I was trying to segment thalamic nuclei using segmentThalamicNuclei.sh after a preprocessing using fMRIPrep 23.1.4 with fs recon-all. But it turned out with an error regarding mri_robust_register.
Log shown below.
------------------------------
PROCESSID 41966
PROCESSOR x86_64
OS Darwin
ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1
Darwin liu-imac 23.0.0 Darwin Kernel Version 23.0.0: Fri Sep 15 14:42:42 PDT 2023; root:xnu-10002.1.13~1/RELEASE_X86_64 x86_64
------------------------------
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
setenv SUBJECTS_DIR /Users/xingyuliu/dataset/neuro/MPG/ds001168_custom/derivatives/sourcedata/freesurfer
cd /Users/xingyuliu/dataset/neuro/MPG/ds001168_custom/derivatives/sourcedata/freesurfer
/Applications/freesurfer/7.4.1/bin/segmentThalamicNuclei.sh sub-01 /Users/xingyuliu/dataset/neuro/MPG/ds001168_custom/derivatives/sourcedata/freesurfer
#--------------------------------------------
#@# Thalamic Nuclei processing Wed Oct 11 13:29:13 EDT 2023
------------------------------------------
Setting up environment variables
---
DYLD_LIBRARY_PATH is .:/Applications/freesurfer/7.4.1/MCRv97//runtime/maci64:/Applications/freesurfer/7.4.1/MCRv97//bin/maci64:/Applications/freesurfer/7.4.1/MCRv97//sys/os/maci64:/Applications/freesurfer/7.4.1/lib/gcc/lib:
Registering imageDump.mgz to mask from ASEG
/Applications/freesurfer/7.4.1/bin//fs_run_from_mcr /Applications/freesurfer/7.4.1/bin///mri_convert /Users/xingyuliu/dataset/neuro/MPG/ds001168_custom/derivatives/sourcedata/freesurfer/sub-01/tmp/THnuclei_v13_useTwoComponents_1_T1//THDEbinaryMask.mgz aux.mgz -odt float -vs 1 1 1 -rt nearest >/dev/null: Signal 127
mv: aux.mgz: No such file or directory
/Applications/freesurfer/7.4.1/bin//fs_run_from_mcr /Applications/freesurfer/7.4.1/bin///mri_robust_register --mov imageDump.mgz --dst /Users/xingyuliu/dataset/neuro/MPG/ds001168_custom/derivatives/sourcedata/freesurfer/sub-01/tmp/THnuclei_v13_useTwoComponents_1_T1//THDEbinaryMask_autoCropped.mgz -lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat 50 >/dev/null: Signal 127
Error using SegmentThalamicNuclei (line 249)
Problem with mri_robust_register
Darwin liu-imac 23.0.0 Darwin Kernel Version 23.0.0: Fri Sep 15 14:42:42 PDT 2023; root:xnu-10002.1.13~1/RELEASE_X86_64 x86_64
Thalamic nuclei exited with ERRORS at Wed Oct 11 13:29:23 EDT 2023
------------------------------