DOC: Document the PET notebook

[jhlegarreta]

Document the PET notebook: add markdown cells explaining the steps.

[jhlegarreta]

Still not true as the data does not use datalad yet, but it will eventually (related to issue #112).

[jhlegarreta]

@mnoergaard I would be grateful if you could review this PR. There is a number of things that I do not fully understand, and may require separate work (i.e. issues and PRs)

• What is the purpose of the below statement ? The split is done internally by PETMotionEstimator and the data_train, and data_test are not used. Maybe it was a simple example ?

data_train, data_test = pet_dataset.lofo_split(15)

• In the statement

model = PETModel(dataset=pet_dataset, timepoints=pet_dataset.midframe, xlim=7000)

Why is xlim given a seemingly arbitrary value? Documenting the class may help clarifying this. Further down the notebook pet_dataset.total_duration is used to set the value for xlim.

• Is the below statement necessary?

model.fit_predict(None)

• There is something missing in the before/after correction plot because the PET_before is not being shown.

• Slightly related to the above, wouldn't it be better if we could propose (or leverage nireports if possible) a GIF with a flickering between uncorrected vs corrected? Otherwise the difference between the two can be hard to tell.

• Are we sure that data_test[0] is the data after motion correction in the following statement?

nifti_img_after = nb.Nifti1Image(data_test[0], pet_dataset.affine)

data_test it is assigned by the lofo_split call but it is never used? Maybe the before_mc and after_mc NIfTI filenames are swapped?

• It seems weird to first make the correction with a given model instance, and then instantiate the estimator with a new model, isn't it?

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.10%. Comparing base (9b36f58) to head (22fb641).
⚠️ Report is 2 commits behind head on main.

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  Coverage   82.10%   82.10%           
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  Files          37       37           
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  Branches      224      224           
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  Partials       46       46           

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[jhlegarreta]

typecheck issues are unrelated (x-ref #204 (comment)); CI errors are unrelated (x-ref #204 (comment)).

Most questions in #197 (comment) are no longer relevant after having merged PR #204, some will be addressed in PR #203, and visualization questions will be addressed after the more pressing questions about the PET estimator, and overall, the results in the notebook are addressed. Merging to move forward.