Hello,
I am new to FastSurfer and I am encountering problems running the pipeline. FastSurfer runs with no errors but some files appear to be missing or empty. I do not understand what is happening.
It is similar to this issue but I cannot find the solution: [Freesurfer] -qcache error
Example of empty files (not exhaustive):
- lh.white.H
- lh.white.K
- rh.white.H
- rh.white.K
- aparc.DKTatlas+aseg.mgz
- aparc+aseg.mgz
Command used:
docker run --gpus all -v "\adni2bids":/data \
-v "\adniFastSurfer":/output \
-v "Code":/fs_license \
--rm --user 0 deepmi/fastsurfer:latest \
--fs_license /fs_license/license.txt \
--t1 "/data/sub-002S0413/anat/sub-002S0413_run-11_T1w.nii.gz" \
--sid sub-002S0413 --sd /output \
--parallel --3T --allow_root
Relevant log outputs (up to 20 lines):
Below, you can find part of the output of recon-all.log where I see that some of the files get removed:
#@# Curv .H and .K lh Fri Jan 17 12:23:43 UTC 2025
/output/sub-002S0413/surf
mris_curvature -w -seed 1234 lh.white.preaparc
setting seed for random number generator to 1234
total integrated curvature = 19.314*4pi (242.712) --> -18 handles
ICI = 139.6, FI = 1331.8, variation=21129.465
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...mris_curvature done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
rm -f lh.white.K
ln -s lh.white.preaparc.K lh.white.K```
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