Hi Lars - Just like you have to do before you run any freesurfer programs, you'll have to run a script that comes with freesurfer and sets up all the necessary environment variables. See: http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration

Hope this helps, a.y

PS: Please send emails about tracula usage to the freesurfer list (cc'd here) and not to me personally. This makes sure the answers get archived so that people can search for answers to common questions. Thanks!

On Thu, 10 Oct 2013, Lars M. Rimol wrote:

Dear Dr. Yendiki,

I am trying to learn how to do Tracula analyses and was wondering about one thing:

According to the tutorial, all I need to do is set up the various configuration files. However, when I try to run the example data set, with

trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial

it complains: "FSLDIR: Undefined variable."

FSL dir doesn't seem to be defined in any of the configuration files provided in the tutorial. Is it necessary to install FSL in order to use Tracula? And where do I set the FSLDIR variable?

Thank you!

yours,

Dr. Lars M. Rimol