To allow multiple images to be processed in parallel, in the mindboggle() function in mindboggle123 set the working directory to be the current working directory.

Author: binarybottle

mindboggle/mindboggle123

@@ -219,7 +219,8 @@ def mindboggle(subjectid, fsdir, antsdir, antsseg, out, args, num_threads=1):
     DATA = os.path.join(fsdir, subjectid)
     ants = os.path.join(antsdir, subjectid, antsseg)
 
-    all_args = ' '.join([DATA, '--out', out, '--ants', ants, args])
+    all_args = ' '.join([DATA, '--out', out, '--ants', ants,
+                         '--workdir', os.getcwd(), args])
 
     if num_threads > 1:
         all_args += ' --plugin MultiProc --plugin_args "dict(n_procs={0})"'.\