This looks like an error inside of fmriprep to me. If you want our help, please recreate the error using just the FS tools
On 10/11/2023 2:08 PM, Xingyu Liu wrote:
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Dear freesurfer experts,
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
Thank you very much for your help! Best, Xingyu
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