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Hello FreeSurfer Developers,

I am attempting to run the Freesurfer recon-all longitudinal pipeline via an Apptainer image built from the official Freesurfer Docker image.

The relevant portion of my slurm bash script is:

echo "--- Stage 3: Longitudinal processing ---"
for TP in "${TIMEPOINTS[@]}"; do
    CROSS_ID="${SUBJECT_ID}_${TP}"
    LONG_ID="${CROSS_ID}.long.${TEMPLATE_ID}"
    echo "  Processing longitudinal stream for '${TP}' as '${LONG_ID}' ..."
    apptainer exec \
        -B "${SUBJECTS_DIR}:/subjects" \
        "${FREESURFER_IMAGE}" /bin/bash -c "cd /subjects && \
        recon-all \
            -long ${CROSS_ID} ${SUBJECT_ID} \
            -all \
            -threads ${THREADS} \
            -sd /subjects" \
        || { echo "Error: longitudinal processing failed for time point '${TP}'."; exit 1; }
done


  ERROR:  
mri_mask -transfer 255 -keep_mask_deletion_edits -xform /subjects/sub-SAY118/mri/transforms/sub-SAY118_ses-B_to_sub-SAY118.lta wm.mgz /subjects/sub-SAY118_ses-B/mri/wm.mgz wm.mgz

transfer mask voxels=255 to dst vol
Transferring mask edits ('1' voxels) to dst vol
transform file name is /subjects/sub-SAY118/mri/transforms/sub-SAY118_ses-B_to_sub-SAY118.lta
DoAbs = 0
Applying transform to the mask volume
maskval=255, outval=255
Writing masked volume to wm.mgz...done.
cp -p /subjects/sub-SAY118/mri/filled.mgz /subjects/sub-SAY118_ses-B.long.sub-SAY118/mri/filled.mgz
cp: preserving permissions for '/subjects/sub-SAY118_ses-B.long.sub-SAY118/mri/filled.mgz': Invalid argument
Linux ccc0425.campuscluster.illinois.edu 5.14.0-570.76.1.el9_6.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Dec 17 04:36:29 EST 2025 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-SAY118_ses-B.long.sub-SAY118 exited with ERRORS at Thu Mar 26 18:31:16 CDT 2026

For more details, see the log file /subjects/sub-SAY118_ses-B.long.sub-SAY118/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 


1) FreeSurfer version: 8.1.0 on Apptainer (1.4.5-2.el9) built from Docker image (https://hub.docker.com/layers/freesurfer/freesurfer/8.1.0/images/sha256-9a8b19158567e267b23b5d661883f2d075a6a2a68243b6ed3b3a05e53873e897)
2) Platform: RHEL 9.6 x86_64-linux
3) uname -a: Linux cc-login5.campuscluster.illinois.edu 5.14.0-570.76.1.el9_6.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Dec 17 04:36:29 EST 2025 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached