Taylor Salo

[DOC] Document additional analysis designs for non-parametric methods

3

Closes #3159. Instead of adding a new example that uses `permuted_ols` with a one-sample design, I added more documentation about designs and linked to an existing one-sample example using `non_parametric_inference`...

[ENH] Add DeprecationWarning for 3D masker.transform inputs

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Closes #2726, closes #3132, and closes #2724. Changes proposed in this pull request: - Fix docstrings of masker classes' `inverse_transform` methods to make it clear that 1D inputs are allowed,...

Optimize TFCE calculation or replace with probabilistic TFCE

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The TFCE method we implemented in #3196 is very slow. The probabilistic TFCE measure implemented in MNE seems to be faster, although I haven't directly compared them. We should look...

Document the types of inference models in the user guide

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I'm thinking that we should add a bit of narrative doc to explain the zoology of inference models (cluster size, cluster mess, one-and two-sided, parametric and non-parametric etc.) _Originally posted...

Add "add changelog entry" to auto-comment PR template

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I think it would be great to add an item about adding a whatsnew/changelog entry to the checklist in the [auto-comment workflow](https://github.com/nilearn/nilearn/blob/0eb1340212c6db5aac07ae31b3061bde5c9f7432/.github/workflows/auto-comment.yml). I am primarily requesting this because I often...

[DOC] Combine similar two-session GLM examples

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Closes #2771. Changes proposed in this pull request: - Combine plot_fiac_analysis.py and plot_fixed_effects.py into plot_two_session_model.py. - Update a link in first_level_model.rst that originally went to plot_fiac_analysis.py.

Use custom sorting for sphinx-gallery examples

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I believe that the documentation currently orders the examples within each section based on its default sorting method, which is [NumberOfCodeLinesSortKey](https://sphinx-gallery.github.io/stable/gen_modules/sphinx_gallery.sorting.html#sphinx_gallery.sorting.NumberOfCodeLinesSortKey). This means that the examples are currently ordered from...

Create or enhance example with parametric and duration modulation

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I think a good introduction to modulation would be to use reaction time, as in [Grinband et al. (2008)](https://doi.org/10.1016/j.neuroimage.2008.07.065). We could walk through how orthogonalization should be used with modulated...

Streamline the release process

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I think we could use integrations and Actions to simplify the release process, with most of the work happening on GitHub instead of on the release maker's local machine. We've...

[DOC] Add documentation page on denoising approaches

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Closes None, but stems from #819. Changes proposed in this pull request: - Add page on denoising strategies. I still need to figure out how to better integrate it into...