Pointers for ANTs registration

I’m trying to figure out what the best way is to do the following. I’d be grateful for feedback on whether this is a good idea or not, or if there are better ways to do it. I would also be really grateful if you can give me some examples on how to do these steps.

  • I want to create a common MNI template with ANTs using T1 data. For that I can get inspired by this workflow:
    Can I use the registration information to register the functional scans to this template?
  • If this works I would proceed to the next step where I would crop only parts of the thalamus and brainstem of the registered T1 images using a mask and fsl.ApplyMask. The functional data would also be cropped in this way.
  • I would then re-register the cropped T1 images to each other. My assumption is this second registration results in a much better overlap of subcortical structures than would a registration that needs to include the cortex and cerebellum. This step also resamples the data to 0.5 mm isovoxel (how can I specify this?).
  • I would apply this new registration to the cropped functional data, again resampling to 0.5 mm isovoxel.
  • The next step would be first level estimation using the functional data.