freesurfer crash because cannot create symbolic links in CIFS

[danielkimmel]

Hello,

I'm running fmriprep-docker.py under CIFS. The pipeline completes when skipping freesurfer, but when I include freesurfer, I get the error listed below. The issue appears to be that FS is attempting to create a symbolic link, which CIFS does not support. There are some workarounds proposed when using stand-alone freesurfer:
http://www.biac.duke.edu/forums/topic.asp?TOPIC_ID=1532

I tried to implement the above recommendation (which involves copying various directories from $FREESURFER_HOME to $SUBJECTS_DIR) by copying the recommended directories to the freesurfer output directory (i.e., [fmriprep_target]/freesurfer), but the same error occurred.

Unfortunately, I'm relatively stuck using CIFS...

I imagine I'm not the only one who may experience this problem (i.e., running fmriprep with freesurfer under CIFS). Do you have a recommended solution?

Thanks very much,
Daniel

#@# Curv .H and .K rh Mon Jul 23 10:10:23 UTC 2018
/out/freesurfer/sub-18050101/surf

 mris_curvature -w rh.white.preaparc 

total integrated curvature = 4.495*4pi (56.487) --> -3 handles
ICI = 139.9, FI = 1628.7, variation=25027.919
writing Gaussian curvature to ./rh.white.preaparc.K...done.
writing mean curvature to ./rh.white.preaparc.H...done.
rm -f rh.white.H
ln -s rh.white.preaparc.H rh.white.H
Linux 22ae7b51e7c1 3.10.0-862.2.3.el7.x86_64 #1 SMP Wed May 9 18:05:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-18050101 exited with ERRORS at Mon Jul 23 10:10:26 UTC 2018

For more details, see the log file /out/freesurfer/sub-18050101/scripts/recon-all-rh.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:
ln: failed to create symbolic link 'rh.white.H': Operation not supported
Return code: 1

[oesteban]

I'm upstreaming this issue to Nipype - nipy/nipype#2663.

I may be wrong, but there is not much we can do in FMRIPREP proper about this problem. Please reopen if I'm missing something out.

[effigies]

I actually think it'd be easier here. Setting custom subject directories is already supported by nipype, so we would just need a flag that indicates we should make a temporary directory and add a data sink. It would be mutually exclusive with reusing FreeSurfer subjects.