Thanks.
Yes, that is what I thought. I typically use the code below to translate the data in 3d space.
3drefit -dxorigin 20 epi.nii.gz
But I am not sure how to set the orientation using 3drefit. Especially, if I get the rotation parameters below after manually nudging the data.
3drotate -quintic -rotate -8.78I -29.47R 5.78A -ashift -7.42S 9.39L 4.00P -prefix ??? inputdataset
So the step would be
(1) manually translate and rotate data
(2) run 3dAllineate
(3) concatenate transformations (nudge + affine)
I think the rotation part is the key barrier for me here. Can you provide some code how to do that?
Best
Ruyuan
