Merge pull request #1 from Remi-Gau/remi-repro_research

some small tweaks on your pull request
learn-neuroimaging · Apr 8, 2020 · 7ab036d · 7ab036d
2 parents fb2054f + 684fa5c
commit 7ab036d
Showing 1 changed file with 55 additions and 26 deletions.
diff --git a/docs/reproducible_neuroimaging_research.md b/docs/reproducible_neuroimaging_research.md
@@ -1,25 +1,38 @@
 # Reproducible neuroimaging research
 
-## Reproducible neuroimaging tools   
 
-####Tools:   
+## Reproducible neuroimaging tools
+
+
+### Tools:   
 
 * [ReproNim](http://www.reproducibleimaging.org/index.html) - A Center for Reproducible Neuroimaging Computation (a good site to get up to date on doing reproducible neuroimaging research
 * [Code-ocean](https://codeocean.com/) - A research collaboration platform that uses docker containers to let you run your analysis online
-####Presentations:    
 
-* [Improving the Reproducibility of Neuroimaging Research](https://neurohackademy.org/course/improving-the-reproducibility-of-neuroimaging-research/) by Russ Poldrack within Neurohackweek 2016 (1 hr 23 min)
-* [GNU Make for Neuroimaging Workflows](https://neurohackademy.org/course/gnu-make-for-neuroimaging-workflows/) by Tara Madhyastha within Neurohackweek 2016 (48 min)
-* [Introduction to web technologies](https://neurohackademy.org/course/introduction-to-web-technologies/) by Anisha Keshavan within Neurohackademy 2018 (56 min)
-* [Neuroimaging pipelines](https://neurohackademy.org/course/neuroimaging-pipelines-2/) by Satra Ghosh within Neurohackweek 2017 (1 hr 33 min)
-* [Reproducibility in fMRI: What is the problem? 1](https://neurohackademy.org/course/reproducibility-in-fmri-what-is-the-problem-2/) by Russ Poldrack within Neurohackweek 2017 (1 hr 40 min)
-* [Same Data - Different Software - Different Results? Analytic Variability of Group fMRI Results](https://www.pathlms.com/ohbm/courses/8246/sections/12541/video_presentations/116000) by Alexander Bowring (12 mins)
-* [Software pipelines for reproducible neuroimaging](https://neurohackademy.org/course/software-pipelines-for-reproducible-neuroimaging/) by Satra Ghosh and Chris Gorgolewski within Neurohackademy 2016 (1 hr 14 min)
-* [Neuroimaging Workflows & Statistics for reproducibility](https://www.pathlms.com/ohbm/courses/8246/sections/12542/video_presentations/115885) by Dorota Jarecka, Satrajit Ghosh, Celia Greenwood and Jean-Baptiste Poline at OHBM (3 hr 45 min)
-* [Tools from the Center for Open Neuroscience](https://www.youtube.com/watch?v=RBaJn2Xtqzg&index=8&t=2278s&list=PLEE6ggCEJ0H0KOlMKx_PUVB_16VoCfGj9) by Yaroslav Halchenko within MIND 2018 (59 min)
 
+#### Presentations
+
+* [Improving the Reproducibility of Neuroimaging Research](https://neurohackademy.org/course/improving-the-reproducibility-of-neuroimaging-research/) by Russ Poldrack within Neurohackweek 2016
+    - duration: 1 hr 23 min
+* [GNU Make for Neuroimaging Workflows](https://neurohackademy.org/course/gnu-make-for-neuroimaging-workflows/) by Tara Madhyastha within Neurohackweek 2016
+    - duration: 48 min
+* [Introduction to web technologies](https://neurohackademy.org/course/introduction-to-web-technologies/) by Anisha Keshavan within Neurohackademy 2018
+    - duration: 56 min
+* [Neuroimaging pipelines](https://neurohackademy.org/course/neuroimaging-pipelines-2/) by Satra Ghosh within Neurohackweek 2017
+    - duration: 1 hr 33 min
+* [Reproducibility in fMRI: What is the problem? 1](https://neurohackademy.org/course/reproducibility-in-fmri-what-is-the-problem-2/) by Russ Poldrack within Neurohackweek 2017
+    - duration: 1 hr 40 min
+* [Same Data - Different Software - Different Results? Analytic Variability of Group fMRI Results](https://www.pathlms.com/ohbm/courses/8246/sections/12541/video_presentations/116000) by Alexander Bowring
+    - duration: 12 min
+* [Software pipelines for reproducible neuroimaging](https://neurohackademy.org/course/software-pipelines-for-reproducible-neuroimaging/) by Satra Ghosh and Chris Gorgolewski within Neurohackademy 2016
+    - duration: 1 hr 14 min
+* [Neuroimaging Workflows & Statistics for reproducibility](https://www.pathlms.com/ohbm/courses/8246/sections/12542/video_presentations/115885) by Dorota Jarecka, Satrajit Ghosh, Celia Greenwood and Jean-Baptiste Poline at OHBM
+    - duration: 3 hr 45 min
+* [Tools from the Center for Open Neuroscience](https://www.youtube.com/watch?v=RBaJn2Xtqzg&index=8&t=2278s&list=PLEE6ggCEJ0H0KOlMKx_PUVB_16VoCfGj9) by Yaroslav Halchenko within MIND 2018
+    - duration: 59 min
 
-####Tutorials/instructions/slides:    
+
+#### Tutorials/instructions/slides    
 
 * [Advance Unix and Make](https://neurohackademy.org/course/advance-unix-and-make/) by Valentina Staneva and Tara Madhyastha within Neurohackweek 2016
 * [CRN resources](https://neurohackademy.org/course/crn-resources/) by Chris Gorgolewski within Neurohackweek
@@ -29,14 +42,18 @@
 
 
 ## The Brain Imaging Data Structure (BIDS)
-* [The Brain Imaging Data Structure (BIDS)](https://neurohackademy.org/course/the-brain-imaging-data-structure-bids/) presented by Chris Gorgolewski within Neurohackademy 2018 (56 min)
+
+* [The Brain Imaging Data Structure (BIDS)](https://neurohackademy.org/course/the-brain-imaging-data-structure-bids/) presented by Chris Gorgolewski within Neurohackademy 2018
+    - duration: 56 min
 * [BIDS website](http://bids.neuroimaging.io/) - A simple and intuitive way to organize and describe your neuroimaging and behavioral data
 * [BIDS apps](https://bids-apps.neuroimaging.io/apps/) - Portable neuroimaging pipelines that understand BIDS datasets
 * [BIDS starter kit](https://github.com/bids-standard/bids-starter-kit) - Collection of tutorials, wikis, and templates to get you started with creating BIDS compliant datasets
 
 
 ## Open-data platforms
-####Platforms to get data from:   
+
+
+### Platforms to get data from   
 
 * [OpenNeuro](https://openneuro.org/) - A free and open platform for sharing MRI, MEG, EEG, iEEG, and ECoG data
 * [INDI](http://fcon_1000.projects.nitrc.org/) - International Neuroimaging Data-Sharing Initiative for rawdata
@@ -48,26 +65,38 @@
 * [Wikipedia](https://en.wikipedia.org/wiki/List_of_neuroscience_databases) - Wikipedia list of neuroscience databases
 * [ElectrophysiologyData](https://github.com/voytekresearch/OpenData) - Open datasets in electrophysiology
 
-####Presentations:   
 
-* [Allen Institute Data and Software](https://neurohackademy.org/course/allen-institute-data-and-software/) by Nicolas Cain within Neurohackweek 2017 (53 min)
-* [Allen Institute Datasets](https://neurohackademy.org/course/allen-institute-datasets/) by Terri Gilbert within Neurohackweek 2016 (1 hr 8min)
-* [Allen Institute RNAseq data](https://neurohackademy.org/course/allen-institute-rnaseq-data/) by Jeremy Miller within Neurohackweek 2016 (52 min)
-* [AllenSDK and the Allen Brain Observatory](https://neurohackademy.org/course/allensdk-and-the-allen-brain-observatory/) by Nicolas Cain and Justin Kiggins within Neurohackademy 2018 (1 hr 42 min)
-* [Integrating Allen Institute Datasets with MRI data](https://neurohackademy.org/course/integrating-allen-institute-datasets-with-mri-data/) by Kirstie Whitaker within Neurohackweek 2016 (28 min)
+#### Presentations   
+
+* [Allen Institute Data and Software](https://neurohackademy.org/course/allen-institute-data-and-software/) by Nicolas Cain within Neurohackweek 2017
+    - duration: 53 min
+* [Allen Institute Datasets](https://neurohackademy.org/course/allen-institute-datasets/) by Terri Gilbert within Neurohackweek 2016
+    - duration: 1 hr 8 min
+* [Allen Institute RNAseq data](https://neurohackademy.org/course/allen-institute-rnaseq-data/) by Jeremy Miller within Neurohackweek 2016
+    - duration: 52 min
+* [AllenSDK and the Allen Brain Observatory](https://neurohackademy.org/course/allensdk-and-the-allen-brain-observatory/) by Nicolas Cain and Justin Kiggins within Neurohackademy 2018
+    - duration: 1 hr 42 min
+* [Integrating Allen Institute Datasets with MRI data](https://neurohackademy.org/course/integrating-allen-institute-datasets-with-mri-data/) by Kirstie Whitaker within Neurohackweek 2016
+    - duration: 28 min
 
-####Other:    
+#### Other    
 
 * [Challenges to open data and how to respond](https://github.com/mozillascience/open-data-training/blob/master/Materials/Handouts/ODChallengesQI.md)
 
 
 ## Other tools for reproducible data-science
-* [From interactive exploration to reproducible data science: Jupyter, Binder, Travis and friends.](https://neurohackademy.org/course/from-interactive-exploration-to-reproducible-data-science-jupyter-binder-travis-and-friends/) by Fernando Perez within Neurohackademy 2018 (1 hr 25 min)
-* [Jupyter tutorial](https://www.youtube.com/watch?v=CSkTJRNBTME&index=3&t=4s&list=PLEE6ggCEJ0H0KOlMKx_PUVB_16VoCfGj9) by Eshin Jolly within MIND 2018 (31 min)
+
+* [From interactive exploration to reproducible data science: Jupyter, Binder, Travis and friends.](https://neurohackademy.org/course/from-interactive-exploration-to-reproducible-data-science-jupyter-binder-travis-and-friends/) by Fernando Perez within Neurohackademy 2018
+    - duration: 1 hr 25 min
+* [Jupyter tutorial](https://www.youtube.com/watch?v=CSkTJRNBTME&index=3&t=4s&list=PLEE6ggCEJ0H0KOlMKx_PUVB_16VoCfGj9) by Eshin Jolly within MIND 2018
+    - duration: 31 min
 
 
 ## Containers
-* [Docker for scientists 1](https://neurohackademy.org/course/docker-for-scientists/) by Chris Gorgolewski within Neurohackweek 2016 (1 hr 13min)
+
+* [Docker for scientists 1](https://neurohackademy.org/course/docker-for-scientists/) by Chris Gorgolewski within Neurohackweek 2016
+    - duration: 1 hr 13 min
 * [Docker for scientists 2](https://neurohackademy.org/course/docker/) by Chris Gorgolewski within Neurohackweek
-* [Docker tutorial](https://www.youtube.com/watch?v=hUvYdXo5MfU&index=17&t=0s&list=PLEE6ggCEJ0H0KOlMKx_PUVB_16VoCfGj9) by Lucy Owen within MIND 2018 (20 min)
+* [Docker tutorial](https://www.youtube.com/watch?v=hUvYdXo5MfU&index=17&t=0s&list=PLEE6ggCEJ0H0KOlMKx_PUVB_16VoCfGj9) by Lucy Owen within MIND 2018
+    - duration: 20 min
 * [Neurodocker](https://github.com/kaczmarj/neurodocker) allows you to easily create containers suited to your neuroimaging needs. Here is a [tutorial](https://miykael.github.io/nipype_tutorial/notebooks/introduction_neurodocker.html) on how to use it.