nipreps / fmriprep
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.
nipreps / fmriprep
mne-tools / mne-python
MNE: Magnetoencephalography (MEG) and Electroencephalography (EEG) in Python
Slicer / Slicer
Multi-platform, free open source software for visualization and image computing.
ANTsX / ANTs
Advanced Normalization Tools (ANTs)
nilearn / nilearn
Machine learning for NeuroImaging in Python
braindecode / braindecode
Deep learning software to decode EEG, ECG or MEG signals
rordenlab / dcm2niix
dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC
fieldtrip / fieldtrip
The MATLAB toolbox for MEG, EEG and iEEG analysis
ANTsX / ANTsPy
A fast medical imaging analysis library in Python with algorithms for registration, segmentation, and more.
freesurfer / freesurfer
Neuroimaging analysis and visualization suite
dipy / dipy
DIPY is the paragon 3D/4D+ medical imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.
nipy / nipype
Workflows and interfaces for neuroimaging packages
nipy / nibabel
Python package to access a cacophony of neuro-imaging file formats
gallantlab / pycortex
Pycortex is a python-based toolkit for surface visualization of fMRI data
ruoyuw22-byte / NeuroMorph-Assessment
An automated structural MRI morphometry system integrating CAT12 processing, brain tissue quantification, visualization, and automated report generation.
KeWang0622 / MRFoundry
MRI research guidance for coding agents — composable skills, established tools, and evidence-linked research memory. Install: npx skills add KeWang0622/MRFoundry