PyPulseq
PyPulseq: A Python Package for MRI Pulse Sequence Design - Published in JOSS (2019)
Virtual Scanner
Virtual Scanner: MRI on a Browser - Published in JOSS (2019)
Brainchop
Brainchop: In-browser MRI volumetric segmentation and rendering - Published in JOSS (2023)
mrivis
mrivis: Medical image visualization library for neuroscience in python - Published in JOSS (2018)
MRdataset
MRdataset : A unified and user-friendly interface to medical imaging datasets - Published in JOSS (2024)
tacmagic
tacmagic: Positron emission tomography analysis in R - Published in JOSS (2019)
FijiRelax
FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t - Published in JOSS (2023)
fsbrain
R library for structural neuroimaging. Provides high-level functions to access (read and write) and visualize surface-based brain morphometry data for individuals and groups.
mriqc
Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
KomaMRI
Koma is a Pulseq-compatible framework to efficiently simulate Magnetic Resonance Imaging (MRI) acquisitions. The main focus of this package is to simulate general scenarios that could arise in pulse sequence development.
freesurferformats
GNU R package for reading and writing neuroimaging file formats. Not limited to FreeSurfer anymore, despite its name.
pymialsrtk
The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ and Python processing and workflow tools necessary to perform motion-robust super-resolution fetal MRI reconstruction in the BIDS Apps framework.
smriprep
Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)
csg_mri_pipelines
MRI preprocessing and analysis pipelines and tools for the study of disorders of consciousness
https://github.com/bids-apps/freesurfer
BIDS app wrapping recon-all from FreeSurfer
https://github.com/lren-chuv/airflow-imaging-plugins
Set of plugins helping to work with imaging data in Airflow.
https://github.com/ottaviadipasquale/react-fmri
REACT: Receptor-Enriched Analysis of functional Connectivity by Targets
https://github.com/bids-apps/mrtrix3_connectome
Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalisation, using the MRtrix3 software package.
https://github.com/agahkarakuzu/sunrise
NumPy, SciPy, MRI and Music | Presented at ISMRM 2021 Sunrise Educational Session
https://github.com/brainlesion/preprocessing
preprocessing tools for multi-modal 3D brain imaging
https://github.com/brainlesion/deep_quality_estimation
Quality estimation for BraTS glioma segmentation models
pituitary-segmentation-tool
This repository contains code that normalizes head MRIs segments the pituitary gland.
nifreeze
A flexible framework for volume-wise artifact estimation and correction across multiple 4D neuroimaging modalities (diffusion MRI, functional MRI, and PET)
3DQLayers
3DQLayers: Volumetric Layer Based Analysis for Quantitative Renal MRI - Published in JOSS (2025)
GIRFReco.jl
GIRFReco.jl: An Open-Source Pipeline for Spiral Magnetic Resonance Image (MRI) Reconstruction in Julia - Published in JOSS (2024)
qMRLab
qMRLab: Quantitative MRI analysis, under one umbrella - Published in JOSS (2020)
model_seg_mouse-sc_wm-gm_t1
White and grey matter segmentation on T1-weighted exvivo mouse spinal cord
eCobidas
Working repository to turn the COBIDAS guidelines to report methods and results in neuroimaging into a user friendly checklist
prolesa-net-a-multi-channel-3d-architecture-for-prostate-mr-lesion-segmentation-with-multi-scale-ch
ProLesA-Net: a Deep learning model For Prostate Lesion Segmentation from bi-parametric MR-Images
https://github.com/beatawereszczynska/t1wir_to_t1wsr
Simulating T1-weighted saturation recovery MRI images for arbitrary values of TR from a set of T1-weighted inversion recovery MRI images. (Python 3)
https://github.com/bids-apps/hcppipelines
A BIDS App for minimal preprocessing using the HCP Pipelines
https://github.com/cpp-lln-lab/fmri_workshop_201911
Slides and Practicals material for the workshop run by the CPP lab in UCLouvain in 2019
mri-education-resources
Resources for learning the principles of magnetic resonance imaging (MRI)
https://github.com/agahkarakuzu/bids2nf
Emits nextflow channels from Brain Imaging Data Structure data.
breastdcedl
BreastDCEDL Pretreatment MRI scans of 2070 Breast cancer patients. A Deep Learning-Ready DCE-MRI Breast Cancer Dataset from I-SPY2 and I-SPY1 trials (1,2 and DUKE.
aladdin_cmr_la
Source code for Aladdin, a complete workflow for 3D MRI left atrium motion analysis
dl-direct
DL+DiReCT - Direct Cortical Thickness Estimation using Deep Learning-based Anatomy Segmentation and Cortex Parcellation
https://github.com/beatawereszczynska/tiandte_wish
Calculating theoretical MRI images with both TI (T1-weighting) and TE (T2-weighting) of choice, from separate T1-weighted and T2-weighted sets of images. (Python 3)
https://github.com/beatawereszczynska/ti_te_wish
Simulating T1- and T2-weighted MRI images with arbitrary values of TI or TE, respectively. (Python 3)
https://github.com/bids-apps/brainsuite
BrainSuite's structural, diffusion, and functional MRI processing pipelines with QC functionalities.
https://github.com/bids-apps/oppni
runs fast optimization of preprocessing pipelines for BOLD fMRI
https://github.com/bids-apps/mindboggle
Improve the accuracy, precision, and consistency of automated labeling and shape analysis of human brain image data
compresso
Compresso: Efficient Compression of Segmentation Data For Connectomics
https://github.com/bids-apps/afni_proc
prototype AFNI bids app implmenting participant level preprocessing with afni_proc.py
https://github.com/brainlesion/aurora
Segmentation models for cancer metastasis in brain MR
mri_k-space-derived_details_edges
k-space based details/edges detection in MRI images with optional k-space based denoising and detail control (on the example of Agilent FID data). (Python 3)
MRI-NUFFT
MRI-NUFFT: Doing non-Cartesian MRI has never been easier - Published in JOSS (2025)
https://github.com/john-veillette/niseq
group sequential tests for neuroimaging
https://github.com/abel-research/openlimbtt
An Open-Source, synthetic transtibial residual limb anatomic dataset
https://github.com/agahkarakuzu/rrsg2020-dashboard
Dashboard for ISMRM RRSG 2020 Challenge, powered by Plotly-Dash, deployed to Heroku via GH-Actions.
https://github.com/brainlesion/modsort
manual sorting GUI for identifying MR sequences
https://github.com/cbica/nichart
The neuro-imaging brain aging chart [niCHART] is a comprehensive solution to analyze standard structural and functional brain MRI data across studies. [niCHART] and the associated pre-processing tools implement computational morphometry, functional signal analysis, quality control, statistical harmonization, data standardization, interactive visual
https://github.com/bids-apps/cpac
BIDS Application for the Configurable Pipeline for the Analysis of Connectomes (C-PAC)
swelling_tablet_fronts_d_k_from_mri_t2_or_img
Tool for calculating swelling tablet eroding front's diffusion rate D and the rate of the swelling k from time series of either T2-maps or MRI images in FDF or Text Image format. (Python 3)
https://github.com/0rc0/neuromet_mp2rage_pypes
Pipelines for structural analysis for NeuroMet Project
k-space_wght_msk_for_mri_denoising
k-space weighting and masking for denoising of MRI image without blurring or losing contrast, as well as for brightening of the objects in the image with simultaneous noise reduction (on the example of Agilent FID data). (Python 3)
https://github.com/abtinmy/clustered-fl-brainage
Official implementation of paper "Brain Age Estimation Using Structural MRI: A Clustered Federated Learning Approach"
https://github.com/aa14av/ufab-587
University of Florida Aging Brain Template of 587 Older Adult T1w Images
superres-mri
Portable, modular, reusable, and reproducible processing pipeline software for fetal brain MRI super-resolution
https://github.com/aswendt-lab/aidaqc
An automated and simple tool for fast quality analysis of animal MRI
https://github.com/control-toolbox/medicalresonanceimaging.jl
Optimal control in Medical Resonance Imaging by Nuclear Magnetic Resonance
deepinv
DeepInverse: a PyTorch library for solving imaging inverse problems using deep learning
https://github.com/brainlesion/stroke_segmentor
stroke segmentation in MRI data
https://github.com/beatawereszczynska/k-space_masking_for_mri_denoising
Graduate k-space masking for MRI image denoising and blurring (on the example of Agilent FID data). (Python 3)
https://github.com/antsx/antsr
R interface to the ANTs biomedical image processing library
