Summary of what happened:
Hi all,
First time seeing this in FreeSurfer, but for a particular dataset I am working with, whenever I run recon-all, the process jumps straight to the end without actually processing anything (see log below). Nothing is immediately obvious about why these data may be treated differently.
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity exec -e -B $scratch,$license:/usr/local/freesurfer/.license $FS_IMG \
recon-all -i $t1 -hires -openmp 8
Version:
7.4.1, but also replicated in 7.3.2
Environment (Docker, Singularity, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
BIDS, but that’s not quite relevant here
Relevant log outputs (up to 20 lines):
INFO: hi-res volumes are conformed to the min voxel size
fs-check-version --s sub-00228190 --o /tmp/tmp.qgLaRk
Thu Dec 21 15:58:21 EST 2023
setenv SUBJECTS_DIR /om2/scratch/tmp/smeisler/mri_proc/sub-00228190/data/derivatives/freesurfer
cd /om2/scratch/tmp/smeisler/mri_proc/sub-00228190
/usr/local/freesurfer/bin/fs-check-version --s sub-00228190 --o /tmp/tmp.qgLaRk
-rwxrwxr-x 1 root root 18565 Jun 13 2023 /usr/local/freesurfer/bin/fs-check-version
freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460
$Id$
Linux node066 4.18.0-372.9.1.el8.x86_64 #1 SMP Tue May 10 14:48:47 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
pid 410135
Current FS Version freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460
Subject does not have a bstampfile, copying /usr/local/freesurfer/build-stamp.txt
Subject FS Version: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460
No constraints on version because REQ=UnSet and FsVerFile=NotThere
#@#% fs-check-version match = 1
fs-check-version Done
INFO: SUBJECTS_DIR is /om2/scratch/tmp/smeisler/mri_proc/sub-00228190/data/derivatives/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
Linux node066 4.18.0-372.9.1.el8.x86_64 #1 SMP Tue May 10 14:48:47 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
hostname: Command not found.
/om2/scratch/tmp/smeisler/mri_proc/sub-00228190/data/derivatives/freesurfer/sub-00228190
mri_convert /om2/scratch/tmp/smeisler/mri_proc/sub-00228190/fs_files/t1.nii.gz /om2/scratch/tmp/smeisler/mri_proc/sub-00228190/data/derivatives/freesurfer/sub-00228190/mri/orig/001.mgz
mri_convert /om2/scratch/tmp/smeisler/mri_proc/sub-00228190/fs_files/t1.nii.gz /om2/scratch/tmp/smeisler/mri_proc/sub-00228190/data/derivatives/freesurfer/sub-00228190/mri/orig/001.mgz
reading from /om2/scratch/tmp/smeisler/mri_proc/sub-00228190/fs_files/t1.nii.gz...
TR=8.05, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /om2/scratch/tmp/smeisler/mri_proc/sub-00228190/data/derivatives/freesurfer/sub-00228190/mri/orig/001.mgz...
/om2/scratch/tmp/smeisler/mri_proc/sub-00228190/data/derivatives/freesurfer/sub-00228190/mri/transforms /om2/scratch/tmp/smeisler/mri_proc/sub-00228190/data/derivatives/freesurfer/sub-00228190
/om2/scratch/tmp/smeisler/mri_proc/sub-00228190/data/derivatives/freesurfer/sub-00228190
Started at Thu Dec 21 15:58:21 EST 2023
Ended at Thu Dec 21 15:58:27 EST 2023
#@#%# recon-all-run-time-hours 0.002
hostname: Command not found.
recon-all -s sub-00228190 finished without error at Thu Dec 21 15:58:27 EST 2023
done
/net/vast-storage.ib.cluster/scratch/vast/gablab/smeisler/slurm_scratch/ravi/fs