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. JIGLESIASGONZALEZ@mgh.harvard.edu Date: Wednesday, May 14, 2025 at 2:25 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Nolan, Jackson JNOLAN5@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://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

Yeah the plan is to fix, recompile, and distribute the fix

-- Juan Eugenio Iglesias http://www.jeiglesias.com

From: Toms, Robert Robert.Toms@UTDallas.edu Date: Wednesday, May 14, 2025 at 12:33 PM To: Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu, Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: Hippocampal Subvolumes Error -- segmentHA_T1_long

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Nolan, Jackson JNOLAN5@mgh.harvard.edu Sent: Wednesday, May 14, 2025 12:13 PM To: Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@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. JIGLESIASGONZALEZ@mgh.harvard.edu Date: Wednesday, May 14, 2025 at 2:25 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Nolan, Jackson JNOLAN5@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://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