Glad it worked. We'll have to make sure this agrees better with non-MGH installations in the next release.
On Fri, 1 Jul 2011, Jared Saletin wrote: > Hi Anastasia, > > That did the trick! Thanks so much! > > Cheers, > Jared > On Jun 30, 2011, at 12:28 PM, Anastasia Yendiki wrote: > >> >> 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
