Skip to content

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

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Closed
wants to merge 192 commits into from
Closed

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

wants to merge 192 commits into from

Conversation

yifan0330
Copy link
Contributor

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

yifan0330 and others added 30 commits June 16, 2022 17:07
@yifan0330
add cbmr.py file
153584d
@yifan0330
create a design matrix function for cbmr
59a3742
@yifan0330
add test file for cbmr
3371a98
@yifan0330
modify pre-process and training function in cbmr
8d2a151
@yifan0330
modify the dataset.anotations in cbmr
d014234
@yifan0330
add documentation in utils functions
f741eeb
@yifan0330
update model structure
e326758
@yifan0330
update optimizer function
85a6d11
@yifan0330
[skip ci][wip] update loss function
fe80124
@yifan0330
update _fit function in CBMR
3edaa74
@yifan0330
[wip][skip ci] allow other data types as pre-process inputs
cadffa6
@yifan0330
use a sparse array instead of numpy
c632d29
@yifan0330
[skip ci][wip] allow for multiple-group cbmr
a22048d
@yifan0330
[skip ci][wip] fix conflict to merge
ab450fa
@yifan0330
solve conflicts
0f2a93a
@yifan0330
[skip CI][wip] modify settings in pre_process
b3ee6f1
@yifan0330
[skip ci][wip] implemented group-wise CBMR and fix problems
0262c66
@yifan0330
[skip ci][wip] add results as inputs to MetaResults
7fd47bc
@yifan0330
Merge branch 'main' of https://github.com/neurostuff/NiMARE into enha…
b2b84a4 
…nce_cbmr
@yifan0330
[skip ci][wip] modify standardization of group moderators
48d4b57
@yifan0330
[skip ci][wip] implement NB regression
5e6107f
@yifan0330
[skip ci][wip]remove vox2idx function and simplify the code
c686558
@yifan0330
[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 25 commits April 27, 2023 21:52
edit example file for cbmr
cabdfce
remove the standardize_field function as it's replicated in the Stand…
e7bc4c1 
…ardizeField class
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
@jdkent
fix merge
6a7b4c9
@jdkent
fix names of notebooks
93cff60
@jdkent
remove functorch (it was absorbed into torch)
4bbe51e
@jdkent
[skip ci] merge
8e34a5c
fix math mode and links in cbmr example.
b36ef7d
fix math mode
5ab8a2b
@yifan0330
add a test with none moderator variable for CBMRInference
c442bda
@yifan0330
add a separate test for moderators=None
20e8908
@yifan0330
merge from upstream, solve conflict
e026add
@yifan0330
Replace functorch.hessian by torch.func.hessian to remove pytorch war…
3730e4b 
…ning message when running cbmr.
@yifan0330
Merge branch 'fix_cbmr' of https://github.com/yifan0330/NiMARE into f…
0dbe8e9 
…ix_cbmr
@yifan0330
solve lint error
668311e
@yifan0330
fix a bug with L-BFGS algorithm and speed up the execution time
9e34484
@yifan0330
Merge branch 'main' of https://github.com/neurostuff/NiMARE into fix_…
b3fb1e2 
…cbmr
@yifan0330
fix lint code error
c68866e
@yifan0330
fix a lint error
2531c19
@yifan0330
add a notebook for comparing cbmr and cbma
ff5bdc3
@codecov
Copy link

codecov bot commented Sep 9, 2023 •
edited
Loading

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
Copy link
Contributor Author

Closed in favour of #835

@yifan0330 yifan0330 closed this Sep 15, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
4 participants
@yifan0330 @jdkent @JulioAPeraza @tsalo