Merge pull request #13 from smeisler/fmap_sym

Allow fmaps to be symlinked
suyashdb · Aug 1, 2022 · 1009641 · 1009641
2 parents 8640cbe + f1af2f8
commit 1009641
Showing 1 changed file with 7 additions and 1 deletion.
diff --git a/hcp2bids/main.py b/hcp2bids/main.py
@@ -193,7 +193,13 @@ def hcp2bids(input_dir, output_dir, s_link = False):
         for fieldmap in fieldmaplist:
             parentdir = os.path.split(os.path.dirname(fieldmap))[1]
             dst = fmap + parentdir +'_'+ os.path.split(fieldmap)[1]
-            shutil.copy(fieldmap, dst)
+
+            if s_link:
+                if not os.path.islink(dst):
+                    os.symlink(os.path.realpath(fieldmap), dst)
+            else:
+                shutil.copy(fieldmap, dst)
+
         print("done with fMAPs for --", subjects)
 
         func_list = glob.glob(os.path.join(subj_raw, 't*/*tfMRI*'))