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 CautionHi 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
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