ReproNim's Repositories

abcd-apps from BrainLife -- just a DataLad superdataset to catalog them all

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Working with a dockerfile setup for antspy

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ants_seg_to_nidm

ANTS-based structural segmentation exporter to NIDM

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Some artwork (logos etc)

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babs-demo-ohbm2025

A demo for OHBM 2025 educational course on BABS

⭐ 3 🌐 Public

brainhack_ohbm18

materials for ReproNim part of TrainTrack

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BrainVerse is an electronic laboratory notebook built as an open-source, cross-platform desktop application to help researchers manage, track and share information in a comprehensive format.

⭐ 29 🌐 Public

carmin-cmdline-demo

A demo for CARMIN API if implemented for cmdline in bash (just a prototype ATM)

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coco2019-training

Training materials for the ReproNim day at https://coastal-coding.github.io

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Containers "distribution" for reproducible neuroimaging

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containers-artwork

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Playground for scripts to ease working with NDA via DataLad

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an example protocol which serves as default protocol in schema-ui

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DGPA_workshop_2022

The repository for the ReproNim "Reproducible Neuroimaging" workshop, organized and conducted for the DGPA in spring 2022.

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ds000003-bids2nda-demo

Demo case on: bids2nda on part of dataset, datalad run/rerun, etc

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Fork of the original OpenNeuro dataset, in order to make proper BIDS for the ReproNim/OHBM 2022 Educational course.

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FAIR_neuroimaging_with_NIDM

FAIR neuroimaging with the Neuroimaging Data Model and PyNIDM

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fsl_seg_to_nidm

Converts structural segmentation outputs from FSL's FIRST and FAST tool to NIDM

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Docker images for GraphDB 8

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hbcd-loris2reproschema

HBCD LORIS format to ReproSchema format

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hbcd-redcap2rs_old

this repo is archived, please go to https://github.com/ReproNim/hbcd-redcap2rs for the most updated information

⭐ 0 🌐 Public 📦 Archived

how-would-repronim-1

Companion notebook for "How would ReproNim" Volume 1

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how-would-repronim-4

Companion notebook to "How would ReproNim" Volume 4

⭐ 1 🌐 Public

HowWouldReproNim

Sphinx for rendering the "How Would ReproNim Do That?" series of documents

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NIDMification of kwyk output

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OpenNeuroLab MetaSearch App

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module-dataprocessing

A module for reproducible data processing

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module-FAIR-data

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Module i: An Introduction to Reproducible Neuroimaging training module

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module-reproducible-basics

Module 0: Reproducible Basics

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The statistics for reproducible neuroimaging

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module-template

A template for ReproNim teaching modules

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Generate custom Docker and Singularity images, and minimize existing containers

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nobrainer-benchmarkit

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ohbm2018-training

⭐ 3 🌐 Public 📦 Archived

OHBMEducation-2022

Repo for the OHBM Education 1/2 day course entitled: "How to Write a Re-Executable Publication"

⭐ 3 🌐 Public

openneuro-tools

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OpenNeuroDerivatives-NIDM

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openneurolab-metasearch-dataset

DataLad (git-annex) dataset containing neuroimaging data used by https://github.com/OpenNeuroLab/metasearch

⭐ 1 🌐 Public

probable-journey

Interactive agents for science

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promo_materials

Repo for promotional materials

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reproducible-imaging

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Materials for ReproFlow: ReproNim tools to establish scalable and automated MRI and behavioral data acquisition and QC

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reproflow-data-sync

DataLad dataset with all samples of recorded "ReproEvents", "ReproStim", etc data for purpose of calibration and establishing processing

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Infrastructure and code for the ReproNim ReproHub JupyterHub effort. Forked from ABCD-ReproNim/reprohub which was forked from dandihub

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A setup for automatic generation of shareable, version-controlled BIDS datasets from MR scanners

⭐ 49 🌐 Public

reproin-publications

Poster and publications for ReproIn

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A repo for developing the ReproNim inventory of training resources.

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Centralization of the issues discovered with reprolake prototypes etc

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reprolib-server

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ReproMan (AKA NICEMAN, AKA ReproNim TRD3)

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Container images for ReproMan & slurm CI

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A service to monitor data acquisition etc to alert if anything goes wrong

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repronim.github.io

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WiP for a replacement website

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Date-based snapshotting of PyPI

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A standardized form generation and data collection schema to harmonize results by design across projects.

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reproschema-agents

multi-agent framework for reproschema

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reproschema-backend

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reproschema-builder

a javascript library to build reproschema activity-set and corresponding activities

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reproschema-demo

A demo for the reproschema paper

⭐ 0 🌐 Public 📦 Archived

reproschema-demo-protocol

A demo protocol for the ReproSchema paper

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reproschema-diff

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reproschema-library

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reproschema-protocol-cookiecutter

A cookiecutter for reproschema protocols.

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reproschema-server

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UI to render ReproSchema based protocols and assessments.

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reproschema2cde

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A POSIX shell script to assist in guaranteeing reproducible non-deterministic computation(s)

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Shell (bash only ATM) configuration to facilitate reproducible research

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Automated capture of audio-visual stimuli into BIDS datasets

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reprostim-sessions

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A location to hold potential RerpNim How would you solve simple things ideas and drafts. Perhaps they will graduate into the official ReproNim How Would document...

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Collection (git-annex/DataLad dataset) of educational videos

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ReproZip is a tool that simplifies the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science.

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schema.repronim.org

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segstats_jsonld

Script to Export Freesurfer-based Parcellation/Segmentation Stats and Provenance as JSON-LD and NIDM

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An ABCD-ReproNim project to prototype methods and procedures for handling (restricted) ABCD data using NIDM to create a ReproPond that can be integrated with similar data from other sources. We will use the Child Behavior Checklist (CBCL) as a test case, but the results should be generalizable to any NDA-hosted data schema.

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sfn2018-training

Materials for SfN 2018 training event

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simple2_NIDM_examples

ReproNim simple2 NIDM files for ABIDE/ADHD200 available from datalad

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The ultra-simple ReproNim simple tutorial.

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simple_workflow

A very simple, re-executable neuroimaging publication (code)

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simple_workflow-02

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SOBPHack-042025

Website for SOBP BrainHack - 2025

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SOBPHack-052024

Website for SOBP BrainHack - 2024

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Repo for the process of adding "stuff" (ie the results of fmriprep, etc. processing) to the NIDM graph.

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SumarizeFmriprep

A script to generate a session summary from a fmriprep* (fmriprep-babies, nibabies, fmriprep, etc.) analysis

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a mix of instructions and scripts to try BABS using slurm in a container (podman)

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test-hpc-cluster

[UNDER CONSTRUCTION] Setup(s) to spin off HPC clusters playgrounds for testing.

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Generalized regression testing of scientific workflows

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