Issue creating symbolic links when running fastsurfer-gpu.sif

[f4bry]

Question/Support Request

Dear experts, running fastsurfer-gpu.sif I am getting the following error:

================== Creating orig and rawavg from input =========================

python-s /fastsurfer/recon_surf/../FastSurferCNN/data_loader/conform.py -i /output/sub-01/mri/orig.mgz --check_only --vox_size min --verbose
Reading input: /output/sub-01/mri/orig.mgz ...
A min-conformed image must satisfy the following criteria:
 - Dimensions 256x256x256:        True
 - Voxel Size 1.0x1.0x1.0:        True
 - Orientation LIA:               True
 - Dtype uint8:                   True
Input /output/sub-01/mri/orig.mgz is already conformed! Exiting.

@#@FSTIME  2024:03:06:00:05:46 python-s N 7 e 0.25 S 0.02 U 0.22 P 98% M 41140 F 0 R 6798 W 0 c 5 w 46 I 282 O 0 L 1.56 1.83 1.40
@#@FSLOADPOST 2024:03:06:00:05:47 python-s N 7 1.56 1.83 1.40
python-s /fastsurfer/recon_surf/../FastSurferCNN/data_loader/conform.py -i /output/sub-01/mri/aparc.DKTatlas+aseg.deep.mgz --check_only --vox_size 1.0 --dtype any --verbose
Reading input: /output/sub-01/mri/aparc.DKTatlas+aseg.deep.mgz ...
A conformed image must satisfy the following criteria:
 - Dimensions 256x256x256:        True
 - Voxel Size 1.0x1.0x1.0:        True
 - Orientation LIA:               True
Input /output/sub-01/mri/aparc.DKTatlas+aseg.deep.mgz is already conformed! Exiting.

@#@FSTIME  2024:03:06:00:05:47 python-s N 9 e 0.21 S 0.02 U 0.18 P 98% M 41148 F 0 R 6800 W 0 c 5 w 45 I 210 O 0 L 1.56 1.83 1.40
@#@FSLOADPOST 2024:03:06:00:05:47 python-s N 9 1.56 1.83 1.40
The voxel size 1.0 is not less than 0.999, so we are proceeding with standard options.
mri_convert /output/sub-01/mri/orig.mgz /output/sub-01/mri/orig.mgz
mri_convert /output/sub-01/mri/orig.mgz /output/sub-01/mri/orig.mgz
reading from /output/sub-01/mri/orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /output/sub-01/mri/orig.mgz...
@#@FSTIME  2024:03:06:00:05:47 mri_convert N 2 e 0.81 S 0.02 U 0.78 P 99% M 25840 F 16 R 5436 W 0 c 5 w 30 I 3506 O 13240 L 1.56 1.83 1.40
@#@FSLOADPOST 2024:03:06:00:05:48 mri_convert N 2 1.52 1.82 1.40
mri_convert /output/sub-01/mri/aparc.DKTatlas+aseg.deep.mgz /output/sub-01/mri/aparc.DKTatlas+aseg.orig.mgz
mri_convert /output/sub-01/mri/aparc.DKTatlas+aseg.deep.mgz /output/sub-01/mri/aparc.DKTatlas+aseg.orig.mgz
reading from /output/sub-01/mri/aparc.DKTatlas+aseg.deep.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /output/sub-01/mri/aparc.DKTatlas+aseg.orig.mgz...
@#@FSTIME  2024:03:06:00:05:48 mri_convert N 2 e 0.82 S 0.01 U 0.80 P 99% M 42244 F 0 R 9535 W 0 c 9 w 1 I 0 O 648 L 1.52 1.82 1.40
@#@FSLOADPOST 2024:03:06:00:05:48 mri_convert N 2 1.52 1.82 1.40
ln -sf orig.mgz rawavg.mgz
ln: failed to create symbolic link 'rawavg.mgz': Operation not permitted
Command exited with non-zero status 1
@#@FSTIME  2024:03:06:00:05:49 ln N 3 e 0.00 S 0.00 U 0.00 P 75% M 1716 F 1 R 91 W 0 c 1 w 12 I 120 O 0 L 1.52 1.82 1.40
@#@FSLOADPOST 2024:03:06:00:05:49 ln N 3 1.52 1.82 1.40

I change the permissions to the output folder (777) and I tried to run it as a root (--allow_root), but I still got this message ln: failed to create symbolic link 'rawavg.mgz': Operation not permitted. Same thing with different input volumes.

Any suggestion to debug it?
Thank you,
f4b

Environment

• FastSurfer Version: lates
• FreeSurfer Version: 6.0
• OS: Ubuntu 22.04.4 LTS
• CPU: Intel(R) Core(TM) i9-10980XE CPU @ 3.00GHz
• GPU: GeForce RTX 3080 Lite Hash Rate

Execution

Run Command:

singularity exec --nv \
                 --no-home \
                 -B /imaging/rawT1/sub-01/T1:/data \
                 -B //imaging/fastsurfer_output:/output \
                 -B /usr/local/freesurfer:/fs \
                  /mnt/wsdata/softwares/fastsurfer-gpu.sif \
                  /fastsurfer/run_fastsurfer.sh \
                 --fs_license /fs/license.txt \
                 --t1 /data/T1.nii.gz \
                 --sid sub-01 --sd /output

[dkuegler]

This operation creates a symbolic link in the mri subfolder. Most likely you are using a file system that does not support soft links?

Can you maybe check whether you can create the symbolic link from the terminal? Because this command should really do the same thing inside singularity as on the terminal...
Talking about ln -sf orig.mgz rawavg.mgz here.

[f4bry]

This operation creates a symbolic link in the mri subfolder. Most likely you are using a file system that does not support soft links?

Can you maybe check whether you can create the symbolic link from the terminal? Because this command should really do the same thing inside singularity as on the terminal... Talking about ln -sf orig.mgz rawavg.mgz here.

You are right, the file system in that drive doesn't allow soft links. Thank you!

[m-reuter]

Maybe we can check if soft links work in our code and if not create copies ? (in a future release)

[dkuegler]

Can you tell us, which file system you used that was affected?

[f4bry]

Can you tell us, which file system you used that was affected?

Sure. The drive is mounted with:

UUID=6387-4CBD /mnt/wsdata exfat defaults,uid=1000,gid=1006,umask=0002 0

[dkuegler]

Hopefully, #473 fixes similar issues in the future. I am going to close this issue for now, feel free to reopen if there are additional comments.