From: Chunling Hu <huchunling99@gmail.com>
Date: Monday, March 16, 2026 at 4:04 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] segmentHA_T2.sh ERROR:cannot find transform file

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Freesurfer experts,

I encountered an issue while using segmentHA_T2.sh. I am using Freesurfer 7.3, and the command I executed was:

segmentHA_T1.sh SUB01 /home/huchunling/HP5T/SUB01_PID_20260313_132311_0037_43/sPID202603131323110037-0301-00001-000001-01.nii T2 1

Referring to the solution provided in a previous email, I ensured that the input file is a single frame rather than a multi‑frame image. Therefore, I need your help to identify where the problem lies.

Best regards,

Chunling Hu

The error message I received is as follows:

------------------------------
USER huchunling
HOST fox-c06
PROCESSID 2744600
PROCESSOR x86_64
OS Linux
Linux fox-c06 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:03:14 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
------------------------------

#--------------------------------------------
#@# Hippocampal Subfields processing (T1+T2) left 2026年 03月 16日星期一 13:34:54 CST
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/opt/fox_cloud/share/app/imaging/freesurfer7.3/MCRv97//runtime/glnxa64:/opt/fox_cloud/share/app/imaging/freesurfer7.3/MCRv97//bin/glnxa64:/opt/fox_cloud/share/app/imaging/freesurfer7.3/MCRv97//sys/os/glnxa64:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/thinlinc/lib64:/opt/thinlinc/lib:/opt/fox_cloud/share/app/imaging/freesurfer7.3/MCRv97//sys/opengl/lib/glnxa64:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/thinlinc/lib64:/opt/thinlinc/lib
Registering norm.mgz to additional volume
makeIsotropic WARNING: not different enough, won't reslice!
CostFunctions::centroid is NAN (empty image? n = 0 )
ERROR: cannot find transform file /home/huchunling/HP5T/OUTPUT/freesurfer_subjects/SUB01/mri/transforms/T1_to_T2.v22.lta
gzip: /home/huchunling/HP5T/OUTPUT/freesurfer_subjects/SUB01/tmp/hippoSF_T1T2_v22_T2_left//T2resampledLikeT1.mgz.gz: No such file or directory
ERROR: problem reading fname
SWITCH expression must be a scalar or a character vector.

Error in myMRIread>load_mgh (line 550)

Error in myMRIread>myMRIread_aux (line 92)

Error in myMRIread (line 63)

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 192)

MATLAB:badSwitchExpression
Command exited with non-zero status 249
@#@FSTIME 2026:03:16:13:34:54 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 22.89 S 3.89 U 7.50 P 49% M 1468976 F 0 R 705152 W 0 c 399 w 16444 I 0 O 288120 L 0.20 0.33 0.40
@#@FSLOADPOST 2026:03:16:13:35:17 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 0.65 0.43 0.44
Linux fox-c06 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:03:14 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

T2 hippocampal subfields exited with ERRORS at 2026年 03月 16日星期一 13:35:17 CST