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This post can be disregarded. I had removed the output and working directories from a previous run with the brainstem unlabeled. But I didn't realize there was a separate working directory for freesurfer. Once I removed that second working directory and re-ran with the brainstem labeled, it ran fine.
________________________________ From: Dierker, Donna donna@wustl.edu Sent: Monday, June 29, 2026 1:39 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] infant_recon_all: could not open aseg.16.mgz
External Email - Use Caution Hi infant freesurfer gurus,
I need help with infant_recon_all. I have existing third-party segmentations for six month old babies' T1w's. I have relabeled them with label indices that bibsnet would output. Then I tried running nibabies like so:
docker run --rm -i -u 1697:10 -v /usr/local/pkg/freesurfer7.3/.license:/opt/freesurfer/license.txt:ro -v /my_file_system/rawdata:/data:ro -v /my_file_system/derivatives/nibabies:/out -v /my_file_system/work/nibabies/sub-01:/work -v /my_file_system/derivatives/bibsnet:/deriv1 nipreps/nibabies:25.2.1 /data /out participant --participant-label 01 -s 6mo -w /work --verbose --derivatives /deriv1 --anat-only --fd-spike-threshold 0.2 --age-months 6 --surface-recon-method infantfs --cifti-output 91k --debug registration --project-goodvoxels --multi-step-reg --norm-csf --omp-nthreads 8 --mem 300000 --nprocs 8 --stop-on-first-crash --output-spaces fsLR MNIInfant:cohort-3 MNI152NLin6Asym:res-2 anat
It runs 30-60 minutes and seems to make some surfaces before bailing like so:
writing spherical brain to /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/surf/lh.qsphere.nofix spherical transformation took 0.0770 hours FSRUNTIME@ mris_sphere 0.0770 hours 8 threads #VMPC# mris_sphere VmPeak 929720 mris_sphere done /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/surf /work/nibabies_26_0_wf/single_subject_sub-01_ses-6mo_wf/infant_single_t1w_fit_wf/infantfs_surface_recon_wf/reconall cp /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/surf/lh.qsphere.nofix lh.qsphere.nofix cp /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/surf/rh.qsphere.nofix rh.qsphere.nofix /work/nibabies_26_0_wf/single_subject_sub-01_ses-6mo_wf/infant_single_t1w_fit_wf/infantfs_surface_recon_wf/reconall mri_or /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.right.41.mgz /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.left.2.mgz /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/wo rk/aseg.16.mgz /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/wm.nonscaled.mgz processing 3 input files processing input volume 1 of 3: /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.right.41.mgz processing input volume 2 of 3: /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.left.2.mgz processing input volume 3 of 3: /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.16.mgz error: mghRead(/out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.16.mgz, -1): could not open file Segmentation fault (core dumped) I suspect aseg.16.mgz is the Brain-Stem, and these third-party segmentations did not separate the brainstem into pons, medulla, and midbrain, so I left the brainstem unlabeled. But after running into this issue, I tried relabeling the brainstem to label index 16 and ran nibabies again -- same error.
I have been looking at these web pages for possible work-arounds, but I could use some help, if you have any ideas:
https://secure-web.cisco.com/1_99iL8k-GK1MhALtq2irh-LWmKZk6I_fFWoE2dliho2ZwZ...
https://secure-web.cisco.com/1uoBOawnMrnPRx7SqEwRJIdUI2UbRdZ7aFYo0eYxupdgOp4...
Sorry for the long message and odd question, but as you know this timepoint is very challenging, and the segmentations are otherwise promising.
Thank you for any ideas you have for working around this issue,
Donna
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