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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
637 stars 295 forks source link

Copy fsaverage instead of symlinking #535

Closed chrisgorgo closed 7 years ago

chrisgorgo commented 7 years ago 
[chrisgor@sherlock-ln04 login_node /oak/stanford/groups/russpold/data/ds000030_R1.0.3_preprocessed_0.4.4/freesurfer]$ ls -al
total 1088
drwxr-s---+ 268 chrisgor russpold 20480 May  9 13:07 .
drwxr-s---+   5 chrisgor russpold  4096 May  5 13:27 ..
lrwxrwxrwx    1 chrisgor russpold    34 May  5 18:07 fsaverage -> /opt/freesurfer/subjects/fsaverage
drwxr-s---+   8 chrisgor russpold  4096 May 31  2011 fsaverage5
drwxrws---+  10 chrisgor russpold  4096 May  9 19:11 sub-10159
drwxrws---+  10 chrisgor russpold  4096 May  9 02:29 sub-10171
drwxrws---+  10 chrisgor russpold  4096 May  7 08:44 sub-10189
drwxrws---+  10 chrisgor russpold  4096 May  9 01:32 sub-10193

See https://github.com/BIDS-Apps/freesurfer/blob/master/run.py#L142

effigies commented 7 years ago

Oh, this is a consequence of this change, which doesn't copy fsaverage unless it's a target space. recon-all symlinks if it doesn't exist. I'll make sure fsaverage is always copied.