Registering mask from CEST image to T2 image

SCT
1

I have acquired T2 images and CEST images with a smaller FOV and larger voxel size. I have segmented the T2 image to create a mask and then registered one CEST image to the T2 using sct_register_multimodal and then transform the mask into CEST space using sct_apply_transfo. I would like to register the CEST space mask to the T2 space so that I know where on the T2 image the CEST mask corresponds to. The CEST image is acquired at a different angle compared to the T2 image. How can I do this?

2

Hi @Victoria987,

If I understand correctly, you’ve already registered the T2 image to the CEST image, meaning that you should have two output warp_* files, corresponding to forward (T2 → CEST) and backward (CEST → T2) transformations. If you want to register your CEST mask on your T2, you can simply use sct_apply_transfo and select your backward transformation.

4

Hi,

Thanks. Another question - the CEST mask has 14 slices. Is there a way to visualize/identify these different slices once I’ve transformed it back to the T2?

5

I’m missing a bit of context here, but one thing you can do is split your CEST mask into multiple, single-slice, masks, and then apply the transformation to get each of these masks in the T2 space.

Another thing you can do is assign a specific value of the CEST mask per slice (eg 1, 2, 3) and then apply the transformation (making sure to use nearest neighbour interpolation to maintain the discrete values)

6

How would I assign a specific value of the CEST mask per slice and apply the transformation (using nearest neighbour interpolation to maintain the discrete values)?