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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://secure-web.cisco.com/1GMjaUSYMADxEvuh_FFhFfAbSBBzgybK7V6lw15ats7NTGs_...

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://secure-web.cisco.com/1K2pk1aF9FT_qJ0WJsOIvvpzbsUGgA6Zkg-tP0nUWsOS3lY...) 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

Thank you!

Paul Camacho, Ph.D.

Data Scientist Biomedical Imaging Center Beckman Institute for Advanced Science & Technology University of Illinois at Urbana-Champaign

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