External Email - Use Caution Dear Eugenio and Jackson,
Thanks for your help! Can you confirm that the output is accurate? For context, we'll be processing >14,000 subjects' longitudinal data on our university's HPC cluster (so at this rate we may end up with 300+ with the same problem), and we have a full matlab license. If there is a way to recompile and have these not error out, please let me know! Thanks, Robert ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Nolan, Jackson <jnol...@mgh.harvard.edu> Sent: Wednesday, May 14, 2025 12:13 PM To: Iglesias Gonzalez, Juan E. <jiglesiasgonza...@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampal Subvolumes Error -- segmentHA_T1_long 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. <jiglesiasgonza...@mgh.harvard.edu> Date: Wednesday, May 14, 2025 at 2:25 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Cc: Nolan, Jackson <jnol...@mgh.harvard.edu> 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://secure-web.cisco.com/1fSpKx_yH2lsd2KxtoXU-3auXZ5elj-ZWEct3DmzXAJ4QFoyJnxCkudhSYj4nfZ_9WTpkVR36t25CfcAz8u7qw6HuQ1BMMpKI3eIORi4mXuiPvRs1loqnShPjgwi8rz2D_QuhC3OeUlmUZuOFhVbOcM0cRJ_KS1RjJFhulKuwtcvlS8P87_-YA8YrRv7D7aWp29N9zY2STmkD-74dxesIyRAh2Nap-a7HtVjjENtrHM9KQjqY6TqZXPdD5xbCV-tKWDDCv6BXGQeiPbNW-xjwMoHF819eNwsCD5Gqpv_IDTLPVRoYCPouZp7bgTrkBIer/http%3A%2F%2Fwww.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Toms, Robert <robert.t...@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
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