Hi Jared - We haven't reproduced this error on our end. So if I understand it correctly, replacing "bedpostx_seychelles" with "bedpostx" in trac-all would solve the problem?
a.y On Wed, 29 Jun 2011, Jared Saletin wrote: > Hi Anatasia, > > Thank you for the response. > > I've reformatted the files and -prep ran fine. > > I'm receiving a similar error to some other users upon running -bedp > > Where bedpostx fails immediately > > I wanted to point out, and wonder if other folks have had any luck, that if I > try running bedpostx from FSL directly on the dmri folder, it starts > normally. I can then kill the bedpostx process, and relaunch trac-all -bedp > -c ... and things seem to be continuing... > > It still returns the "unexpected operator" errors that other users have > reported but it does not break to a command prompt anymore, and instead > beings return the "0 slices processed" ... iterating message. > > I'm curious, has anyone else had luck navigating around this bedpostx error? > Or would it be best to just run bedpostx separately in FSL and return to > trac-all after the bedpostx processing is complete? > > Thanks again! > Jared > > > On Jun 28, 2011, at 3:24 PM, Anastasia Yendiki wrote: > >> >> 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 >>> >> >> >> 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. >> > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
