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?
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.
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?
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)
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)?