Thanks for catching this, Robert. It’s a small bug that does not affect the results on the cases that didn’t crash. Jackson: I just submitted a PR. Do we need to recompile, or does this happen automatically? Cheers, /E
-- Juan Eugenio Iglesias http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Toms, Robert Robert.Toms@utdallas.edu Date: Tuesday, May 13, 2025 at 10:05 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal Subvolumes Error -- segmentHA_T1_long
External Email - Use Caution Dear FreeSurfer Community,
I'm longitudinally processing a significant amount of secondary scan data, to get hippocampal subvolumes for a study I'm working on.
Of the hundreds of scans I've processed so far, 18 have failed on line 2136 of SegmentSubfieldsT1Longitudinal.m--a subprocess of the segmentHA_T1_long command-- all with the same final lines:
####### Fitting mesh to image data mask took, at this global iteration and time point, 20.7436 seconds Transforming points Transforming points Wrote image to file image_tp_1.mgz Computing shift introduced by kvlRead Constructing image-to-world transform from header information (asmr1.mgz) Constructing image-to-world transform from header information (/mnt/md0/ScratchPad_/ABCD/Package_1234721/image03/derivative/freesurfer/freesurfer8.0.0/NDARINVGCPTFXEV_long/tmp/hippoSF_T1_long.v22_right/imageDump.mgz) Wrote image to file asmr2.mgz This file does not contain MRI parameters This file does not contain MRI parameters Unable to perform assignment because the left and right sides have a different number of elements.
Error in SegmentSubfieldsT1Longitudinal (line 2136)
MATLAB:matrix:singleSubscriptNumelMismatch Command exited with non-zero status 249 #######
I've searched the list and no similar errors have been reported. Does anyone know what may be the problem?
I'll attach a couple of the long-hippocampal-subfields.log's in case they can be of help.
FreeSurfer version: 8.0.0
System: Ubuntu 22.04.5 LTS, 512GB RAM
Thanks,
Robert