Merge pull request #180 from CoBrALab/updates

Added seeds to MELODIC runs to ensure reproducibility.

Author: Gab-D-G

rabies/analysis_pkg/analysis_functions.py

@@ -222,7 +222,7 @@ def run_group_ICA(bold_file_list, mask_file, dim):
 
     from rabies.preprocess_pkg.utils import run_command
     out_dir = os.path.abspath('group_melodic.ica')
-    command = f'melodic -i {file_path} -m {mask_file} -o {out_dir} -d {dim} --report'
+    command = f'melodic -i {file_path} -m {mask_file} -o {out_dir} -d {dim} --report --seed=1'
     rc = run_command(command)
     IC_file = out_dir+'/melodic_IC.nii.gz'
     return out_dir, IC_file

rabies/conf_reg_pkg/mod_ICA_AROMA/ICA_AROMA_functions.py

@@ -200,7 +200,7 @@ def runICA(fslDir, inFile, outDir, melDirIn, mask, dim, TR):
                                 '--ICs=' + melIC,
                                 '--mix=' + melICmix,
                                 '--outdir=' + melDir,
-                                '--Ostats --mmthresh=0.5']))
+                                '--Ostats --mmthresh=0.5 --seed=1']))
 
     else:
         # If a melodic directory was specified, display that it did not contain all files needed for ICA-AROMA (or that the directory does not exist at all)
@@ -216,7 +216,7 @@ def runICA(fslDir, inFile, outDir, melDirIn, mask, dim, TR):
                             '--outdir=' + melDir,
                             '--mask=' + mask,
                             '--dim=' + str(dim),
-                            '--Ostats --nobet --mmthresh=0.5 --report',
+                            '--Ostats --nobet --mmthresh=0.5 --report --seed=1',
                             '--tr=' + str(TR)]))
 
     # Get number of components