External Email - Use Caution
It looks like you started recon-all by copying in mri/orig/001.mgz. I saw multiple runs of recon-all that were run on top of each other.
Can you try to restart clean by providing the input on the command line ‘recon-all -s <subjid> -I <input> -all’?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Justin Kasowski Sent: Wednesday, June 28, 2023 7:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all ends with error
External Email - Use Caution Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2023:06:28:16:19:10 mri_mask N 5 e 0.51 S 0.01 U 0.44 P 89% M 74240 F 0 R 2972 W 0 c 3 w 760 I 0 O 0 L 0.13 0.04 0.01 @#@FSLOADPOST 2023:06:28:16:19:11 mri_mask N 5 0.13 0.04 0.01 #-------------------------------------------- #@# Fill Wed Jun 28 16:19:11 PDT 2023 /mnt/c/Users/BigBrain/documents/Subjects/sub-049/mri
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /usr/local/freesurfer/7.2.0/SubCorticalMassLUT.txt -auto-man filled.auto.mgz filled.mgz ../tmp/filled.edits.txt wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... error: volume size must be greater than 0 in every dimension Command exited with non-zero status 1
The error implies aseg.presurf.mgz or talairach.lta have a 0 dimension, but neither do. mri_info for aseg.presurf is below, I've attached the log and talairach.lta files:
bigbrain@DESKTOP-EDQPTKK:/mnt/c/Users/BigBrain/Documents/Subjects/sub-049/mri$ mri_info aseg.presurf.mgz Volume information for aseg.presurf.mgz type: MGH dimensions: 256 x 256 x 256