Which registration strategy is better among DTI, T1 and template space?

Hi experts,
Recently, I am working on analysis of DTI images. And I want to perform tractography between some ROIs. I have a HCP1065 template and ROIs on it. So which below registration is better? I am not sure.

  1. Regestrate native T1 image to native DTI(b=0) image and get T1_to_DTI image first. Then regestrate template image to this “T1_to_DTI image” and get template_to_DTI matrix(for registration). Finally apply this matrix to the ROIs to generate ROIs_in_native. And perform tractography between these ROIs_in_native on the DTI images.
  2. Regestrate native DTI(b=0) image to native T1 image and get DTI_to_T1 image first. Then regestrate T1 image to template and get T1_to_template matrix(for registration). Then apply this matrix to the DTI_to_T1 image and generate DTI_to_T1_to_template images. Finally perform tractography between the ROIs on the “DTI_to_T1_to_template images”.
  3. Any other strategies?

I tried the first strategy via ANTs, and it seems that the registration is quite good (both T1 to DTI and Template to T1_to_DTI). But I can’t check the warped ROIs because there is deformation.
Anyway, I am not sure what solution is a common way for this kind of tractography analysis. So I hope experts could give me some advice and reasons.
Best wishes,

Hi Roger,

You probably want to run the tractography on the native, undistorted DTI space, so I recommend you follow your first path, with some minor modifications to deal with the deformations:

If you collected fieldmaps, you want to correct the distortions in the diffusion-weighted images (DWI) to then register the DWI into the T1 using a rigid-body transformation. If you don’t have fieldmaps, I think ANTs allows you to do a distorted-DWI to T1 non-linear registration, but this is less than ideal.

Then you compute the registration of the T1 into the template. After that, you want to concatenate both transformations into a single one (undistorted DWI → template). Finally, you invert that transformation, and you can transform your template ROIs into the undistorted DWI, and perform the tractography in the undistorted DWI space.