applywarp and non-linear transformations

AFNI Message Board
1

Hi there,

So I had a question.
I have two transformations:

  1. T1-weigted image in standard space TRANSFORM
  2. T1-weighted to T2-weighted-epi (Diffusion weighted space) TRANSFORM

I transformed these using the flirt and fnirt tool.
But now I would like to concatenate these two transformations together, but inverse both of them before concatenating so I would have the following two tranformations instead:

  1. standard space in T1-weigted space TRANSFORM
  2. T1-weighted to T2-weighted-epi (Diffusion weighted space) TRANSFORM

and then concatenate them so that I have a final product of:
standard space to T2-weighted-epi (Diffusion weighted space) TRANSFORM

SO, my question is: how can I do that?
Should I use the applywarp command and then invwarp? to inverse the transforms correctly? also would invwarp, inverse the --affine as well?

I normally would do
convert_xfm -omat standardspace_to_T2w_epi concat standard space in T1-space_TRANSFORM T1-weighted_T2-weighted-epi_TRANSFORM

But I want a nonlinear transformation, so convert_xfm is not the right thing in this particular example

2

Hi, Sondos-

Within AFNI, using things such as 3dAllineate/align_epi_anat.py and 3dQwarp, this could be done and addressed here. However, FSL tools such as flirt and fnirt have their own formats, structure, etc., and you will have to address these questions to those developers.

–pt