This is a bit tricky as you need a volume as a template that has the dimensions/resolution you want. One fast and dirty way to do it is to upsample the orig to 0.5mm, eg mri_convert --upsample 2 orig.mgz orig.us2.mgz You can then run mri_vol2vol --mov T2.nii.gz --lta reg.lta --targ orig.us2.mgz --o t2.us2.mgz It might complain that the output volume in the lta file does not match the target volume; if this causes it to fail, I can give you a work-around
On 2/25/2022 12:23 PM, Tisdall, Dylan wrote: > External Email - Use Caution > > Hi all, > > Thanks again for all the help so far with getting my data registered and > surfaces extracted. I have one further issue that I'm hoping to get help with. > > I've used bbregister to align my T2 scan with the surfaces from my T1 scan. > However, the output is resampled down to 1mm iso and a 256^3 volume; I'd like > to keep the native 0.8 mm resolution and FOV if possible (acknowledging, of > course, there's actually some blurring in the interpolation, but just for the > sake of nominal consistency). > > I tried to work around this by applying the .lta output by bbregister to my > T2 scan (with the goal of eventually using the --out-like flag to specify the > sampling resolution, but not doing that yet): > > mri_transform T2_SPACE.nii.gz T2_SPACE_transform.lta T2_SPACE_warped.nii.gz > > However, when I load the resulting output volume (T2_SPACE_warped.nii.gz) in > freeview, it has swapped axes. Strangely, this isn't the case with the output > volume generated by bbregister... it's well-aligned with the surfaces. > Similarly, if I load the T2_SPACE.nii.gz into freeview, and apply > T2_SPACE_transform.lta as part of the load command, the volume is > well-aligned. > > So what's different about how mri_transform applies that .lta file, compared > to bbregister and freeview? > > Is there a way to just get bbregister to resample my T2 scan with the > original resolution and FOV, so I can avoid applying mri_transform > altogether? I don't see an --out-like option for bbregister, but is there a > different flag? > > > Thanks again, > Dylan > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
