Hello- I'm having a consistent problem running multiple subjects through tracula. I am able to run single subjects through all steps but whenever I try to run it on multiple subjects I get the same error about a syntax error and one of the items it wants to copy being a directory so its not being copied. I can't figure out what in my configuration file is incorrect. I'm attaching the configuration file to this email.
I'm only trying to get the first few steps done at the moment so command I run is: trac-all -corr -qa -intra -inter -masks -c Tracula_config
And it outputs this:
*set: Syntax Error.* INFO: SUBJECTS_DIR is /Volumes/KramerLab/Projects/HealthAging/FAST/Freesurfer/v5.3 INFO: Diffusion root is /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014 Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/scripts/dmrirc.local -log /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/scripts/trac-all.log -cmd /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Mar 11 10:08:12 CDT 2014 mri_convert /Volumes/KramerLab/Users/banducc2/forTracula/DTI/F109_1/data.nii.gz /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/dmri/dwi_orig.nii.gz mri_convert /Volumes/KramerLab/Users/banducc2/forTracula/DTI/F109_1/data.nii.gz /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Volumes/KramerLab/Users/banducc2/forTracula/DTI/F109_1/data.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998367, -0.00222992, -0.0570763) j_ras = (0, 0.999238, -0.0390395) k_ras = (-0.0571199, 0.0389758, 0.997606) writing to /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/dmri/dwi_orig.nii.gz... cp /Volumes/KramerLab/Users/banducc2/forTracula/DTI/F109_1 /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/dmri/dwi_orig.mghdti.bvecs *cp: /Volumes/KramerLab/Users/banducc2/forTracula/DTI/F109_1 is a directory (not copied).* Darwin sarahsmacpro.vp.illinois.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Tue Mar 11 10:08:38 CDT 2014
Thanks, Sarah Banducci University of Illinois, Urbana