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