Fmriprep coregistration & normalisation T2 * TSE image

We run fmriprep 21.0.1 on the HPC (using singularity). We would like to coregister and normalise our anatomical T2w & TSE (=partial scan) scans together with our T1w image. Is this possible in fmriprep (and how)?


Fmriprep does not use T2 weighted images (except for in Freesurfer recon-all).

However, you can register your T2 to your T1 (using ANTs for example) and multiply that transform by the transforms output by fmripre to get your other images in the same standard spaces as your T1.


If robust tool/parameter selections are made for coregistering other anatomical modalities to T1w, then we could add them to sMRIPrep without too much difficulty. There’s an open issue for T2w/FLAIR:

If you do what @Steven suggests, please report back (here or on that issue) with modality and command that work well for you.

Thanks, I will try this:)

I’ll try these and get back to you. Thanks for your suggestions