That warning in and of itself is not critical, but it does suggest that the initial registration failed. I assume the registration still looks bad? Does this happen on a bunch of data sets or just this one? There are a couple of more steps. First, you can run with --init-fsl and check the initial registration to verify that it is way off. To do this, run with --init-reg-out and check that registration with tkregister2. If that is bad, you can can try two things. First, if you have spm and matlab, you can use --init-spm. Second, you can tweak the initial registration by hand to get it "close" (ie, within 5mm and 5deg), then use --init-reg
doug
Hansen, Kathleen (NIH/NIMH) [F] wrote:
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" greve@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.