Open Source Teaching & Projects

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Below you’ll find an overview (most likely not complete) of the open source projects I’m involved in. The section is divided into teaching related resources, projects I initiated or maintain and amazing projects I’m contributing to.

Teaching

Whenever I teach, I try my best to make all respective materials available online, free for everyone to use. Depending on the event at hand, this might be slides, jupyter notebooks, jupyter books or a combination thereof. Below are some of the resources I created for workshops and courses.

Workshops

I have been involved in a number of workshops, ranging from Introduction Python and Virtualization over Neuroimaging analyses to Machine Learning/Deep Learning in Cognitive Neuroscience and Reproducibility. Below are some of the resources I created for these workshops.

Clean and Reproducible Code for Machine & Deep Learning - NeuromatchJupyterBookcontributorssizeissuespulls
Reproducible Machine & Deep Learning - ReproNimJupyterBookcontributorssizeissuespulls
Introduction to Python for Open & Reproducible NeuroDataScience - NOWA SchoolJupyterBookcontributorsissuesmerge-requests 
Brain decoding - Machine & Deep Learning - MAINJupyterBookcontributorssizeissuespulls
Reproducible Neuroimaging - DGPAJupyterBookcontributorssizeissuespulls
Neuroimaging and NeuroDataScience - Weizmann Institute of ScienceJupyterBookcontributorssizeissuespulls
A primer on machine/deep learning with a focus on NeuroscienceJupyterBookcontributorssizeissuespulls
Brainhack 2020 showcasescontributorssizeissuespulls 
PyBraincontributorssizeissuespullsDocker Hub
Montreal Brainhack schoolcontributorssizeissuespulls 
Neuroimaging and NeuroDataScience - MarburgcontributorssizeissuespullsDocker Hub
Neuroimaging and NeuroDataScience - MagdeburgcontributorssizeissuespullsDocker Hub
Neuroimaging analyses in PythoncontributorssizeissuespullsDocker Hub
Introduction to & Visualization with Python)contributorssizeissuespulls 
Open and Reproducible Neuroscience using PythoncontributorssizeissuespullsDocker Hub

Courses

Besides workshops, I also teach/taught courses regarding the same topics at different universities . Below are some of the resources I created for these courses.

T32 Cognitive Brain Mapping Group: data & design workshopsJupyterBookcontributorssizeissuespulls
Cognitive and Computational Neuroscience - Machine & Deep learningJupyterBookcontributorssizeissuespulls
Python for PsychologistsJupyterBookcontributorssizeissuespulls
Practical lab course - introduction to research & cognitive neuroscienceJupyterBookcontributorssizeissuespulls
Methodological working in the neurosciencesJupyterBookcontributorssizeissuespulls
Foundations of Neuro Data ScienceJupyterBookcontributorssizeissuespulls

Core developer and/or maintainer

Developing and maintaining open-source software in the realm of NeuroDataScience is a big part of my daily work. Besides super interesting, it’s a great way to support the community and help everyone being less dependent on proprietary software. Below are some of the projects I initiated or maintain.

PeerHerholz/responsible_AI_resourcescontributorssizeissuespullsDocker Hub
C0C0AN/ConapcontributorssizeissuespullsDocker Hub
C0C0AN/ALPACAcontributorssizeissuespullsDocker Hub
C0C0AN/audiometry_mricontributorssizeissuespullsDocker Hub
BIDS-Apps/freesurfercontributorssizeissuespullsDocker Hub
PeerHerholz/BIDSonymcontributorssizeissuespullsDocker Hub
G0RELLA/gorella_overviewcontributorssizeissuespulls 

Contributor

In addition to developing and maintaining, I’m trying my best to contribute to other projects as well. Below are some of the projects I contributed to.

bids-standard/bids-specificationcontributorssizeissuespulls
bids-standard/bids-starter-kitcontributorssizeissuespulls
datalad-handbook/bookcontributorssizeissuespulls
MICA-MNI/micapipecontributorssizeissuespulls
MICA-MNI/BrainSpacecontributorssizeissuespulls
MICA-MNI/BrainStatcontributorssizeissuespulls
HBClab/NiBetaSeriescontributorssizeissuespulls
miykael/fmriflowscontributorssizeissuespulls
miykael/atlasreadercontributorssizeissuespulls
miykael/parcellation_fragmentercontributorssizeissuespulls
nilearn/nilearncontributorssizeissuespulls
ReproNim/repronim.github.iocontributorssizeissuespulls
PsychoinformaticsLab/plierscontributorssizeissuespulls
nipy/mindbogglecontributorssizeissuespulls
brainhackorg/brainhack_jupyter_bookcontributorssizeissuespulls
murraylab/brainsmashcontributorssizeissuespulls