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 FSL v3.2 is distributed with Freesurfer, which is a bit out of date.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 > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
