Confused about sct_apply_transfo (why do I need a destination file?)

SCT
1

Dear all

Here is what I want to do:
I have a multi-echo acquisition, where I need the individual echoes (scan A echo 1…n) to further processing, but the SNR is realtively poor. To get a better coregistration, I created the mean of these to boost SNR (scan A_mean), to coregister to an anatomical scan (scan B).
Now I want to go back and apply the transformation of A2B to the individual echoes.

If I understand right, then sct_apply_transfo (sic?) is the right tool to do this. But it is asking for a destination file. My understanding was that the warp field contains everything needed to warp from one space to another. What is the destination file used for?

Or am i misunderstanding something?

SCt version: 4.0.0 beta2
BW
Daniel

2

Hi @Daniel_Papp

The forward warping field (ITK-based) is defined in the physical coordinate system so we need to know in which destination (voxel-based coordinate) you want your images to be interpolated to.

In your case, the destination image would be scan B.

Cheers,
Julien

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