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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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
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