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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
