NeuroImaging PREProcessing toolS

All

59 repositories

niworkflows
Public
Common workflows for MRI (anatomical, functional, diffusion, etc)
Python
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Apache License 2.0
•54•106•79•10•Updated Dec 1, 2025Dec 1, 2025
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•3•Updated Dec 1, 2025Dec 1, 2025
petprep
Public
PETPrep: A Robust Preprocessing Pipeline for PET Data
Jupyter Notebook
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Apache License 2.0
•13•17•18•11•Updated Nov 30, 2025Nov 30, 2025
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
•5•5•39•22•Updated Nov 29, 2025Nov 29, 2025
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 ensuring the reproducibility of the results.
image-processing neuroimaging fmri bids brain-imaging fmri-preprocessing
HTML
•
Apache License 2.0
•308•701•307•8•Updated Nov 26, 2025Nov 26, 2025
smriprep
Public
Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)
image-processing mri surface-reconstruction image-segmentation image-registration structural-mri
Python
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Apache License 2.0
•47•156•63•7•Updated Nov 24, 2025Nov 24, 2025
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
•20•10•20•7•Updated Nov 24, 2025Nov 24, 2025
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
•28•43•36•9•Updated Nov 24, 2025Nov 24, 2025
nipreps-book
Public
Dockerfile
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Apache License 2.0
•7•8•0•0•Updated Nov 24, 2025Nov 24, 2025
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
•134•341•80•13•Updated Nov 24, 2025Nov 24, 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•0•Updated Nov 24, 2025Nov 24, 2025
fmriprep_stats
Public
Automatic reports summarizing usage stats from Sentry.io
Jupyter Notebook
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Apache License 2.0
•1•4•0•3•Updated Nov 18, 2025Nov 18, 2025
nipreps.github.io
Public
The NiPreps landing page
Python
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Creative Commons Zero v1.0 Universal
•11•3•10•2•Updated Nov 17, 2025Nov 17, 2025
identity
Public
A repository of NiPreps identity files
Python
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Creative Commons Zero v1.0 Universal
•0•0•0•0•Updated Nov 10, 2025Nov 10, 2025
acres
Public
Resource-loading utility for Python
python resources
Python
•
Apache License 2.0
•1•0•1•0•Updated Nov 3, 2025Nov 3, 2025
fmripost-aroma
Public
Run ICA-AROMA on fMRIPrep derivatives
fmri fmriprep fmri-preprocessing
Python
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Apache License 2.0
•4•21•21•5•Updated Nov 1, 2025Nov 1, 2025
skeleton
Public
A generic project skeleton for Python projects.
Python
•
Apache License 2.0
•37•1•0•0•Updated Oct 28, 2025Oct 28, 2025
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 ensuring the reproducibility of the results.
preprocessing bids diffusion-mri magnetic-resonance-imaging bids-apps
Python
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Apache License 2.0
•25•73•18•0•Updated Oct 27, 2025Oct 27, 2025
nibabies
Public
fMRIPrep Lifespan - A robust, transparent workflow tailored for neonate and infant MRI
neuroimaging fmri infant
Python
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Apache License 2.0
•14•36•33•1•Updated Oct 22, 2025Oct 22, 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
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 Oct 14, 2025Oct 14, 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•4•4•0•Updated Oct 13, 2025Oct 13, 2025
presentations
Public
A common resource for talks, courses and presentations
CSS
•
Creative Commons Zero v1.0 Universal
•0•0•0•0•Updated Oct 9, 2025Oct 9, 2025
fmripost-phase
Public
An attempt at an fMRIPost workflow for handling phase data
fmri fmriprep fmri-preprocessing
Python
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Apache License 2.0
•1•3•10•3•Updated Oct 1, 2025Oct 1, 2025
fmripost-template
Public template
A generic fMRIPost workflow
Python
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Apache License 2.0
•4•0•6•5•Updated Oct 1, 2025Oct 1, 2025
fmripost-resample
Public
Python
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Apache License 2.0
•1•0•0•2•Updated Oct 1, 2025Oct 1, 2025
fmripost-tedana
Public
A BIDS App for the tedana workflow
Python
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MIT License
•5•3•11•3•Updated Oct 1, 2025Oct 1, 2025
Cookiecutter
Public template
Template for NiPreps repositories
Apache License 2.0
•1•0•4•0•Updated Sep 16, 2025Sep 16, 2025
migas-server
Public
Python
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Apache License 2.0
•1•3•6•0•Updated Jul 17, 2025Jul 17, 2025
qkay
Public
Manager for the quality assessment of large neuroimaging studies
HTML
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Apache License 2.0
•3•5•11•7•Updated Jul 15, 2025Jul 15, 2025