add a notebook for comparison between CBMR and CBMA on neurosynth dataset by yifan0330 · Pull Request #833 · neurostuff/NiMARE

yifan0330 · 2023-09-09T18:53:27Z

Closes # .

Changes proposed in this pull request:

Compare spatial convergence between pain studies and non-pain studies (in Neurosynth dataset) via CBMR and MKDA Chi-square analysis

…nce_cbmr

…ning message when running cbmr.

…ix_cbmr

…cbmr

codecov · 2023-09-09T19:51:30Z

Codecov Report

Patch coverage: 100.00% and project coverage change: +0.17% 🎉

Comparison is base (0864fd2) 88.67% compared to head (1df7789) 88.84%.
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #833      +/-   ##
==========================================
+ Coverage   88.67%   88.84%   +0.17%     
==========================================
  Files          47       47              
  Lines        6020     5997      -23     
==========================================
- Hits         5338     5328      -10     
+ Misses        682      669      -13

Files Changed	Coverage Δ
nimare/meta/cbmr.py	`78.32% <ø> (ø)`
nimare/meta/models.py	`90.29% <100.00%> (+2.47%)`	⬆️

... and 1 file with indirect coverage changes

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

yifan0330 · 2023-09-15T10:46:32Z

Closed in favour of #835

yifan0330 and others added 30 commits June 16, 2022 17:07

add cbmr.py file

153584d

create a design matrix function for cbmr

59a3742

add test file for cbmr

3371a98

modify pre-process and training function in cbmr

8d2a151

modify the dataset.anotations in cbmr

d014234

add documentation in utils functions

f741eeb

update model structure

e326758

update optimizer function

85a6d11

[skip ci][wip] update loss function

fe80124

update _fit function in CBMR

3edaa74

[wip][skip ci] allow other data types as pre-process inputs

cadffa6

use a sparse array instead of numpy

c632d29

[skip ci][wip] allow for multiple-group cbmr

a22048d

[skip ci][wip] fix conflict to merge

ab450fa

solve conflicts

0f2a93a

[skip CI][wip] modify settings in pre_process

b3ee6f1

[skip ci][wip] implemented group-wise CBMR and fix problems

0262c66

[skip ci][wip] add results as inputs to MetaResults

7fd47bc

Merge branch 'main' of https://github.com/neurostuff/NiMARE into enha…

b2b84a4

…nce_cbmr

[skip ci][wip] modify standardization of group moderators

48d4b57

[skip ci][wip] implement NB regression

5e6107f

[skip ci][wip]remove vox2idx function and simplify the code

c686558

[skip ci][wip]develp CNB model

171d5a6

adjustment to Firth penalty

b786a3d

Merge branch 'main' of https://github.com/neurostuff/NiMARE into enha…

f7cc042

…nce_cbmr

Merge branch 'main' of https://github.com/neurostuff/NiMARE into enha…

1a822d6

…nce_cbmr

[skip CI][wip] implement index2voxel function

e051015

[skip CI][wip] add implementation for SE of regression coefficient

c38aa31

[skip CI][WIP] implementing CBMRInference

27a8c8e

[skip CI][wip] implement spatial homogeneity test

c0da20d

Yifan Yu and others added 23 commits April 29, 2023 15:59

use pass instead of return in the abstract methods

ab751a5

added a test for StandardizeField class.

a95e116

edit example file of cbmr methods.

4705c47

fix linter error.

d48cd41

fix a linter error.

677e6a5

fix a linter error

d3487f5

fix merge

6a7b4c9

fix names of notebooks

93cff60

remove functorch (it was absorbed into torch)

4bbe51e

[skip ci] merge

8e34a5c

fix math mode and links in cbmr example.

b36ef7d

fix math mode

5ab8a2b

add a test with none moderator variable for CBMRInference

c442bda

add a separate test for moderators=None

20e8908

merge from upstream, solve conflict

e026add

Replace functorch.hessian by torch.func.hessian to remove pytorch war…

3730e4b

…ning message when running cbmr.

Merge branch 'fix_cbmr' of https://github.com/yifan0330/NiMARE into f…

0dbe8e9

…ix_cbmr

solve lint error

668311e

fix a bug with L-BFGS algorithm and speed up the execution time

9e34484

Merge branch 'main' of https://github.com/neurostuff/NiMARE into fix_…

b3fb1e2

…cbmr

fix lint code error

c68866e

fix a lint error

2531c19

add a notebook for comparing cbmr and cbma

ff5bdc3

yifan0330 added 2 commits September 10, 2023 15:29

fix documentation error in notebook

2f4a33f

try not to run this notebook due to memory consideration

1df7789

yifan0330 closed this Sep 15, 2023

jdkent added this to Planning Dec 19, 2025

jdkent moved this to Done in Planning Dec 19, 2025

Navigation Menu

Uh oh!

add a notebook for comparison between CBMR and CBMA on neurosynth dataset - #833

add a notebook for comparison between CBMR and CBMA on neurosynth dataset#833
yifan0330 wants to merge 192 commits into
neurostuff:mainfrom
yifan0330:add_cbmr_comparison

yifan0330 commented Sep 9, 2023

Uh oh!

codecov Bot commented Sep 9, 2023 •

edited

Loading

Uh oh!

yifan0330 commented Sep 15, 2023

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Uh oh!

Conversation

yifan0330 commented Sep 9, 2023

Uh oh!

codecov Bot commented Sep 9, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

yifan0330 commented Sep 15, 2023

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

codecov Bot commented Sep 9, 2023 •

edited

Loading