Register day 1 to one of the anatomicals with bbregister, call output day1.lta

Register day 1 to the same anatomical with bbregister, call output day2.lta

mri_concatenate_lta -invert1 day1.ltaday2.lta day2-to-day1.lta

Check:

tkregisterfv --mov day2.nii --targ day1.nii --reg day2-to-day1.lta

Apply

mri_vol2vol -mov day2.nii --targ day1.nii --reg day2-to-day1.lta --o day2-in-day1.nii

On 03/14/2018 07:05 PM, David Beeler wrote:

Hi,

I have some functional data for the same localizer (dimensions 80x80x38x246) that was acquired in the same subject on two separate days. I would like day 1's raw data to be spatially aligned to the anatomical taken on day 2, but still have the low resolution dimensions of functional space. This question has been asked a couple times before in various forms, but I can't seem to find a clear answer of how to do this correctly.

Anatomicals were collected on both days, so I figured I could do something like this:

mri_vol2vol --nearest --regheader --mov day1-f.nii.gz --targ $SUBJECTS_DIR/S03/mri/brain.mgz --o day1-f-in-day1-3danat.nii.gz

bbregister --s S03_day1 --mov $SUBJECTS_DIR/S03_day2/mri/brain.mgz --reg day1-to-day2.lta --init-fsl --t1 mri_vol2vol --mov $SUBJECTS_DIR/S03_day2/mri/brain.mgz --targ day1-f-in-day1-3danat.nii.gz --o day1-f-in-day2-3danat.nii.gz --reg day1-to-day2.lta --nearest --inv mri_vol2vol --regheader --mov day1-f-in-day2-3danat.nii.gz --targ day2-f.nii.gz --o day1-f-in-day2-func.nii.gz but this is a bad solution because I shouldn't have to actually upsample every time point to high resolution space and then back down again. I figure there must be a way to use the --no-resample flag of mri_vol2vol or something to keep the voxel number (relatively) low and just use the transformation matrix information to go straight from day 1 functional to day 2 functional. Let me know if you have any ideas, thanks! David

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