Dear FreeSurfer experts,

I am running into a problem with hippocampal subfield segmentation with T2 input on a newly installed FreeSurfer 7.4.1 and I really need help. On this subject, recon-all and segmentHA_T1.sh completed successfully, but when I ran segmentHA_T2.sh, I get the following error after a few minutes of processing:

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writing to T2corrected.mgz...

set final LTA type to 1

ERROR: tried to read 51314688, actually read 0

Index in position 1 exceeds array bounds.

Error in applyCropping (line 15)

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 935)

MATLAB:badsubscript

Command exited with non-zero status 249

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This instance of FreeSurfer 7.4.1 is running on Ubuntu 22.04.5 running on VirtualBox 7.1.8 on a Windows 11 Pro for Workstations.

I have tried segmentHA_T2 with two different T2 input images (axial and coronal), and get the same error both times. The images open OK on Matlab. Not sure if this is a problem with the Matlab runtime. I have installed (and re-installed) Matlab runtime R2019b using fs_install_mcr 2019b.  

I have attached the log files for segmentHA_T2 (and also recon-all, which worked OK).

I would greatly appreciate your help. Thank you very much!