Tracula multiple fatal errors: Eddy and MRI binarize (thalamic segmentation) - Freesurfer

29 Nov 2022


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Dear Freesurfer developers,
I am attempting to perform tracula on a single participant but i am running into multiple fatal errors during trac-all prep.
The first fatal error is this one :
eddy_openmp --imain=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/dwi_orig_las.nii.gz --mask=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/lowb_topup_brain_mask.nii.gz --bvecs=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/dwi_orig_las.bvecs --bvals=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/dwi_orig_las.bvals --acqp=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/acqp.txt --index=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/index.txt --data_is_shelled --topup=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/topup --out=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/dwi
eddy_openmp: Command not found.
Darwin gbw-d-m0128.luna.kuleuven.be 21.6.0 Darwin Kernel Version 21.6.0: Thu Sep 29 20:12:57 PDT 2022; root:xnu-8020.240.7~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Tue Nov 29 13:03:33 CET 2022
I checked my FSL installation and there seems to not be anything wrong here, although the command eddy_openmp is missing from the bin folder. If i change the config file to set doeddy = 1 to work with eddy correct this error disappears. But I would prefer to use eddy here instead is there any way to fix this.
Further along i get another fatal error in the mri binarize part of the code which is related to a previous issue found in the mailing archives (https://secure-web.cisco.com/1eL0pyxEECqHmJx6yIaWdwio_XR8d47T_BB4CncFLEYAt8F...
Applying LTAtransformInterp (resample_type 0)
writing to /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dlabel/diff/White-Matter++.bbr.nii.gz...
mri_convert -at /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz
mri_convert -at /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz
reading from /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz...
error: niiRead(): error opening file /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
Darwin gbw-d-m0128.luna.kuleuven.be 21.6.0 Darwin Kernel Version 21.6.0: Thu Sep 29 20:12:57 PDT 2022; root:xnu-8020.240.7~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Tue Nov 29 13:24:02 CET 2022
I wanted to try the proposed solution but i have no permission to edit the files as specified in the thread. Would there be another fix for this.
In the attachment you can find the log and error files of both runs (1 is the eddy error, 2 the mri binarize) and the config file I used.
I am using freesurfer 7.2.0
platform MacOS Monterey 12.6.1
Kind regards,
Ward Deferm
CDP KU Leuven