Hi Sarah - The best way to troubleshoot the configuration file is to source it, make sure that there are no errors, and then echo each variable to make sure it contains what you intended.

For example once you run "source Tracula_config" you'll get an error, and you'll find that you have to correct this line: set dcmlist = (data.nii.gz / to: set dcmlist = (data.nii.gz \

Then check the tutorial to see which variables should contain only one item and which variables can contain a list of items. Hint: check dcmroot, bvecfile, bvalfile.

Hope this helps, a.y

On Tue, 11 Mar 2014, Sarah Banducci wrote:

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/scrip ts/dmrirc.local -log/Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/scrip ts/trac-all.log -cmd/Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/scrip ts/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