Error:autorecon_surfs0 and autorecon_surfs1

Software Support
, ,
1

Summary of what happened:

I had problems trying to run fmriprep, I processed a total of 6 subjects, the data organization format of these 6 subjects passed BIDS verification, because it only contains T1w images, so my code limited anat only, and found out at runtime that my subjects had problems running FreeSurfer. I open the corresponding log file and the error message is as follows

Command used

$BIDS_DIR = “E:\alldata397”
$OUT_DIR = “E:\testoutput1”
$maxConcurrentJobs = 2

       docker run --rm `
        -v "${BIDS_DIR}:/data:ro" `
        -v "${OUT_DIR}:/out" `
        -v "E:\license.txt:/opt/freesurfer/license.txt:ro" `
        nipreps/fmriprep:latest /data /out participant `
        --participant-label $sub `
        --anat-only

I ran fmriprep on the Windows system through the Poweshell(WSL2) to run the docker command, the specific code is shown in the figure above, I omitted the parallel processing of the test code process, it seems that using fmriprep-docker can not be parallel, so I used the docker original command

Relevant log outputs :

/out/sourcedata/freesurfer/sub-001/surf

 mris_curvature -w -seed 1234 lh.white.preaparc 

setting seed for random number generator to 1234
total integrated curvature = 14.718*4pi (184.952) --> -14 handles
ICI = 146.4, FI = 1464.7, variation=23095.380
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
Linux c8a33c5e5e81 5.15.90.1-microsoft-standard-WSL2 #1 SMP Fri Jan 27 02:56:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-001 exited with ERRORS at Sat Oct 14 19:55:18 UTC 2023

For more details, see the log file /out/sourcedata/freesurfer/sub-001/scripts/recon-all-lh.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    Stderr:
ln: failed to create symbolic link 'lh.white.H': Operation not permitted
    Traceback:
RuntimeError: subprocess exited with code 1.

Relevant log outputs2:

#@# Curv .H and .K lh Sat Oct 14 19:55:11 UTC 2023
/out/sourcedata/freesurfer/sub-001/surf

 mris_curvature -w -seed 1234 lh.white.preaparc 

setting seed for random number generator to 1234
total integrated curvature = 14.718*4pi (184.952) --> -14 handles
ICI = 146.4, FI = 1464.7, variation=23095.380
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
Linux c8a33c5e5e81 5.15.90.1-microsoft-standard-WSL2 #1 SMP Fri Jan 27 02:56:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-001 exited with ERRORS at Sat Oct 14 19:55:18 UTC 2023

For more details, see the log file /out/sourcedata/freesurfer/sub-001/scripts/recon-all-lh.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    Stderr:
 ln: failed to create symbolic link 'lh.white.H': Operation not permitted
    Traceback:
RuntimeError: subprocess exited with code 1.
2

Hi @Holland and welcome to neurostars!

If you want to only process anatomical data, you can also use smriprep (which is what fmriprep uses internally).

In regards to your errors, this looks like it could be a drive permission issue. I see you don’t have a work directory specified. Please add a working directory with the -w flag and try again.

Best,
Steven

1 Like
3

Hi steven thank you very much for the suggestion, I found after debugging that it is the disk I am running on is not NTFS system; At the same time, I successfully ran it after modifying the code to mount the work volume before runing docker, thanks again.