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