On 08/13/2018 03:02 PM, Ben M wrote:

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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?

Yes

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?

Yes. You may need info here to decode it: https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems

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?

It reslices the mov into the anatomical space. What do you mean when you "load" them?

Best, Ben