Hi Glad can you send us the full command line you are using and screen output?
thanks Bruce On Tue, 11 Jul 2017, Paul Glad Mihai wrote: > Dear List, > > I've been quite frustrated with the BBRegister results when trying to > register a partial field of view EPI mean functional image to a T1 scan. > I've tried different init arguments (fsl, spm, header) and none really > work. I've found that the initial registration is causing the problem, > since the T1 and mean EPi are in reasonable alignment, but not perfect. > As soon as it passes the initial alignment it's totally off and > obviously fails in the BBR step. I have no full head EPI, unfortunately. > I have a full head scout which seems to be a T1 image with really poor > contrast. If I try to register this to the T1 through BBRegister it > works. But if I use it as an intermediate file it still fails. What can > I do? How does the intermediate file come into play? Will it get > registered to the T1 initially and then the resulting matrix is used > further? I also tried to feed the resulting registration matrix as > init-reg but that didn't work either. > > Is there a way to skip the initial registration? > > Can I mask the T1 image with the FoV of the functional scan if they are > initially in reasonable alignment? Would that work? Would that mean that > I have to re-run ReconAll with the masked T1? > > Would love to hear back from someone. > > Regards, > Glad > _______________________________________________ Freesurfer mailing list [email protected] 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.
