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Hi Freesurfer Experts,
I’m attempting to run Tracula and receiving the same error for both Tracula 6.0.
Note: I have also tried updating to Freesurfer 7.2 and running recon-all (which runs without issue) and then Tracula (which returns the same error as 6.0), so I don’t think version is my issue.
I have gotten Tracula 6.0 to run in the past on the machine I’m using now and I have not made any major modifications or updates since then.
Here is the set of commands I am passing to Tracula:
export FREESURFER_HOME=/Applications/freesurfer/6.0.0 source $FREESURFER_HOME/SetUpFreeSurfer.sh export TUTORIAL_DATA=/Users/kayti/Desktop/Projects/MIND/Freesurfer6 export SUBJECTS_DIR=$TUTORIAL_DATA/02_Data/01_recon_all cd $SUBJECTS_DIR trac-all -prep -c $TUTORIAL_DATA/01_Protocols/dmrirc.mind95
And here is the full text of my config file:
setenv SUBJECTS_DIR $SUBJECTS_DIR set subjlist = (A201) set dcmlist = (/Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all/A201/dwi_preprocessed.nii) set bveclist = (/Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all/A201/dwi_preprocessed.bvec) set bvallist = (/Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all/A201/dwi_preprocessed.bval) set dob0 = 0 set doeddy = 0 set intrareg = 2 set interreg = 2
And here is the full text of the error message:
domainname: Command not found.
: Command not found.
set: Variable name must begin with a letter.
does not exist.DIR /Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all
I have ensured that the directory above DOES exist.
I have seen other posts in these forums with this issue and I have tried all of the fixes I’ve found: removing trailing/extraneous spaces, correcting my paths, etc.
Does anyone have any ideas why this is happening?
Thank you!
Ryn Thorn (she/her) Lab Manager Medical University of South Carolina Department of Neurology Center for Biomedical Imaging 135 Cannon St. CS101 Charleston, SC 29425