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