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
