Merge pull request #45 from shots47s/master

Creating symbolic links for the template directories is safer than checking if directories exist while running multiple instances in same directory.

run.py

@@ -10,6 +10,7 @@
 from warnings import warn
 import pandas as pd
 import re
+import errno
 
 def run(command, env={}, ignore_errors=False):
     merged_env = os.environ
@@ -177,15 +178,16 @@ def run(command, env={}, ignore_errors=False):
 
 # running participant level
 if args.analysis_level == "participant":
-    if not os.path.exists(os.path.join(output_dir, "fsaverage")):
-        run("cp -rf " + os.path.join(os.environ["SUBJECTS_DIR"], "fsaverage") + " " + os.path.join(output_dir, "fsaverage"),
-            ignore_errors=True)
-    if not os.path.exists(os.path.join(output_dir, "lh.EC_average")):
-        run("cp -rf " + os.path.join(os.environ["SUBJECTS_DIR"], "lh.EC_average") + " " + os.path.join(output_dir, "lh.EC_average"),
-            ignore_errors=True)
-    if not os.path.exists(os.path.join(output_dir, "rh.EC_average")):
-        run("cp -rf " + os.path.join(os.environ["SUBJECTS_DIR"], "rh.EC_average") + " " + os.path.join(output_dir, "rh.EC_average"),
-            ignore_errors=True)
+    fst_links_to_make = ["fsaverage", "lh.EC_average","rh.EC_average"]
+    for fst in fst_links_to_make:
+        try:
+            os.symlink(os.path.join(os.environ["SUBJECTS_DIR"], fst),os.path.join(output_dir, fst))
+        except OSError as e:
+            if e.errno == errno.EEXIST:
+                print("Symbolic link to {0} already exists".format(fst))
+            else:
+                print("ERROR: Symbolic link to {0} unable to be created because: {1}".format(fst,str(e)))
+                raise e
 
     for subject_label in subjects_to_analyze:
         if glob(os.path.join(args.bids_dir, "sub-%s" % subject_label, "ses-*")):