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