Thanks for the suggestions. It is whole-brain epi data. Unfortunately, it was not acquired at the same time as the anatomical. Just for the heck of it I tried substituting --init-header for --init-fsl anyway, and got the same warning about negative G-W contrast.
-Kathleen On 8/19/10 2:39 PM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> wrote: It may have been the initialization that failed. Was the epi acquired at the same time as the anatomical? If so, you might be able to run it with --init-header. Also, is this whole brain or partial field of view? doug On 8/19/10 1:50 PM, Hansen, Kathleen (NIH/NIMH) [F] wrote: > Hello, > > The following command has produced a very wrong registration and a warning: > > bbregister --mov epi.template.strange_G-W_contrast.nii --bold --s D06 > --init-fsl --reg register.strange_G-W_contrast.dat > **** > WARNING: initial G-W contrast is negative, but expecting positive. > If the mov data has a T1 contrast, re-run with --T1 > **** > The file epi.template.strange_G-W_contrast.nii is BOLD fmri data, not > T1-weighted data. As far as I can tell, it is a typical BOLD fmri volume. > Any ideas? > > Thank you, > Kathleen > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ 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
