Dear Sondos,
> 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 would recommend combining transforms 1 and 2 using convertwarp (there is a reasonably good description of how to use it at https://fsl.fmrib.ox.ac.uk/fsl/fsldev/FNIRT/UserGuide#convertwarp), and after that invert that composite transform using invwarp.
Jesper
>
> 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
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