ENH: Implement Jacobian weighting during unwarp [backport gh-391]

[effigies]

Slightly different shaping than in the latest master, but I believe this is the equivalent. It would be good to get a test. @themeo would you be able to test? If you're using fmriprep-docker, it's pretty easy:

$ git clone https://github.com/effigies/sdcflows.git
$ git -C sdcflows checkout bp/2.5.x/391
$ pipx run "fmriprep-docker==23.1.4" [usual arguments] --patch sdcflows=$PWD/sdcflows/sdcflows

This will mount the sdcflows directory into the correct location to be picked up by fMRIPrep.

[themeo]

I'd be happy to give it a spin, but our cluster doesn't have docker (we use singularity). Is it possible to put the patched version together using singularity?

[effigies]

Yes, it's just a little bit less automated. You'll need to add the following flag to your binds, before the image:

-B $PWD/sdcflows/sdcflows:/opt/conda/envs/fmriprep/lib/python3.10/site-packages/sdcflows

You can replace $PWD/sdcflows with the full path to wherever you clone the repository. Note that on the left side of the colon sdcflows should appear twice, like sdcflows/sdcflows:...

[themeo]

This fix led to a dramatic improvement in how fmriprep handles SDC.

original raw bold:

topup/applytopup on the raw image:

fmriprep with the fix:

This is not an entirely clean comparison, as the fmriprep-processed image has also undergone motion correction etc.

Congrats on cracking this!

[amirhusseinab]

Thanks for the fix! The boldref is SDCed now, but the T1w and MNI space outputs are still extra-distorted. Is it because the pipelines are not totally merged? PE-dir is RL, SDC with PEPOLAR.
Raw bold:

fmriprep 23.1.4. "vannila" boldref:

fmriprep 23.1.4. SDC-fixed boldref:

fmriprep 23.1.4 vannila and SDC-fixed T1w space boldref:

[effigies]

This is a good point, this will currently only affect files resampled into boldref space, since the resampling to other spaces is handled differently. I'm currently working on a tool that will resample directly to any volumetric space, but that will only be available with fmriprep 23.2.

[effigies]

This will need to wait for a later fMRIPrep.