Amazon FSx : AWS Launch, run, and scale feature-rich and highly-performant file systems with just a few clicks
ANCP-bids : A Python package to read/write/query/validate BIDS datasets. Lighter weight than PyBids.
Apptainer : Apptainer/Singularity is the most widely used container system for HPC. It is designed to execute applications at bare-metal performance while being secure, portable, and 100% reproducible. Apptainer is an open-source project with a friendly community of developers and users. The user base continues to expand, with Apptainer/Singularity now used across industry and academia in many areas of work.
BEP : BIDS Enhancement Proposal
BIDS : Brain Imaging Data Structure
BIDS-schema : Prospective repository of BIDS schema versions. For now, use current source of truth
BOLD MRI : Blood Oxygen Level Dependent MRI -- basis of most fMRI
BossDB : Brain Observatory Storage Service & Database
Brain Hack : Collaborative workshops, hackathons, etc
CalVer : Versioning based on the date
ChRIS : ChRIS is a fully-open source distributed data and computation platform.
CON : Center for Open Neuroscience
con/tinuous : is a command for downloading build logs and (for GitHub only) artifacts & release assets for a GitHub repository from GitHub Actions, Travis-CI.com, and/or Appveyor.
con/catinate : This doc!
COS : Unaffiliated but friendly, the Center for Open Science and their flagship the Open Science Framework
DataLad : Allows distributed data management under a single interface (git), uses git-annex under the hood.
DANDI : Distributed Archives for Neurophysiology Data Integration
DICOM : Digital Imaging and Communications in Medicine : Primarily for clinical use, does not include research-friendly metadata
Docker : brand name for container platform as a service(PaaS)
DueCredit : Makes it easy to cite code you used. It embeds publication or other references in the original code so they are automatically collected and reported to the user at the necessary level of reference detail for citation.
FAIR : Findable, Accessible, Interoperable, Reproducible
FastSurfer : FastSurfer - a fast and accurate deep-learning based neuroimaging pipeline
fMRI : Functional MRI -- MRI hoping to reflect functioning of the brain, not only anatomy, and typically acquired multiple brain volumes through time to see the change in the signal.
fMRI Prep : NiPreps application for the preprocessing of task-based and resting-state functional MRI (fMRI).
git-annex : git-annex allows managing large files with git, without storing the file contents in git. It can sync, backup, and archive your data, offline and online. Checksums and encryption keep your data safe and secure. Bring the power and distributed nature of git to bear on your large files with git-annex. Used under the hood by DataLad
HeudiConv : heudiconv is a flexible DICOM converter for organizing brain imaging data into structured directory layouts.FastSurfer - a fast and accurate deep-learning based neuroimaging pipeline
jq : filter and pretty print json
Jupyter : Python notebooks (formerly iPython Notebook)
Kubernetes : Container orchestrator
Minder : Mind mapper tool. Used to produce e.g. DataLad standards mindmap
MOC : Mass Open Cloud
NERC : New England Research Cloud
Niceman : now called reproman
NifTI : Neuroimaging Informatics Technology Initiative
NiPreps : (NeuroImaging PREProcessing toolS) application
NWB : Neurodata Without Borders (NWB) is a data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build analysis tools for neurophysiology data. NWB is designed to store a variety of neurophysiology data, including data from intracellular and extracellular electrophysiology experiments, data from optical physiology experiments, and tracking and stimulus data.
NeuroScout : A platform for fast and flexible re-analysis of (naturalistic) fMRI studies
NeuroSynth : Neurosynth is a platform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data. It takes thousands of published articles reporting the results of fMRI studies, chews on them for a bit, and then spits out images that look like this:
Open Brain Consent : Helps make consent forms easier, and easier to share data.
Open Neuro : A free and open platform for validating and sharing BIDS-compliant MRI, PET, MEG, EEG, and iEEG data.
Open Neuroscience : We are a user-driven database of open neuroscience projects. All should be here, add them if they aren't.
Orthanc : Open-source, lightweight DICOM servhttps://www.repronim.org/5stepser
PACS : picture archiving and communication system
Pelican : static site generator (used by CON website)
PBS : 1. Portable Batch System : 2. Psychology and Brain Science @ Dartmouth
Polars : Lightning-fast DataFrame library for Rust and Python
PyBIDs : Python tools for querying and manipulating BIDS datasets.
Pylabber : "XNAT reimplemented in Django" ((C) Chris) ;)
PyMVPA : PyMVPA is a Python package intended to ease statistical learning analyses of large datasets. It offers an extensible framework with a high-level interface to a broad range of algorithms for classification, regression, feature selection, data import and export. It is designed to integrate well with related software packages, such as scikit-learn, shogun, MDP, etc. While it is not limited to the neuroimaging domain, it is eminently suited for such datasets. (Pioneering in machine learning analytics in neuroimaging in 2007-2016, currently not actively developed)
NeuroDebian : NeuroDebian is a distribution of popular neuroscience research software for Debian (and derivatives)
RN/ReproMan : creation and management of computing environments (in Neuroimaging)?
RN/containers : with a collection of popular neuroscience computational tools provided within ready to use containerized environmentshttps://github.com/CenterForOpenScience/modular-file-renderer
RN/reproin : Its goal is to provide a turnkey flexible setup for automatic generation of shareable, version-controlled BIDS datasets from MR scanners. Provides heuristic for HeudiConv and convention for naming exam cards and sequences in the MRI scanner.
RN/reprostim : ReproStim is a video capture and recording suite for neuroimaging and psychology experiments. Its goal is to provide experimenters with a complete record of audio and visual stimulation for every data collection session by making it possible to easily collect high fidelity copies of the actual stimuli shown to each subject in the form of video files that can be stored alongside behavioral or neuroimaging data in public repositories.
RN/neurodocker : Neurodocker is a command-line proghttps://www.repronim.org/5stepsram that generates custom Dockerfiles and Singularity recipes for neuroimaging and minifies existing containers. Its purpose is to make it easier for scientists (and others) to easily create reproducible computational environments.
RN/ReproLake : Cloud storage of metadata about studies and analyses
RN/ReproPond : Local storage of metadata
ReproPub : Publish ReproPond to ReproLake
SemVer : Semantic Versioning
[Singularity] : See Apptainer
SLURM : Simple Linux Utility for Resource Management
TR&D : Technology Research and Development Programs
YODA : YODA's Organigram on Data Analysis : poster : Best practice(s) for organizing and managing digital objects of science
