Hey Eugenio, Unfortunately, this will require a recompile of the tool. None of the Matlab executables are compiled during the build, as this requires a full Matlab license, which we do not want to be a prerequisite to run FS.
Happy to help get the new version rebuild, I’ll just need to confirm with Rob exactly what needs to be supported. Best, Jackson From: Iglesias Gonzalez, Juan E. <[email protected]> Date: Wednesday, May 14, 2025 at 2:25 AM To: Freesurfer support list <[email protected]> Cc: Nolan, Jackson <[email protected]> Subject: Re: Hippocampal Subvolumes Error -- segmentHA_T1_long 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: [email protected] <[email protected]> on behalf of Toms, Robert <[email protected]> Date: Tuesday, May 13, 2025 at 10:05 AM To: [email protected] <[email protected]> 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
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