Hi Jared - Have you looked at $FREESURFER_HOME/bin/dmrirc.example? You can specify bvecfile, bvalfile, and nb0. Currently these are assumed to be the same for all subjects. The format is 3 columns for bvecs, single column for bvals. Otherwise you shouldn't have to do anything else to them (hopefully! :)
a.y
On Tue, 28 Jun 2011, Jared Saletin wrote:
Hi Freesurfer experts,
I was wondering if you all had some advice for getting trac-all up and running.
I'm trying to work up a trac-all configuration file for a group of subjects, previously processed in FSL.
We extracted the Siemens bvec and bval files for the FSL pipeline when importing the dicoms through dicom2nii.
I know FSL bval and bvec files are organized in a different matrix shape from what Trac-all wants.
Has anyone had sucess with transforming these files? Should/do I need to worry about whether to flip the orientation on bvec files as the images seem to get flipped in the early steps of Trac-all?
Also is it possible to feed the configuration file a list of bvec files (for each subject) similar to how we feed it the dicom directory for each subject, or should I create a configuration script for each subject pointing to their bvec file specifically.
Thanks in advance for help!
Cheers, Jared