Frequently Asked Questions
for NIfTI and ANALYZE tools
Orientation related question
Is it possible to use reslice_nii to apply a transform to a nifti volume? for example, if I have a transformation matrix that is the result of a 3D
coregistration of a functional with an anatomical volume, could I use reslice_nii to apply that transformation matrix to the functional volume
to transform it into anatomical space? If so, any chance of some example code? (30-April-2012, Extracted from Mark from MATLAB File
Exchange Comments)
Answer
Sure Mark. You need a reference image by the way, so you can see what will happen before and after you apply the transformation matrix.
Here's the example:
1. Download "avg152T1_RL_nifti.nii" from NIfTI site. I use it as reference image.
2. Load and view how the reference image looks like:
nii = load_nii('avg152T1_RL_nifti.nii');
view_nii(nii);
3. Assume that I have a transformation matrix, which will let the reference image turn 30 degree counter-clockwise on XY plane, here will
be the matrix:
T = [cos(pi/6) -sin(pi/6) 0; sin(pi/6) cos(pi/6) 0; 0 0 1];
4. Get old_xyz from reference image:
rl = load_untouch_nii('avg152T1_RL_nifti.nii');
old_xyz = [rl.hdr.hist.srow_x(1:3);rl.hdr.hist.srow_y(1:3);rl.hdr.hist.srow_z(1:3)];
5. Apply your transformation matrix, and save new_xyz into a new image:
new_xyz = T * old_xyz;
rl.hdr.hist.srow_x(1:3) = new_xyz(1,:);
rl.hdr.hist.srow_y(1:3) = new_xyz(2,:);
评论0