NeuroImaging PREProcessing toolS

All

60 repositories

niworkflows
Public
Common workflows for MRI (anatomical, functional, diffusion, etc)
Python
•
Apache License 2.0
•56•107•85•13•Updated Feb 22, 2026Feb 22, 2026
nibabies
Public
fMRIPrep Lifespan - A robust, transparent workflow tailored for neonate and infant MRI
neuroimaging fmri infant
Python
•
Apache License 2.0
•15•39•34•8•Updated Feb 19, 2026Feb 19, 2026
petprep
Public
PETPrep: A Robust Preprocessing Pipeline for PET Data
Jupyter Notebook
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Apache License 2.0
•13•20•26•13•Updated Feb 19, 2026Feb 19, 2026
smriprep
Public
Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)
image-processing mri surface-reconstruction image-segmentation image-registration structural-mri
Python
•
Apache License 2.0
•47•162•65•6•Updated Feb 18, 2026Feb 18, 2026
fmriprep-rodents
Public
fMRIPrep for Rodents
HTML
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Apache License 2.0
•7•13•11•2•Updated Feb 17, 2026Feb 17, 2026
nireports
Public
The NiPreps' Reporting and Visualization system - report templates and "reportlets"
visualization quality-control reporting neuroimaging brain-imaging qc nipreps
Python
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Apache License 2.0
•22•10•22•6•Updated Feb 16, 2026Feb 16, 2026
sdcflows
Public
Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes
magnetic-resonance-imaging echo-planar-imaging nonlinear-distortions image-artifacts
Python
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Apache License 2.0
•29•44•38•16•Updated Feb 16, 2026Feb 16, 2026
dmriprep
Public
dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensurin…
preprocessing bids diffusion-mri magnetic-resonance-imaging bids-apps
Python
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Apache License 2.0
•25•73•20•1•Updated Feb 14, 2026Feb 14, 2026
nifreeze
Public
A flexible framework for volume-wise artifact estimation and correction across multiple 4D neuroimaging modalities (diffusion MRI, functional MRI, and PET)
mri pet neuroimaging fmri preprocessing dwi brain-imaging magnetic-resonance-imaging positron-emission-tomography dmri
Python
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Apache License 2.0
•7•5•37•20•Updated Feb 13, 2026Feb 13, 2026
fmriprep
Public
fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensurin…
image-processing neuroimaging fmri bids brain-imaging fmri-preprocessing
HTML
•
Apache License 2.0
•310•717•322•15•Updated Feb 10, 2026Feb 10, 2026
mriqcwebapi
Public
Backend of the MRIQC Web API
Python
•
Apache License 2.0
•13•7•3•0•Updated Feb 2, 2026Feb 2, 2026
acres
Public
Resource-loading utility for Python
python resources
Python
•
Apache License 2.0
•1•0•0•0•Updated Feb 1, 2026Feb 1, 2026
fmripost-phase
Public
An attempt at an fMRIPost workflow for handling phase data
fmri fmriprep fmri-preprocessing
Python
•
Apache License 2.0
•1•3•10•4•Updated Feb 1, 2026Feb 1, 2026
fmripost-template
Public template
A generic fMRIPost workflow
Python
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Apache License 2.0
•4•0•6•4•Updated Feb 1, 2026Feb 1, 2026
fmripost-aroma
Public
Run ICA-AROMA on fMRIPrep derivatives
fmri fmriprep fmri-preprocessing
Python
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Apache License 2.0
•5•22•21•3•Updated Feb 1, 2026Feb 1, 2026
fmripost-rapidtide
Public
A BIDS App for running rapidtide on a preprocessed fMRI dataset.
fmri fmriprep fmri-preprocessing
Python
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Apache License 2.0
•1•4•13•4•Updated Feb 1, 2026Feb 1, 2026
mriqc
Public
Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
machine-learning quality-control mri quality-reporter neuroimaging
Python
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Apache License 2.0
•136•348•80•8•Updated Jan 28, 2026Jan 28, 2026
fmriprep_stats
Public
Automatic reports summarizing usage stats from Sentry.io
Jupyter Notebook
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Apache License 2.0
•1•5•0•0•Updated Jan 26, 2026Jan 26, 2026
nipreps.github.io
Public
The NiPreps landing page
Python
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Creative Commons Zero v1.0 Universal
•11•3•10•2•Updated Jan 23, 2026Jan 23, 2026
migas-server
Public
Python
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Apache License 2.0
•1•3•6•0•Updated Jan 23, 2026Jan 23, 2026
identity
Public
A repository of NiPreps identity files
Python
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Creative Commons Zero v1.0 Universal
•0•0•0•0•Updated Jan 3, 2026Jan 3, 2026
fmripost-tedana
Public
A BIDS App for the tedana workflow
Python
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MIT License
•5•3•11•3•Updated Jan 1, 2026Jan 1, 2026
niquery
Public
A principled tool to query open neuroimaging datasets, extract relevant information and create new datasets for research
graphql research mri pet neuroimaging fmri brain-imaging magnetic-resonance-imaging positron-emission-tomography openneuro
Python
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Apache License 2.0
•1•0•5•1•Updated Dec 30, 2025Dec 30, 2025
NORDIC_Raw
Public
Matlab code for performing image reconstruction in MRI and performing the NORDIC denoising
MATLAB
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Other
•26•0•0•0•Updated Dec 18, 2025Dec 18, 2025
version-schemes
Public
setuptools_scm plugin for nipreps version schemes
versioning setuptools-scm
Python
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Apache License 2.0
•0•2•0•1•Updated Dec 15, 2025Dec 15, 2025
presentations
Public
A common resource for talks, courses and presentations
CSS
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Creative Commons Zero v1.0 Universal
•0•0•0•0•Updated Dec 11, 2025Dec 11, 2025
skeleton
Public
A generic project skeleton for Python projects.
Python
•
Apache License 2.0
•37•1•0•0•Updated Dec 9, 2025Dec 9, 2025
nipreps-book
Public
Dockerfile
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Apache License 2.0
•7•8•0•0•Updated Nov 24, 2025Nov 24, 2025
speczeroplus
Public
SPEC0 + 1yr
Python
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BSD 3-Clause "New" or "Revised" License
•54•0•0•0•Updated Oct 21, 2025Oct 21, 2025
migas-py
Public
A ready-to-go python package for communicating with a migas server
Python
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Apache License 2.0
•2•5•4•0•Updated Oct 13, 2025Oct 13, 2025