Integration and validation tests with b=0 only

[oesteban]

Two low-hanging fruit tests using only a b=0:

• Validation:
  • [x] Unit tests of the TrivialB0Model implementation
  • [x] Unit tests of ANTs' config for b=0.
• Integration:
  • [x] Introduce a series of transforms (e.g., copy them from another dataset) and resample the b=0 through that motion series. Then run the whole estimator and check the proximity of the estimated transforms.

[oesteban]

Okay, I've tried to set up some basics, and implemented a unit-test for the TrivialB0Model sketching what we intend to do here:

https://github.com/nipreps/eddymotion/blob/152e0d4aeb6917965ed1821ea1507fb68630fa3b/eddymotion/tests/test_model.py#L29-L42

Unit tests of ANTs' config for b=0.

I see this implemented in test_estimator.py. To do so:

• [ ] Upload an example B0 map (3D)
• [ ] Apply random (and small) rotations and translations on the image. These can be generated with nibabel.eulerangles.euler2mat (e.g., https://github.com/poldracklab/nitransforms/blob/master/nitransforms/tests/test_linear.py#L107). For the resampling, I would use nitransforms.linear.Affine.resample().
• [ ] Run the registration interface loading the parameters from config
• [ ] Check that the error of the affine is below some threshold when transforming points scattered across the volume.

Introduce a series of transforms (e.g., copy them from another dataset) and resample the b=0 through that motion series. Then run the whole estimator and check the proximity of the estimated transforms.

I see this implemented in test_integration.py. To do so:

• [ ] Upload an example B0 map (3D) - or reuse from the previous test
• [ ] Generate a series of moved B0's with the realignment matrices from another, real dataset.
• [ ] Initiate the TrivialB0Model with this B0 map and feed the dwi object with the moved data (simulate perhaps several transforms).

[oesteban]

Hi there! I've uploaded some data under https://github.com/nipreps/eddymotion/tree/main/eddymotion/tests/data, generated by @dPys with FiberFox.

[sebastientourbier]

@oesteban I am progressing! For now, I managed to:

• extract the b0 volume from the sub-01_dwi.nii.gz provided by Céline.
• run AFNI 3dvolreg on the fmri of the first run, first subject of ds000005 (240 time frames) on openneuro with the middle frame as reference. This gives me a text file where one line corresponds to the motion parameters for one time frame.
• make 20 copies of the b0 where I applied the motion parameters from the last 20 frames (with nitransforms), saved in temporary niftis.
• save a unique 4D nifti image that concatenates the original and the moving b0s

I haven't opened a PR yet but here is a quick preview of the motion introduced

What do think?

[dPys]

This looks so awesome.