  0.001 -0.1291 -0.0446   True
+     3     28   -0.086  0.001 -0.1302 -0.0419   True
+     7     14   0.0286  0.446 -0.0162  0.0734  False
+     7     21   0.0197 0.7781 -0.0251  0.0645  False
+     7     28   0.0205 0.7777 -0.0261   0.067  False
+    14     21  -0.0089    0.9  -0.053  0.0352  False
+    14     28  -0.0081    0.9  -0.054  0.0378  False
+    21     28   0.0008    0.9 -0.0451  0.0467  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0432 0.0765 -0.0026  0.089  False
+     0      7   0.0254 0.5353  -0.018 0.0688  False
+     0     14   0.0021    0.9 -0.0396 0.0438  False
+     0     21   0.0028    0.9 -0.0449 0.0505  False
+     0     28   0.0022    0.9 -0.0431 0.0474  False
+     3      7  -0.0178 0.8689 -0.0643 0.0287  False
+     3     14  -0.0411 0.0925  -0.086 0.0037  False
+     3     21  -0.0404 0.1961  -0.091 0.0101  False
+     3     28  -0.0411 0.1433 -0.0893 0.0072  False
+     7     14  -0.0233 0.5943 -0.0658 0.0191  False
+     7     21  -0.0226 0.7292  -0.071 0.0257  False
+     7     28  -0.0232 0.6666 -0.0692 0.0227  False
+    14     21   0.0007    0.9 -0.0461 0.0475  False
+    14     28   0.0001    0.9 -0.0442 0.0444  False
+    21     28  -0.0006    0.9 -0.0506 0.0494  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00320301]	Yes
+Stroke	Sham	14	[0.00637168]	Yes
+Stroke	Sham	21	[0.432966]	No
+Stroke	Sham	28	[0.12970839]	No
+Stroke	Sham	7	[0.02312619]	Yes
+Stroke	Sham	0	[0.8336977]	No

output/Final_Quantitative_output/mixed_model_analysis/rd_CC_SSp_ul-SSp_ul_cut_log.txt

@@ -0,0 +1,67 @@
+Model Name: rd_CC_SSp_ul-SSp_ul_cut
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM  Dependent Variable:  Value   
+No. Observations:    364      Method:              REML    
+No. Groups:          2        Scale:               0.0102  
+Min. group size:     158      Log-Likelihood:      307.7241
+Max. group size:     206      Converged:           Yes     
+Mean group size:     182.0                                 
+-----------------------------------------------------------
+                 Coef.  Std.Err.   z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept         0.629    0.018 34.844 0.000  0.594  0.665
+merged_timepoint -0.002    0.001 -3.643 0.000 -0.003 -0.001
+Group Var         0.001    0.008                           
+===========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.1904  0.001   0.122  0.2589   True
+     0      7  -0.0035    0.9 -0.0759  0.0688  False
+     0     14   0.0378 0.6299 -0.0336  0.1091  False
+     0     21    0.018    0.9 -0.0534  0.0893  False
+     0     28    0.016    0.9 -0.0581  0.0901  False
+     3      7   -0.194  0.001 -0.2612 -0.1267   True
+     3     14  -0.1527  0.001 -0.2189 -0.0865   True
+     3     21  -0.1725  0.001 -0.2387 -0.1063   True
+     3     28  -0.1744  0.001 -0.2436 -0.1053   True
+     7     14   0.0413 0.5327 -0.0289  0.1114  False
+     7     21   0.0215    0.9 -0.0487  0.0916  False
+     7     28   0.0195    0.9 -0.0534  0.0925  False
+    14     21  -0.0198    0.9 -0.0889  0.0493  False
+    14     28  -0.0217    0.9 -0.0937  0.0502  False
+    21     28  -0.0019    0.9 -0.0739    0.07  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3   0.0484 0.0875 -0.0039  0.1007  False
+     0      7   0.0101    0.9 -0.0395  0.0597  False
+     0     14  -0.0082    0.9 -0.0558  0.0395  False
+     0     21   0.0004    0.9 -0.0541  0.0549  False
+     0     28   -0.009    0.9 -0.0607  0.0427  False
+     3      7  -0.0383 0.3042 -0.0914  0.0149  False
+     3     14  -0.0566 0.0214 -0.1078 -0.0053   True
+     3     21   -0.048  0.163 -0.1057  0.0097  False
+     3     28  -0.0574 0.0356 -0.1125 -0.0024   True
+     7     14  -0.0183 0.8785 -0.0668  0.0302  False
+     7     21  -0.0097    0.9  -0.065  0.0455  False
+     7     28  -0.0192 0.8983 -0.0717  0.0333  False
+    14     21   0.0086    0.9 -0.0449  0.0621  False
+    14     28  -0.0009    0.9 -0.0515  0.0498  False
+    21     28  -0.0095    0.9 -0.0666  0.0477  False
+----------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00042224]	Yes
+Stroke	Sham	14	[0.02967025]	Yes
+Stroke	Sham	21	[0.82160274]	No
+Stroke	Sham	28	[0.38104306]	No
+Stroke	Sham	7	[0.05271787]	No
+Stroke	Sham	0	[0.5754265]	No

output/Final_Quantitative_output/mixed_model_analysis/rd_CC_SSp_ul-SSp_ul_log.txt

@@ -0,0 +1,67 @@
+Model Name: rd_CC_SSp_ul-SSp_ul
+           Mixed Linear Model Regression Results
+===========================================================
+Model:               MixedLM   Dependent Variable:   Value 
+No. Observations:    364       Method:               REML  
+No. Groups:          2         Scale:                0.0087
+Min. group size:     158       Log-Likelihood:       inf   
+Max. group size:     206       Converged:            Yes   
+Mean group size:     182.0                                 
+-----------------------------------------------------------
+                 Coef.  Std.Err.   z    P>|z| [0.025 0.975]
+-----------------------------------------------------------
+Intercept         0.000                                    
+merged_timepoint -0.001    0.001 -2.366 0.018 -0.002 -0.000
+Group Var         0.000                                    
+===========================================================
+
+Posthoc Analysis for Stroke:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05 
+====================================================
+group1 group2 meandiff p-adj   lower   upper  reject
+----------------------------------------------------
+     0      3    0.162  0.001  0.0978  0.2262   True
+     0      7   -0.001    0.9 -0.0688  0.0668  False
+     0     14   0.0398   0.52  -0.027  0.1067  False
+     0     21   0.0269 0.8394   -0.04  0.0938  False
+     0     28   0.0359 0.6509 -0.0336  0.1053  False
+     3      7   -0.163  0.001 -0.2261    -0.1   True
+     3     14  -0.1222  0.001 -0.1842 -0.0601   True
+     3     21  -0.1351  0.001 -0.1972 -0.0731   True
+     3     28  -0.1262  0.001  -0.191 -0.0614   True
+     7     14   0.0409 0.4771 -0.0249  0.1066  False
+     7     21   0.0279 0.8031 -0.0379  0.0937  False
+     7     28   0.0369 0.6135 -0.0315  0.1053  False
+    14     21  -0.0129    0.9 -0.0778  0.0519  False
+    14     28   -0.004    0.9 -0.0714  0.0635  False
+    21     28    0.009    0.9 -0.0585  0.0764  False
+----------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0464 0.1115 -0.0057 0.0986  False
+     0      7   0.0307 0.4747 -0.0187 0.0802  False
+     0     14  -0.0005    0.9  -0.048  0.047  False
+     0     21   0.0038    0.9 -0.0505 0.0581  False
+     0     28   0.0044    0.9 -0.0472 0.0559  False
+     3      7  -0.0157    0.9 -0.0687 0.0372  False
+     3     14  -0.0469  0.092  -0.098 0.0042  False
+     3     21  -0.0426 0.2739 -0.1002 0.0149  False
+     3     28   -0.042 0.2391  -0.097 0.0129  False
+     7     14  -0.0312 0.4317 -0.0795 0.0172  False
+     7     21  -0.0269 0.6957  -0.082 0.0282  False
+     7     28  -0.0263 0.6712 -0.0787  0.026  False
+    14     21   0.0043    0.9  -0.049 0.0576  False
+    14     28   0.0049    0.9 -0.0456 0.0554  False
+    21     28   0.0006    0.9 -0.0564 0.0575  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[5.22097049e-05]	Yes
+Stroke	Sham	14	[0.00256078]	Yes
+Stroke	Sham	21	[0.36854534]	No
+Stroke	Sham	28	[0.03823607]	Yes
+Stroke	Sham	7	[0.09533539]	No
+Stroke	Sham	0	[0.84064333]	No

output/Final_Quantitative_output/mixed_model_analysis/rd_CReT_MOp-TRN_ipsilesional_CCcut_log.txt

@@ -0,0 +1,67 @@
+Model Name: rd_CReT_MOp-TRN_ipsilesional_CCcut
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM  Dependent Variable:  Value   
+No. Observations:   364      Method:              REML    
+No. Groups:         2        Scale:               0.0053  
+Min. group size:    158      Log-Likelihood:      426.9526
+Max. group size:    206      Converged:           No      
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef. Std.Err.   z    P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        0.596    0.006 98.914 0.000  0.584  0.608
+merged_timepoint 0.001    0.000  2.324 0.020  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   -0.043 0.1149 -0.0916 0.0055  False
+     0      7   -0.001    0.9 -0.0523 0.0503  False
+     0     14  -0.0041    0.9 -0.0547 0.0464  False
+     0     21    0.022 0.7852 -0.0286 0.0726  False
+     0     28   0.0263 0.6785 -0.0263 0.0788  False
+     3      7    0.042 0.1189 -0.0057 0.0897  False
+     3     14   0.0389 0.1669  -0.008 0.0858  False
+     3     21   0.0651 0.0013  0.0181  0.112   True
+     3     28   0.0693  0.001  0.0203 0.1183   True
+     7     14  -0.0032    0.9 -0.0529 0.0466  False
+     7     21    0.023 0.7404 -0.0268 0.0728  False
+     7     28   0.0272 0.6342 -0.0245  0.079  False
+    14     21   0.0262 0.6228 -0.0229 0.0752  False
+    14     28   0.0304 0.5201 -0.0206 0.0814  False
+    21     28   0.0042    0.9 -0.0468 0.0553  False
+---------------------------------------------------
+Posthoc Analysis for Sham:
+Multiple Comparison of Means - Tukey HSD, FWER=0.05
+===================================================
+group1 group2 meandiff p-adj   lower  upper  reject
+---------------------------------------------------
+     0      3   0.0264 0.7401 -0.0309 0.0837  False
+     0      7  -0.0216 0.8433  -0.076 0.0327  False
+     0     14    0.008    0.9 -0.0441 0.0602  False
+     0     21   0.0019    0.9 -0.0578 0.0615  False
+     0     28  -0.0073    0.9 -0.0639 0.0493  False
+     3      7  -0.0481 0.1681 -0.1062 0.0101  False
+     3     14  -0.0184    0.9 -0.0745 0.0378  False
+     3     21  -0.0246 0.8599 -0.0877 0.0386  False
+     3     28  -0.0337 0.5785  -0.094 0.0266  False
+     7     14   0.0297 0.5785 -0.0234 0.0828  False
+     7     21   0.0235   0.86  -0.037  0.084  False
+     7     28   0.0143    0.9 -0.0431 0.0718  False
+    14     21  -0.0062    0.9 -0.0647 0.0524  False
+    14     28  -0.0153    0.9 -0.0708 0.0401  False
+    21     28  -0.0092    0.9 -0.0717 0.0534  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00432306]	Yes
+Stroke	Sham	14	[0.47621495]	No
+Stroke	Sham	21	[0.33027897]	No
+Stroke	Sham	28	[0.08338487]	No
+Stroke	Sham	7	[0.14275735]	No
+Stroke	Sham	0	[0.99592817]	No

output/Final_Quantitative_output/mixed_model_analysis/rd_CRuT_MOp-RN_ipsilesional_log.txt

@@ -0,0 +1,67 @@
+Model Name: rd_CRuT_MOp-RN_ipsilesional
+          Mixed Linear Model Regression Results
+==========================================================
+Model:              MixedLM   Dependent Variable:   Value 
+No. Observations:   364       Method:               REML  
+No. Groups:         2         Scale:                0.0048
+Min. group size:    158       Log-Likelihood:       inf   
+Max. group size:    206       Converged:            Yes   
+Mean group size:    182.0                                 
+----------------------------------------------------------
+                 Coef.  Std.Err.   z   P>|z| [0.025 0.975]
+----------------------------------------------------------
+Intercept        -0.000                                   
+merged_timepoint  0.001    0.000 3.420 0.001  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  -0.0369  0.176 -0.0819 0.0081  False
+     0      7  -0.0194 0.8297 -0.0669 0.0281  False
+     0     14   0.0113    0.9 -0.0355 0.0582  False
+     0     21   0.0246 0.6386 -0.0223 0.0714  False
+     0     28   0.0354 0.2959 -0.0133  0.084  False
+     3      7   0.0175 0.8509 -0.0267 0.0617  False
+     3     14   0.0482 0.0202  0.0047 0.0917   True
+     3     21   0.0614  0.001   0.018 0.1049   True
+     3     28   0.0723  0.001  0.0268 0.1177   True
+     7     14   0.0307 0.3952 -0.0154 0.0769  False
+     7     21    0.044 0.0715 -0.0021 0.0901  False
+     7     28   0.0548 0.0149  0.0068 0.1027   True
+    14     21   0.0132    0.9 -0.0322 0.0586  False
+    14     28    0.024 0.6646 -0.0232 0.0713  False
+    21     28   0.0108    0.9 -0.0365 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   0.0305 0.6199 -0.0266 0.0877  False
+     0      7  -0.0107    0.9 -0.0649 0.0435  False
+     0     14   0.0179    0.9 -0.0342 0.0699  False
+     0     21   0.0189    0.9 -0.0406 0.0785  False
+     0     28   0.0021    0.9 -0.0544 0.0586  False
+     3      7  -0.0412   0.32 -0.0993 0.0169  False
+     3     14  -0.0127    0.9 -0.0687 0.0434  False
+     3     21  -0.0116    0.9 -0.0747 0.0515  False
+     3     28  -0.0284 0.7217 -0.0886 0.0318  False
+     7     14   0.0285 0.6125 -0.0245 0.0816  False
+     7     21   0.0296 0.6925 -0.0308   0.09  False
+     7     28   0.0128    0.9 -0.0446 0.0702  False
+    14     21   0.0011    0.9 -0.0574 0.0595  False
+    14     28  -0.0158    0.9 -0.0711 0.0396  False
+    21     28  -0.0168    0.9 -0.0793 0.0456  False
+---------------------------------------------------
+Sidak Multiple Comparisons:
+Group1	Group2	TimePoint	PValue	SignificantDifference
+Stroke	Sham	3	[0.00670118]	Yes
+Stroke	Sham	14	[0.8804173]	No
+Stroke	Sham	21	[0.50021618]	No
+Stroke	Sham	28	[0.02589372]	Yes
+Stroke	Sham	7	[0.96367405]	No
+Stroke	Sham	0	[0.50179847]	No