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[REL] v0.3.0 release (#181)
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* update changelog

* modify the zenodo files for this release

* add peer herholz to joss paper

* fix peer affiliation

* address peer comments

* clarify sentence by adding brain
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jdkent authored Aug 30, 2019
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16 changes: 12 additions & 4 deletions .joss/paper.md
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Expand Up @@ -10,9 +10,14 @@ authors:
- name: James D. Kent
orcid: 0000-0002-4892-2659
affiliation: 1
- name: Peer Herholz
orcid: 0000-0002-9840-6257
affiliation: 2
affiliations:
- name: Neuroscience Program, University of Iowa
index: 1
- name: Montréal Neurological Institute
index: 2
date: 30 January 2019
bibliography: paper.bib
---
Expand All @@ -22,9 +27,10 @@ bibliography: paper.bib
You may not be aware of it, but your brain is orchestrating a complex ballet of activity while reading this sentence.
Whether it is following a dot, reading a sentence, interpreting what response is required when presented with a red square; the brain is evaluating input and sending motoric output to perform optimally/efficiently.
We can measure and analyze this flurry of activity using functional Magnetic Resonance Imaging (fMRI).
Traditional fMRI analysis emphasizes what regions are "activated/deactivated" during a task, but does not provide information on which regions are acting in synchrony.
Knowing what regions are synchronous during a task gives insights on the potential organization of the brain.
NiBetaSeries seeks to fill this gap by providing a method to measure how activation patterns between brain regions are correlated across trials.
Traditional fMRI analysis emphasizes what regions are "activated/deactivated" during a task, but does not provide information on which regions are acting in synchrony or are being segregated.
Knowing the synchronous/segregated brain regions during a task gives insights on the potential organization of the brain.
NiBetaSeries seeks to fill this gap by providing a method to measure how activation/deactivation
patterns between brain regions are correlated across trials.
That is to say if region A and region B both show high activity on trial 1, low activity on trial 2, medium activity on trial 3, and so on, then these two regions are highly correlated.

# Background
Expand All @@ -38,7 +44,7 @@ Thus larger betas mean greater activation, and smaller or negative betas mean le
Traditional fMRI analysis will group together all the relevant trial types and give them all one beta estimate, where variance between trials is treated as noise.
NiBetaSeries, on the other hand, gives each trial its own beta estimate treating the variance between trials as the signal of interest.
With the concept of a beta under our belt, The final complication is the multiple methods we can use to derive individual beta estimates.
Two common methods are least squares all (LSA) and least squares separate (LSS).
Two common methods are least squares all (LSA) and least squares separate (LSS) [@Mumford2012;@Turner2012a].
LSA places all the trials in the same GLM, where each trial is a separate predictor.
LSA works well when the trials are far apart in time since the BOLD response takes a long time to return to baseline.
When the trials are close together, however, the bold responses start to overlap and the GLM cannot accurately attribute the variance in the fMRI data to trial 1 or trial 2, leading to unreliable beta estimates.
Expand Down Expand Up @@ -79,6 +85,8 @@ useful for a variety of scientific questions.
# Overview

NiBetaSeries presents as a command line utility written in python following the template of a BIDS-App [@Gorgolewski2017].
NiBetaSeries is available on [pypi](https://pypi.org/project/nibetaseries/) and as an container
on [dockerhub](https://hub.docker.com/r/hbclab/nibetaseries) with [comprehensive documentation](https://nibetaseries.readthedocs.io/en/latest/) complete with interactive examples.
The primary way for users to interact with NiBetaSeries is by typing `nibs` in the command line.
The basic workflow of NiBetaSeries follows these steps (the files can be found in the `workflows` directory):

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59 changes: 1 addition & 58 deletions .zenodo.json
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Expand Up @@ -5,67 +5,10 @@
"affiliation": "Neuroscience Program, University of Iowa",
"orcid": "0000-0002-4892-2659"
},
{
"name": "Rokem, Ariel",
"affiliation": "eScience Institute, University of Washington",
"orcid": "0000-0003-0679-1985"
},
{
"name": "VanderPlas, Jake",
"affiliation": "eScience Institute, University of Washington",
"orcid": "0000-0002-9623-3401"
},
{
"name": "Holdgraf, Chris",
"affiliation": "Berkeley Institute for Data Science, University of California Berkeley",
"orcid": "0000-0002-9420-9301"
},
{
"name": "DeStasio, Krista",
"affiliation": "Social & Affective Neuroscience Laboratory, University of Oregon",
"orcid": "0000-0002-3959-9060"
},
{
"name": "Ludwig, Rita",
"affiliation": "Social & Affective Neuroscience Laboratory, University of Oregon"
},
{
"name": "Martin, Rebecca",
"affiliation": "Hartley Lab, New York University",
"orcid": "0000-0002-5482-1707"
},
{
"name": "Toro-Serey, Claudio",
"affiliation": "Cognition and Decision Lab, Boston University",
"orcid": "0000-0002-5273-2276"
},
{
"name": "Eschenburg, Kristian",
"affiliation": "Integrated Brain Imaging Center, University of Washington"
},
{
"name": "Erramuzpe, Asier",
"affiliation": "Computational Neuroimaging Lab, BioCruces Health Research Institute",
"orcid": "0000-0002-9402-2184"
},
{
"name": "Herholz, Peer",
"affiliation": "Laboratory for Multimodal Neuroimaging, University of Marburg",
"affiliation": "Montréal Neurological Institute",
"orcid": "0000-0002-9840-6257"
},
{
"name": "Blue, Brandon",
"affiliation": "BIL Consultant"
},
{
"name": "Whitaker, Kirstie",
"affiliation": "Research fellow, Turing Institute",
"orcid": "0000-0001-8498-4059"
},
{
"name": "Voss, Michelle",
"affiliation": "Health, Brain, and Cognition Lab, University of Iowa",
"orcid": "0000-0002-3706-7423"
}
],
"keywords": [
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80 changes: 80 additions & 0 deletions .zenodo.tmp.json
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@@ -0,0 +1,80 @@
{
"creators": [
{
"name": "Kent, James D.",
"affiliation": "Neuroscience Program, University of Iowa",
"orcid": "0000-0002-4892-2659"
},
{
"name": "Rokem, Ariel",
"affiliation": "eScience Institute, University of Washington",
"orcid": "0000-0003-0679-1985"
},
{
"name": "VanderPlas, Jake",
"affiliation": "eScience Institute, University of Washington",
"orcid": "0000-0002-9623-3401"
},
{
"name": "Holdgraf, Chris",
"affiliation": "Berkeley Institute for Data Science, University of California Berkeley",
"orcid": "0000-0002-9420-9301"
},
{
"name": "DeStasio, Krista",
"affiliation": "Social & Affective Neuroscience Laboratory, University of Oregon",
"orcid": "0000-0002-3959-9060"
},
{
"name": "Ludwig, Rita",
"affiliation": "Social & Affective Neuroscience Laboratory, University of Oregon"
},
{
"name": "Martin, Rebecca",
"affiliation": "Hartley Lab, New York University",
"orcid": "0000-0002-5482-1707"
},
{
"name": "Toro-Serey, Claudio",
"affiliation": "Cognition and Decision Lab, Boston University",
"orcid": "0000-0002-5273-2276"
},
{
"name": "Eschenburg, Kristian",
"affiliation": "Integrated Brain Imaging Center, University of Washington"
},
{
"name": "Erramuzpe, Asier",
"affiliation": "Computational Neuroimaging Lab, BioCruces Health Research Institute",
"orcid": "0000-0002-9402-2184"
},
{
"name": "Herholz, Peer",
"affiliation": "Montréal Neurological Institute",
"orcid": "0000-0002-9840-6257"
},
{
"name": "Blue, Brandon",
"affiliation": "BIL Consultant"
},
{
"name": "Whitaker, Kirstie",
"affiliation": "Research fellow, Turing Institute",
"orcid": "0000-0001-8498-4059"
},
{
"name": "Voss, Michelle",
"affiliation": "Health, Brain, and Cognition Lab, University of Iowa",
"orcid": "0000-0002-3706-7423"
}
],
"keywords": [
"neuroimaging",
"betaseries",
"analysis",
"fMRI",
"BIDS"
],
"license": "MIT",
"upload_type": "software"
}
102 changes: 69 additions & 33 deletions CHANGELOG.rst
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@@ -1,9 +1,45 @@
.. _changelog:

0.3.0 (August 29, 2019)
=======================

Thanks to @PeerHerholz and @njvack for their contributions on this release.
Special thanks to @snastase for being a great reviewer and improving the project
overall.
This release is special because it will be published in the
Journal of Open Source Software (JOSS).
One condition of this is that the authors on the paper be the only authors in the zenodo file.
I will modify the authors listed on the zenodo file for this release,
but I will add all contributors back on for the subsequent release.

* [ENH] reduce focus on parcellations (#179) @jdkent
* [FIX] generalized -> general linear model description (#178) @jdkent
* [DOC] Add math (#177) @jdkent
* [FIX] remove .git from the binder url (#175) @jdkent
* [FIX] add pypiwin32 as conditional dependency (#173) @jdkent
* [FIX] add readthedocs config file (#174) @jdkent
* [DOC] Minor changes to documentation text (#163) @snastase
* [MAINT] fix tagging/pushing docker images (#160) @jdkent
* [FIX] binder ci triggers (#159) @jdkent
* [ENH] add binder (#158) @jdkent
* [MAINT] Change Install Strategy (#157) @jdkent
* [DOC] Clarify Documentation (#156) @jdkent
* [FIX] Only hyphens for commandline parameters (#155) @jdkent
* [DOC] add concrete example of nibs (#154) @jdkent
* [DOC] add references (#153) @jdkent
* [MAINT] build docs on circleci (#152) @jdkent
* [MAINT] temporary fix to dockerfile (#150) @jdkent
* [MAINT] require python3 (#147) @jdkent
* [ENH] add visualizations (#148) @jdkent
* [ENH] Add Docker and Singularity Support (#140) @PeerHerholz
* [DOC] edit docs (#142) @jdkent
* [DOC] Tiny tweak to README (#141) @njvack
* [WIP] JOSS Paper (#122) @jdkent

0.2.3 (January 29, 2019)
========================

Various documentation and testing changes.
Various documentation and testing changes.
We will be using readthedocs going forward and not doctr.

* [FIX] Remove high_pass references from documentation (#90) @RaginSagan
Expand Down Expand Up @@ -48,7 +84,7 @@ my workflow for making releases.
* [FIX] connect derivative outputs (#61) @jdkent
* [FIX] add CODEOWNERS file (#63) @jdkent
* [FIX] Fix pull request template (#65) @kristianeschenburg
* [ENH]Update CONTRIBUTING.rst (#66) @PeerHerholz
* [ENH] Update CONTRIBUTING.rst (#66) @PeerHerholz
* [FIX] ignore sourcedata and derivatives directories in layout (#69) @jdkent
* [DOC] Added zenodo file (#70) @ctoroserey
* [FIX] file logic (#71) @jdkent
Expand All @@ -66,39 +102,39 @@ my workflow for making releases.
* [MGT] simplify and create deployment (#79)
* [TST] Add more tests (#78)
* [ENH] Reword docs (#77)
* [ENH]: allow confounds to be none (#76)
* various fixes for a real dataset (#75)
* [FIX]: Find metadata (#74)
* [ENH] allow confounds to be none (#76)
* [FIX] various fixes for a real dataset (#75)
* [FIX] Find metadata (#74)
* [FIX] confound removal (#72)
* [WIP, FIX]: file logic (#71)
* [WIP,FIX]: file logic (#71)
* [DOC] Added zenodo file (#70)
* [FIX]: ignore sourcedata and derivatives directories in layout (#69)
* Update CONTRIBUTING.rst (#66)
* Fix pull request template (#65)
* FIX: add CODEOWNERS file (#63)
* FIX: connect derivative outputs (#61)
* run versioneer install (#60)
* Fix issue #29: Add link to Zenodo DOI (#57)
* Fix issue #45: conform colors of labels (#56)
* fix links in readme.rst (#55)
* Added code of conduct (#53)
* Add link to contributing in README (#52)
* removed acknowledgments section of pull request template (#50)
* [TST]: Add functional test (#49)
* [FIX]: remove references to bootstrap (#48)
* FIX: test remove base .travis.yml (#47)
* removed data directory (#40)
* Add pull request template (#41)
* Update issue templates (#44)
* Update contributing (#43)
* README (where's the beef?) (#37)
* change jdkent to HBClab (#38)
* [FIX]: pass tests (#14)
* [ENH]: improve docs (#13)
* add documentation (#11)
* FIX: add graph (#10)
* Refactor NiBetaSeries (#9)
* Refactor (#2)
* [FIX] ignore sourcedata and derivatives directories in layout (#69)
* [DOC] Update CONTRIBUTING.rst (#66)
* [FIX] Fix pull request template (#65)
* [FIX] add CODEOWNERS file (#63)
* [FIX] connect derivative outputs (#61)
* [MAINT] run versioneer install (#60)
* [FIX] Fix issue #29: Add link to Zenodo DOI (#57)
* [FIX] Fix issue #45: conform colors of labels (#56)
* [DOC] fix links in readme.rst (#55)
* [DOC] Added code of conduct (#53)
* [DOC] Add link to contributing in README (#52)
* [DOC] removed acknowledgments section of pull request template (#50)
* [TST] Add functional test (#49)
* [FIX] remove references to bootstrap (#48)
* [FIX] test remove base .travis.yml (#47)
* [ENH] removed data directory (#40)
* [ENH] Add pull request template (#41)
* [ENH] Update issue templates (#44)
* [DOC] Update contributing (#43)
* [DOC] README (where's the beef?) (#37)
* [MAINT] change jdkent to HBClab (#38)
* [FIX] pass tests (#14)
* [ENH] improve docs (#13)
* [DOC] add documentation (#11)
* [FIX] add graph (#10)
* [ENH] Refactor NiBetaSeries (#9)
* [ENH] Refactor (#2)


0.1.0 (2018-06-08)
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