Yes, it does help. If that is the case then I am probably doing something wrong. Could you please confirm/correct the following?
Lets assume that we have one grid point at location (i,j,k) in the initial FA image and we want to warp it to the reference image (FMRIB58_FA). After warping the point will be at (i',j',k') in the reference image space.
Then as far as I understand we need to do the following
(i',j',k',1).T = A*(i,j,k,1).T
where A is a 4x4 matrix which is made by the .mat file left multiplied with the inverse diagonal matrix of the voxel sizes(zooms) of the reference image and right multiplied by the diagonal matrix of the voxel sizes(zooms) of the initial image. At this point
i',j',k' is now at the reference image space but only affine transformed, then we need to update them with the displacements which will do the warping bit
(i',j',k',1).T= (i',j',k',1).T +(d(i',j',k',0),d(i',j',k',1),d(i',j',k',2),1).T
where .T denotes the transpose, d the displacements read from the output nii of fnirtfileutils interpolated at the points i',j',k'
Is there anything else that is necessary?
Do you see any problems with this approach?
Are the displacements in mm (millimetres)?
Thank you,
Eleftherios
Dear Eleftherios,
For learning purposes I am trying to create my own apply warp where you give as an input your FA image, the affine transform and the displacement nifti and then warp the FA image to the FMRIB58_FA template. It seemed to me easier to use fnirtfileutils and
work directly with the displacements(by fnirtfileutils) rather than the intermediate image generated by fnirt.
When I use FSL's command applywarp the registration looks very good however when I visualize the displacements it looks like they are applied in the entire space even outside the unmasked area and having quite large displacements near the foreground/background
edge.
So, here is my question:
Do they displacements need any preprocessing/transformation/masking before applying them to the image to be warped?
No, they don't.
The mask is used to select the voxels from which to use information to obtain/create the warps. It doesn't mean there cannot be warps out there. The reason warps are propagated from within the mask (where there is information) to outside the mask is because
of the "regularisation". The regularisation term enforces smoothness of the warps, so that all other things equal it will chose the smoothest set of warps. The regularisation term is estimated from the entire FOV, not just within the mask. Hence, the smoothest
field is that which changes as little as possible as one goes from inside to outside of the mask.
Hope that helps to clarify things?
Jesper
