This might be easier to do with lta files, eg, when you run tkregister specify --ltaout file.lta. Once you have both LTAs, You can then use mri_concatenate_lta to multiply them together, eg

mri_concatenate_lta file1.lta file2.lta output.lta

output = file2matrix*file1matrix

mri_concatenate_lta can also invert the matrices before doing the computation

On 08/18/2017 03:23 PM, Michael Waskom wrote:

OK I think a way around this is to use tkregister2 to generate a registration between the conformed brain image and the cropped one:

tkregister2 --mov brain.nii --targ brain-crop.nii --regheader --reg anat2crop.dat --noedit

I can then convert this to an FSL-style matrix and use convert_xfm to concatenate the func2anat and anat2crop matrix so it can be applied with a single interpolation.

By the way is it possible to combine two tkreg style matrices in that format? I don't see an obvious option in tkregister2. That is I want to combine a2b.dat and b2c.dat into a2c.dat.

Thanks, Michael

On Fri, Aug 18, 2017 at 2:00 PM, Michael Waskom <mwaskom@nyu.edu mailto:mwaskom@nyu.edu> wrote:

Alternatively, is it possible to pass bbregister a different
target volume that's in register with the surfaces?

On Thu, Aug 17, 2017 at 6:10 PM, Michael Waskom <mwaskom@nyu.edu
<mailto:mwaskom@nyu.edu>> wrote:

    Hi Doug,

    I'd like to use the registration matrix from bbregister to
    transform functional data into a cropped FOV that corresponds
    with the anatomy.

    I thought that bbregister outputs a ras2ras transform, so if I
    could crop the anatomical volume with a correct header
    vox2ras, things should be fine. Is my thinking here wrong?

    Here is roughly what I have done:

    1. Generate a registration matrix to the full anatomy

    bbregister --s subj --mov func.nii --reg reg.dat --t2

    2. Crop the anatomy:

    mri_convert brain.mgz brain.nii
    fslroi brain.nii brain_crop.nii 50 150 50 150 50 150

    (I know this is an fsl tool but I couldn't find an option to
    do exactly this in mri_convert)

    3. Check the output -- looks fine so far

    tkregister2 --mov brain-crop.nii --regheader --s subj --surfs
    --reg /dev/null

    4. Resample the functional volume

    mri_vol2vol --mov func.nii --targ brain_crop.nii --reg reg.dat
    --o func_xfm.nii

    5. Check the output

    tkregister2 --mov func_xfm.nii --regheader --s subj --surfs
    --reg /dev/null

    The resulting functional image is shifted superior about ~20cm

    What am I missing in my understanding of the bbregister and
    header transformation matrices?

    Thanks!
    Michael

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