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Implement cluster mass-based cluster-level Monte Carlo correction for CBMA algorithms #609

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merged 11 commits into from
Dec 16, 2021

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@tsalo tsalo commented Dec 7, 2021

Closes #608.

Changes proposed in this pull request:

  • Add new cluster mass-based Monte Carlo FWE correction, which produces new <z|logp>_desc-mass_level-cluster_corr-FWE_method-montecarlo maps.
  • Rename <z|logp>_level-cluster_corr-FWE_method-montecarlo maps to <z|logp>_desc-size_level-cluster_corr-FWE_method-montecarlo.

To do:

  • Add citation for cluster mass approach (Bullmore 1999).
  • Add versionchanged directive to FWE method.
  • Describe cluster mass approach in docstring.
  • Check results.

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tsalo commented Dec 7, 2021

RTD is failing due to a problem with m2r and mistune.

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codecov bot commented Dec 7, 2021

Codecov Report

Merging #609 (98186b9) into main (c3f2667) will increase coverage by 0.06%.
The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##             main     #609      +/-   ##
==========================================
+ Coverage   85.85%   85.91%   +0.06%     
==========================================
  Files          40       40              
  Lines        4382     4401      +19     
==========================================
+ Hits         3762     3781      +19     
  Misses        620      620              
Impacted Files Coverage Δ
nimare/correct.py 91.95% <ø> (ø)
nimare/diagnostics.py 78.16% <ø> (ø)
nimare/meta/cbma/base.py 94.14% <100.00%> (+0.46%) ⬆️

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@tsalo tsalo added cbma Issues/PRs pertaining to coordinate-based meta-analysis enhancement New feature or request breaking-change PRs that change results or interfaces. labels Dec 10, 2021
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tsalo commented Dec 10, 2021

Renaming the existing cluster size-based maps counts as a breaking change.

@tsalo tsalo changed the title [ENH] Implement cluster mass-based cluster-level Monte Carlo correction Implement cluster mass-based cluster-level Monte Carlo correction for CBMA algorithms Dec 14, 2021
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tsalo commented Dec 16, 2021

The results look the same as cluster size for an example Dataset with 17 studies and FWE correction with 10000 iterations.

image

Also, the cluster size and mass null distributions were correlated at about 0.9, and the cluster mass and max ALE value distributions were correlated at about 0.91. I think I can conclude that the results are what we'd expect.

@tsalo tsalo merged commit 51b871a into neurostuff:main Dec 16, 2021
@tsalo tsalo deleted the cluster-mass branch December 16, 2021 17:53
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Add cluster mass option for Monte Carlo FWE correction methods
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