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 <mwas...@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 <mwas...@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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