TRACULA error: lowb_brain_mask.bbr.nii.gz - Freesurfer

13 Nov 2023


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Hi FreeSurfers,
I am attempting to run tracula on longitudinal DTI data however during trac-all -prep the process fails because it does not generate lowb_brain_mask.bbr.nii.gz from mri_concat.
#-------------------------------------
/Applications/freesurfer/7.3.2/bin/trac-preproc
#-------------------------------------
#@# Intra-subject registration (base template) Mon Nov 13 14:13:56 PST 2023
mri_concat --i /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/aparc+aseg_mask.nii.gz --min --o /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001/dlabel/anatorig/aparc+aseg_mask.nii.gz
ninputs = 1
Checking inputs
nframestot = 1
Allocing output
Done allocing
nframes = 1
Computing min across all frames
Writing to /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001/dlabel/anatorig/aparc+aseg_mask.nii.gz
mri_concat --i /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz --min --o /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz
ninputs = 1
Checking inputs
error: niiRead(): error opening file /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz
ERROR: reading /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz
Darwin PSYC-C02DP05D0833.stanford.edu 22.6.0 Darwin Kernel Version 22.6.0: Wed Oct  4 21:25:26 PDT 2023; root:xnu-8796.141.3.701.17~4/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Mon Nov 13 14:13:58 PST 2023
I am using FreeSurfer 7.3.2 on an iMac Pro running Ventura 13.6.1.
Any suggestions for how to clear this error would be greatly appreciated!
Thank you,
Lauren Stephens
Lauren Stephens, MS
Assistant Clinical Research Coordinator
Department of Psychiatry and Behavioral Science
Stanford University School of Medicine
E: laurenss@stanford.edu
P: (650)-725-1716