Hi Ben, please remember to post the list. Answers below

On 08/14/2018 02:22 PM, Ben M wrote:

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Hi Doug,

Thanks again for your help!

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

I mean when I view the images in fsleyes they don't seem to be very different, but I suppose that's because the reslicing is probably very subtle to see.

I just came across this post https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-February/036120...., in which you suggest running

tkregister2 --mov func.nii --fstarg --reg register.dat --fslregout fsl.mat --noedit

to get an FSL-compatible registration. I'd also like to use fnirt, and for that I need the affine transformation matrix from bbregister. I think if I simply do:

$ bbregister --t2 --lta /data/bbregister/reg.lta --mov /data/mean_func.nii.gz --s 001 $ tkregister2 --mov /data/mean_func.nii.gz --fstarg --reg /data/bbregister/reg.lta --fslregout /data/fsl.mat --noedit

tkregister2 will put the transformation matrix reg.lta in the appropriate format for fnirt, right? Or do I still need to play around with freesurfer's coordinate system?

It should be ok

Best, Ben

On Mon, Aug 13, 2018 at 10:11 PM, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:

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


            External Email - Use Caution

    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
<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




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