Frederick,

Freesurfer uses FSL's motion correction tool 'flirt'. FSL v3.2 is distributed with Freesurfer, which is a bit out of date.

You can download and use the newest FSL if you like. Just set the environment var FSL_DIR before calling Freesurfer setup, like this:

setenv FSL_DIR /whereever/you/installed/fsl source $FREESURFER_HOME/SetUpFreeSurfer.csh

You could even delete the $FREESURFER_HOME/fsl directory if you want to save space.

Nick

On Tue, 2007-04-03 at 10:38 -0400, Frederick Powell wrote:

I would like to run FSL and Freesurfer on my Linux compter. I have noticed that within Freesurfer I have a FSL directory. I have also visited the FSL website and noticed an entire downloadable version of FSL. I would like to be able to use my structural MPRAGE images that I have analyzed in Freesurfer and combine them with DTI images for ROI tractography and FA calculations. Do I need to download the version of FSL from the website? Secondly how should it be sourced so that FSL and Freesurfer are able to run together ( will I encounter any binary issues)? If you could respond with details. I am a novice to installing programs using a Linix machine. I am specifically talking about how to source the program and get it up and running.

Thanks