Transforming DWI images to template using RABIES output?

[geowk]

Hello,

Recently ran RABIES with a t2 and an epi datasets successfully using Fast Commonspace. We also have DWI images for the same rodent and wanted to spatially transform the DWI image to the same template altas as the t2 and epi dataset?

How would one go about doing this? Could we use the transformation matrices from the RABIES output? If so, where are they located?

Your help would greatly be appreciated.

-g

[Gab-D-G]

Hello @geowk,

All the transforms that are applied through RABIES preprocessing are found in the transforms_datasink/ https://rabies.readthedocs.io/en/latest/outputs.html#:~:text=atlas%20in%20commonspace-,transforms_datasink,-/%3A%20datasink%20for. These include the linear (affine) and nonlinear (warp or inverse warp) transforms generated by antsRegistration. Since you are using fast_commonspace, I believe in your case you will have the following outputs: native_to_atlas_affine, native_to_atlas_warp, native_to_atlas_inverse_warp (I realize these ones are not listed in the documentation since fast_commonspace is not the default). The combination of native_to_atlas_affine and native_to_atlas_warp moves an image from anatomical to commonspace. You could apply those, however this will be assuming that your DTI image is overlapping with your t2 already; if this is not the case, you will need to compute an additional image alignment step that is not provided by RABIES.

Hope this helps,
Gabriel