That would be the same as specifying highres.nii.gz as the intermediate registration (--int to bbregister). Is this what you tried? doug
Cris Lanting wrote: > Dear all, > dear Doug, > > >> If you have a partial FOV, then it >> will probably fail. You can test this by running bbregister outside of the >> reg-feat2anat. You can look in the reg-feat2anat for a command line, but it >> should be something like: >> >> bbregister --s subject --mov example_func.nii.gz --bold --init-fsl --reg >> register.dat >> >> If this fails, you have a couple of options. If the functional and >> anatomical were acquired in the same session, then you can use --init-header >> instead of --init-fsl. If they are not but you have a full-brain of anything >> acquired during the same session as the functional, you can pass that as an >> intermediate volume to bbregister (--int). >> >> doug >> >> >> > > I've tried the --init-fsl option and the --init-header but they both > seem to fail. I noticed that there is a --init-reg option; > Is it not an idea to normalise the T1 (mprage) file called > highress.nii.gz (output registerT1.dat) and then in a second step > apply this to a previously registered file > (example_func2highres.nii.gz) using the --init-reg option? > > so, in short, would this approach work? > example_func.nii.gz -> example_func2highres.nii.gz (using flirt or > anything that works) > bbregister --s subject --mov highres.nii.gz --T1 --init-fsl --reg > registerT1.dat > bbregister --s subject --mov example_func2highres.nii.gz --bold > --init-reg registerT1.dat --reg registerfunc.dat > (ps, I haven't tried this yet...) > > Or are there other options.... > > Kind regards, > Cris > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
