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Do the two align in freeview if you just load both of them? If so, then
you can use something like
mri_vol2vol --mov vol1.mgz --targ vol2.mgz --regheader --no-resample --o
new.vol1.mgz
If they do not but you have a registration, then you can use a similar
command, eg,
mri_vol2vol --mov vol1.mgz --targ vol2.mgz --reg yourreg.lta
--no-resample --o new.vol1.mgz
On 8/18/2023 11:34 AM, Proulx, Jean Sebastien wrote:
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Dear Freesurfers!
I have two single-slice images that were acquired with different head
positions.
Thanks to a fancy AutoAlign-like routine at the scanner (areg by Paul
Wighton), the fov of the second image tracked the movement of the
head—the brain nicely aligns when overlaying the two untouched image
grids with e.g. fslview.
To leverage this online registration and properly visualize images in
freeview, I need the fov position in header of the second image to be
the same as in the header of the first image—basically pretending the
head did not move and the two images were acquired with the exact same
scanner-space fov position. So far I achieved that in a somewhat
inelegant way by loading the first header in matlab with MRIread.m and
manually adding the volume data from the second image before saving
with MRIwrite.m.
That however does not work when the second image have different voxel
and matrix sizes—e.g. my second image has twice the resolution of the
first and gets blown up to twice the size in freeview after my
makeshift header change :-(
I suspect a better solution could use mri_vol2vol with an appropriate
registration matrix, but I don't know how to get the appropriate matrix.
Any suggestions?
thanks a lot for the help and
Have a very good day!
Sébastien
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