antsRegistration create transforms


I have multi-echo fMRI data that I am processing using FMRIPREP 21.0.0 + Tedana 0.0.11. In fmriprep, I used --output-spaces func T1w which gave me the func-anat transform file. I then submitted the minimally processed echo-wise images to tedana in their original ‘scanner’ space following the recommendation in the documentation. I did not keep the working directory for these subjects.

  1. I plan to keep my rest run in T1w space (they are already closely aligned), so I ran this command adapted from @tsalo 's pull request here (thanks!) and using the fmriprep-calculated func-anat transform. Unfortunately this is changing the image shape (fsleyes - space-scanner: 80x80x48 3mm iso voxels; space-T1w: 50x60x48 3mm iso voxels) in a seemingly suboptimal way (signal stretched to skull). The new dimensions match the boldref, which seems accurate to the man page’s description of the --reference. So I am misunderstanding how to ensure the images are coregistered?

Script here: normalize.txt (2.0 KB)

blue is the space-T1w image; red is the space-scanner image on the T1w

  1. For task runs, I’d like to calculate the transform between T1w and a custom template image (YAOAn100) without re-running fmriprep entirely. I want this transform to do the func->anat and anat->template normalization that was described in the pull request. What ants command or fmriprep subcommand/workflow (?) could produce that after the fact?

I’m not wed to ants but figured it couldn’t hurt to keep close to the fmriprep methods.

Thanks for your time,