and the registration? On 05/28/2014 08:46 AM, Weber, Wade (weberw) wrote: > Hi Doug, > > It ran completely through to the end, but when I open up and inspect the data > there is nothing there except for a few white/grey voxels. > > Wade > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Tuesday, May 27, 2014 6:45 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] dt_recon error > > > Did it actually fail? If not, does the registration look ok? That msg should > just be a warning doug > > On 05/27/2014 02:06 PM, Weber, Wade (weberw) wrote: >> Hi all, >> >> I have been trying to work with DTI data in FreeSurfer for the first >> time. We acquire our data on a 4T Varian and reconstruct into AFNI >> format (BRIK/HEAD files). I set up the bval and bvec files >> successfully and ran the "dt_recon" script. It seemed to run fine >> until I got an fslregister error saying "G-W contrast is negative but >> expecting positive." It says to try running with the "--T1" flag. The >> problem is that I'm not sure which line I put the flag into. I tried >> re-running the dt_recon line again with the --T1 flag, but it did not >> work. >> >> I know I may not be giving enough information, so if anyone needs more >> information, just let me know what you want to know. >> >> Thanks in advance! >> >> Wade Weber >> >> University of Cincinnati >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
