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 <mwas...@nyu.edu > <mailto: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 > <mailto: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 > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
