add a notebook for comparing cbmr and cbma on neurosynth #835

yifan0330 · 2023-09-15T10:45:43Z

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

codecov · 2023-09-15T11:58:26Z

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All modified lines are covered by tests ✅

Comparison is base (d0b4c0f) 0.00% compared to head (63e6e4c) 89.07%.

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@@            Coverage Diff            @@
##           main     #835       +/-   ##
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+ Coverage      0   89.07%   +89.07%     
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  Files         0       48       +48     
  Lines         0     6113     +6113     
=========================================
+ Hits          0     5445     +5445     
- Misses        0      668      +668

see 48 files with indirect coverage changes

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jdkent

just some spelling errors to fix for now!

jdkent · 2023-09-19T10:04:23Z

examples/02_meta-analyses/12_compare_cbmr_and_cbma.py

+# of spatial intensity between pain studies and non-pain studies in Neurosynth.
+# The null hypothesis assumes spatial intensity estimations of two groups are equal
+# at voxel level, $H_0: \mu_{1j}=\mu_{2j}, j=1,\cdots,N$, where $N$ is number of
+# voxels within brain mask, $j$ is the index of voxel. Areas with significant p-vaules


Suggested change

# voxels within brain mask, $j$ is the index of voxel. Areas with significant p-vaules

# voxels within brain mask, $j$ is the index of voxel. Areas with significant p-values

jdkent · 2023-09-19T10:05:02Z

examples/02_meta-analyses/12_compare_cbmr_and_cbma.py

+# The null hypothesis assumes spatial intensity estimations of two groups are equal
+# at voxel level, $H_0: \mu_{1j}=\mu_{2j}, j=1,\cdots,N$, where $N$ is number of
+# voxels within brain mask, $j$ is the index of voxel. Areas with significant p-vaules
+# (siginificant difference in spatial intensity estimation between two groups) are


Suggested change

# (siginificant difference in spatial intensity estimation between two groups) are

# (significant difference in spatial intensity estimation between two groups) are

jdkent · 2023-09-19T10:06:03Z

examples/02_meta-analyses/12_compare_cbmr_and_cbma.py

+# voxels within brain mask, $j$ is the index of voxel. Areas with significant p-vaules
+# (siginificant difference in spatial intensity estimation between two groups) are
+# highlighted. We found that estimated activation level are significantly different
+# in ... between pain group and non-pain group.


Suggested change

# in ... between pain group and non-pain group.

# in ... between the pain group and non-pain group.

jdkent · 2023-09-19T10:06:33Z

examples/02_meta-analyses/12_compare_cbmr_and_cbma.py

+# Run MKDA on Neurosynth dataset
+# -----------------------------------------------------------------------------
+# For the purpose of justifying the validity of CBMR framework, we compare the estimated
+# spatial covergence of activation regions between pain studies and non-pain fMRI studies


Suggested change

# spatial covergence of activation regions between pain studies and non-pain fMRI studies

# spatial convergence of activation regions between pain studies and non-pain fMRI studies

jdkent · 2023-09-19T10:07:08Z

examples/02_meta-analyses/12_compare_cbmr_and_cbma.py

+)
+
+###############################################################################
+# This figure (displayed as z-statistics map) shows MKDA spatial covergence of


Suggested change

# This figure (displayed as z-statistics map) shows MKDA spatial covergence of

# This figure (displayed as a z-statistic map) shows MKDA spatial convergence of

jdkent · 2023-09-19T10:08:02Z

examples/02_meta-analyses/12_compare_cbmr_and_cbma.py

+coordinate-based meta-analysis (CBMA) in NiMARE
+
+CBMR is a generative framework to approximate smooth activation intensity function and investigate
+the effect of study-level moderators (e.g., year of pubilication, sample size, subtype of stimuli).


Suggested change

the effect of study-level moderators (e.g., year of pubilication, sample size, subtype of stimuli).

the effect of study-level moderators (e.g., year of publication, sample size, subtype of stimuli).

jdkent · 2023-09-19T10:08:24Z

examples/02_meta-analyses/12_compare_cbmr_and_cbma.py

+This tutorial is intended to provide an intuitive comparison of CBMA and MKDA results on
+neurosynth dataset.
+
+For more detailed introduction to CBMR implementation in NiMARE, see the `CBMR tutoral


Suggested change

For more detailed introduction to CBMR implementation in NiMARE, see the `CBMR tutoral

For more detailed introduction to CBMR implementation in NiMARE, see the `CBMR tutorial

jdkent · 2023-09-19T10:09:00Z

examples/02_meta-analyses/12_compare_cbmr_and_cbma.py

+
+For more detailed introduction to CBMR implementation in NiMARE, see the `CBMR tutoral
+<https://nimare.readthedocs.io/en/latest/auto_examples/02_meta-analyses/11_plot_cbmr.html>`_ and
+`documatation <https://nimare.readthedocs.io/en/latest/generated/nimare.meta.cbmr.html>`_.


Suggested change

`documatation <https://nimare.readthedocs.io/en/latest/generated/nimare.meta.cbmr.html>`_.

`documentation <https://nimare.readthedocs.io/en/latest/generated/nimare.meta.cbmr.html>`_.

jdkent · 2023-09-19T10:09:28Z

examples/02_meta-analyses/12_compare_cbmr_and_cbma.py

+###############################################################################
+# Download the Neurosynth Dataset
+# -----------------------------------------------------------------------------
+# Neurosynth is a large-scale functional magnetic resonance imaing (fMRI) database.


Suggested change

# Neurosynth is a large-scale functional magnetic resonance imaing (fMRI) database.

# Neurosynth is a large-scale functional magnetic resonance imaging (fMRI) database.

yifan0330 · 2023-09-19T15:00:33Z

just some spelling errors to fix for now!

Sorry for the spelling errors! I've fixed them now

…neurosynth_notebook

jdkent · 2023-09-20T15:21:47Z

examples/02_meta-analyses/13_compare_cbmr_and_cbma.py

+neurosynth_dset = download_abstracts(neurosynth_dset, "example@example.edu")
+neurosynth_dset.save(os.path.join(out_dir, "neurosynth_dataset_with_abstracts.pkl.gz"))


think this bit can be removed, we are not using abstracts for this notebook

jdkent

Sorry for changing my mind about this, could you add a .ipynb notebook to misc-notebooks with the cells executed? Since this notebook is a bit intensive it would be nice to have a version of this where the code is already run and visible.

add a notebook for comparing cbmr and cbma on neuroth

a62a695

yifan0330 mentioned this pull request Sep 15, 2023

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

Closed

jdkent changed the title ~~add a notebook for comparing cbmr and cbma on neuroth~~ add a notebook for comparing cbmr and cbma on neurosynth Sep 15, 2023

jdkent requested changes Sep 19, 2023

View reviewed changes

fix some spelling error

47a3e16

yifan0330 added 3 commits September 19, 2023 23:55

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

21b659d

…neurosynth_notebook

change notebook name

263f9e9

reformalize codes with black

d2cb58a

jdkent reviewed Sep 20, 2023

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jdkent requested changes Sep 20, 2023

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yifan0330 added 7 commits September 26, 2023 19:44

add executed cbmr-pain notebook in misc-notebooks

a8612c3

modify some of parameters in cbmr notebook

b20d7dc

fix the dependency error of numpy version

bca5d6d

fix the dependency error of numpy version

9ab374a

fix the dependency error of numpy version

09abdf1

fix the dependency error of numpy version

c5b29ce

set up loose criteria for cbmr optimization

63e6e4c

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add a notebook for comparing cbmr and cbma on neurosynth #835

add a notebook for comparing cbmr and cbma on neurosynth #835

yifan0330 commented Sep 15, 2023

codecov bot commented Sep 15, 2023 •

edited

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yifan0330 commented Sep 19, 2023

jdkent Sep 20, 2023

jdkent left a comment

	# voxels within brain mask, $j$ is the index of voxel. Areas with significant p-vaules
	# voxels within brain mask, $j$ is the index of voxel. Areas with significant p-values

	# (siginificant difference in spatial intensity estimation between two groups) are
	# (significant difference in spatial intensity estimation between two groups) are

	# in ... between pain group and non-pain group.
	# in ... between the pain group and non-pain group.

	# spatial covergence of activation regions between pain studies and non-pain fMRI studies
	# spatial convergence of activation regions between pain studies and non-pain fMRI studies

	# This figure (displayed as z-statistics map) shows MKDA spatial covergence of
	# This figure (displayed as a z-statistic map) shows MKDA spatial convergence of

	the effect of study-level moderators (e.g., year of pubilication, sample size, subtype of stimuli).
	the effect of study-level moderators (e.g., year of publication, sample size, subtype of stimuli).

	For more detailed introduction to CBMR implementation in NiMARE, see the `CBMR tutoral
	For more detailed introduction to CBMR implementation in NiMARE, see the `CBMR tutorial

	`documatation <https://nimare.readthedocs.io/en/latest/generated/nimare.meta.cbmr.html>`_.
	`documentation <https://nimare.readthedocs.io/en/latest/generated/nimare.meta.cbmr.html>`_.

	# Neurosynth is a large-scale functional magnetic resonance imaing (fMRI) database.
	# Neurosynth is a large-scale functional magnetic resonance imaging (fMRI) database.

		neurosynth_dset = download_abstracts(neurosynth_dset, "example@example.edu")
		neurosynth_dset.save(os.path.join(out_dir, "neurosynth_dataset_with_abstracts.pkl.gz"))

add a notebook for comparing cbmr and cbma on neurosynth #835

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yifan0330 commented Sep 15, 2023

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codecov bot commented Sep 15, 2023 •

edited