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[ENH] Add support for multivariate coherency method (canonical coherence) #163

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Mar 25, 2024
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b2f05e0
[ENH] Added CaCoh
tsbinns Nov 19, 2023
027701f
[MAINT] Switched to numpy for computing phis
tsbinns Nov 21, 2023
a743c75
[DOC] Improved internal CaCoh comments
tsbinns Nov 21, 2023
9419a91
Merge branch 'main' into cacoh
tsbinns Nov 25, 2023
b755dce
[BUG] Fix incorrect CaCoh n_seeds after SVD
tsbinns Nov 27, 2023
261aa41
Merge branch 'main' into cacoh
tsbinns Nov 28, 2023
2982dc5
Merge branch 'main' into cacoh
tsbinns Nov 28, 2023
8fa75d2
[MAINT] Updated authorship
tsbinns Nov 28, 2023
949ac3f
[MAINT] Updated authorship
tsbinns Nov 28, 2023
bc491a8
fix: update class methods for cacoh
orabe Nov 30, 2023
0960238
fix: implement class methods for cacoh
orabe Nov 30, 2023
b4230cc
Add email address
orabe Nov 30, 2023
f688c33
chore: reuse multivar tests for cacoh method
orabe Dec 1, 2023
8519442
[BUG] Fixed tests and flake
tsbinns Dec 1, 2023
e93fb47
[MAINT] Black format changed code
tsbinns Dec 11, 2023
4e1234a
[MAINT] Merge branch 'main' into cacoh
tsbinns Dec 11, 2023
788dddf
[MAINT] Ignore black formatting in git blame
tsbinns Dec 11, 2023
4296e54
[BUG] Fix missing/incorrect multivariate tests
tsbinns Dec 11, 2023
888e82d
[MAINT] Improve test code readability
tsbinns Dec 11, 2023
ec25d7d
Switched to complex CaCoh
tsbinns Dec 11, 2023
3d281ff
[BUG] Fix failing tests h5py version mismatch
tsbinns Dec 11, 2023
488c0d8
Revert "[BUG] Fix failing tests h5py version mismatch"
tsbinns Dec 11, 2023
f9ff2ac
Added author
tsbinns Dec 11, 2023
a247161
Merge branch 'mne-tools:main' into cacoh
tsbinns Dec 15, 2023
1cb52ad
Revert "[MAINT] Ignore black formatting in git blame"
tsbinns Dec 15, 2023
8393f5a
Merge branch 'main' into cacoh
adam2392 Dec 15, 2023
ee7fda7
Merge branch 'main' into cacoh
adam2392 Jan 17, 2024
a2ad531
Merge branch 'main' into cacoh
tsbinns Jan 24, 2024
cc81cc4
Update changelog file
orabe Jan 31, 2024
11f7775
Add new authors to CITATION file
orabe Jan 31, 2024
513e15a
Update authors file
orabe Jan 31, 2024
2a2a8ed
add a new author
orabe Jan 31, 2024
257a324
Add docstring for _invsqrtm function
orabe Jan 31, 2024
45458e9
Update docstring for _MultivariateCohEstBase
orabe Jan 31, 2024
f886297
add draft for cacoh example
orabe Feb 2, 2024
4652a44
(cacoh-example): consider spatial patterns, include references, link …
orabe Feb 2, 2024
ab3c64b
Add reference
tsbinns Feb 4, 2024
ac3d3f6
Update whats_new log message
tsbinns Feb 4, 2024
5aadfdb
Update version citation file
tsbinns Feb 4, 2024
d792c3a
Add preliminary CaCoh vs. MIC example
tsbinns Feb 4, 2024
cdca613
Update MIC/MIM example
tsbinns Feb 4, 2024
5cb9c44
Update docstrings
tsbinns Feb 4, 2024
5cb370a
Redraft CaCoh example
tsbinns Feb 4, 2024
0c90cfa
Update CaCoh example
tsbinns Feb 5, 2024
8789416
Merge branch 'main' into cacoh
tsbinns Feb 5, 2024
e0d6cd2
Update multivariate examples
tsbinns Feb 6, 2024
d69dc21
Fix CITATION.cff
tsbinns Feb 18, 2024
aa8c307
Update docstrings
tsbinns Feb 18, 2024
8ff932c
Update examples
tsbinns Feb 18, 2024
e095b35
Replace N.B. with Note
tsbinns Feb 19, 2024
8652da4
Reword cohy comparison example
tsbinns Feb 19, 2024
81ffefe
Update CaCoh & MIC/MIM examples
tsbinns Feb 19, 2024
e9497ff
Update CaCoh example
tsbinns Feb 19, 2024
1022e83
Remove empty line CaCoh example
tsbinns Feb 19, 2024
2d46f69
Update examples from review
tsbinns Feb 19, 2024
34af00a
Add simulation function
tsbinns Feb 20, 2024
9be5e8f
D comes before E
tsbinns Mar 1, 2024
0559e9a
Mark TODO replace simulations
tsbinns Mar 4, 2024
286c18d
Replace trivial simulations
tsbinns Mar 4, 2024
fb2e580
Apply suggestions from code review
tsbinns Mar 4, 2024
358004a
Add suggestion from code review
tsbinns Mar 4, 2024
2499023
Merge branch 'pr-sim_con' of https://github.com/tsbinns/mne-connectiv…
tsbinns Mar 4, 2024
5509a28
Fix black formatting
tsbinns Mar 4, 2024
46d40cd
Fix thresholds for new RNG settings
tsbinns Mar 4, 2024
e51d130
Fix missing object references
tsbinns Mar 4, 2024
61bb7b0
Merge branch 'mne-tools:main' into pr-sim_con
tsbinns Mar 6, 2024
97a3651
Merge branch 'mne-tools:main' into pr-sim_con
tsbinns Mar 12, 2024
673bd3a
Merge branch 'main' into cacoh
tsbinns Mar 12, 2024
f87edae
Refactor multivariate methods for connectivity classes
tsbinns Mar 12, 2024
0056820
Revert "Refactor multivariate methods for connectivity classes"
tsbinns Mar 12, 2024
2d756fb
Add CaCoh as multivariate method to classes
tsbinns Mar 12, 2024
fdd532d
Merge branch 'pr-sim_con' into cacoh
tsbinns Mar 18, 2024
95cd343
Update examples to use simulation function
tsbinns Mar 18, 2024
3b55901
Merge branch 'main' into cacoh
tsbinns Mar 19, 2024
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11 changes: 9 additions & 2 deletions CITATION.cff
Original file line number Diff line number Diff line change
Expand Up @@ -20,8 +20,15 @@ authors:
- given-names: "Alexandre"
family-names: "Gramfort"
orcid: https://orcid.org/0000-0001-9791-4404
- given-names: "Thomas Samuel"
family-names: "Binns"
orcid: https://orcid.org/0000-0003-0657-0891
- given-names: "Mohammad"
family-names: "Orabe"
orcid: https://orcid.org/0009-0004-7177-799X


title: "mne-connectivity"
version: 0.2.0
date-released: 2022-01-13
version: 0.6.0
date-released: 2024-12-06
url: "https://github.com/mne-tools/mne-connectivity"
2 changes: 2 additions & 0 deletions doc/authors.inc
Original file line number Diff line number Diff line change
Expand Up @@ -14,3 +14,5 @@
.. _Thomas Binns: https://github.com/tsbinns
.. _Tien Nguyen: https://github.com/nguyen-td
.. _Richard Köhler: https://github.com/richardkoehler
.. _Mohammad Orabe: https://github.com/orabe
.. _Mina Jamshidi: https://github.com/minajamshidi
20 changes: 20 additions & 0 deletions doc/references.bib
Original file line number Diff line number Diff line change
Expand Up @@ -82,6 +82,16 @@ @article{HaufeEtAl2013
year = {2013}
}

@article{HaufeEtAl2014,
author={Haufe, Stefan and Meinecke, Frank and G{\"o}rgen, Kai and D{\"a}hne, Sven and Haynes, John-Dylan and Blankertz, Benjamin and Bie{\ss}mann, Felix},
doi = {10.1016/j.neuroimage.2013.10.067},
journal={NeuroImage},
pages={96--110},
title={On the interpretation of weight vectors of linear models in multivariate neuroimaging},
volume={87},
year={2014},
}

@article{HippEtAl2012,
author = {Hipp, Joerg F and Hawellek, David J and Corbetta, Maurizio and Siegel, Markus and Engel, Andreas K},
doi = {10.1038/nn.3101},
Expand Down Expand Up @@ -268,6 +278,16 @@ @article{VinckEtAl2015
year = {2015}
}

@article{ViriyopaseEtAl2012,
author={Viriyopase, Atthaphon and Bojak, Ingo and Zeitler, Magteld and Gielen, Stan},
doi={10.3389/fncom.2012.00049},
journal={Frontiers in Computational Neuroscience},
pages={49},
title={When long-range zero-lag synchronization is feasible in cortical networks},
volume={6},
year={2012}
}

@article{Whittle1963,
author = {Whittle, Peter},
doi = {10.1093/biomet/50.1-2.129},
Expand Down
5 changes: 4 additions & 1 deletion doc/whats_new.rst
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ Version 0.7 (in dev)
Enhancements
~~~~~~~~~~~~

-
- Add support for a new multivariate connectivity method (canonical coherence; ``cacoh``) in :func:`mne_connectivity.spectral_connectivity_epochs` and :func:`mne_connectivity.spectral_connectivity_time` by `Thomas Binns`_ and `Mohammad Orabe`_ and `Mina Jamshidi`_ (:pr:`163`).

Bug
~~~
Expand All @@ -38,6 +38,9 @@ API

Authors
~~~~~~~
* `Thomas Binns`_
* `Mohammad Orabe`_
* `Mina Jamshidi`_


:doc:`Find out what was new in previous releases <whats_new_previous_releases>`
Expand Down
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