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Hi Doug,
Thank you very much for your response, it helped me a lot. I checked the examples of mri_vol2vol and for functional-to-structural registration I think I should do
$ bbregister --t2 --lta /data/bbregister/reg.lta --mov /data/mean_func.nii.gz --s 001 $ mri_vol2vol --lta /data/bbregister/reg.lta --mov /data/mean_func.nii.gz --fstarg --o func2anat.nii.gz --no-resample
If I understood correctly, this will align mean_func with the structural image (orig.mgz I think). Is this correct?
I have two follow up questions if you don't mind:
1 - I'd like to get the file describing the affine registration of the functional to structural space for subsequent preprocessing. I think this should be the reg.lta (or reg.dat) file from the bbregister step, shouldn't it? This file contains the transformation matrix from functional to structural, is that correct? 2 - does mri_vol2vol actually physically move the -mov image? I think it does, which is the --o func2anat image above. However when I load the mean_func and func2anat images, they don't seem to be different in terms of orientation. I suppose it's because it's difficult to see the transformation with the naked eye?
Best, Ben