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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:
------ 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 ------
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!
Best regards, Shams
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Shams Rashid, PhD
Instructor
Diagnostic, Molecular and Interventional Radiology
BioMedical Engineering & Imaging Institute (BMEII)
Icahn School of Medicine at Mount Sinai
1470 Madison Ave 1st floor, S1-116 New York, NY 10029