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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