Fmri Python Packages

nilearn

Machine learning for NeuroImaging in Python

hedtools

Python validation, summary, and analysis tools for HED (Hierarchical Event Descriptors).

tedana

TE-dependent analysis of multi-echo fMRI

junifer

Forschungszentrum Jülich Neuroimaging Feature Extractor

neurocaps

A Python package for performing Co-Activation Patterns (CAPs) analyses on resting-state and task-based fMRI data.

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.

fmriprep-docker

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.

neurora

A Python Toolbox for Multimode Neural Data Representation Analysis - A Representational Analysis Toolbox for Neuroscience, including Neural Pattern Similarity (NPS), Representational Similarity Analysis (RSA), Spatiotemporal Pattern Similarity (STPS) & Inter-Subject Correlation (ISC)

pynets

A Reproducible Workflow for Structural and Functional Connectome Ensemble Learning

visualqc

Assistive tool for the quality control of neuroimaging data

brainiak

Brain Imaging Analysis Kit

rshrf

Resting state HRF estimation from BOLD-fMRI signal

topoconscious

Persistent homology pipeline for detecting neural correlates of consciousness from fMRI — H0/H1/H2, Wasserstein + Müller-Lyer timelines, HMM decoding, topological transfer entropy.

multiecho

Combine multi-echoes from a multi-echo fMRI acquisition.

nibabies-wrapper

A wrapper for generating Docker and Apptainer/Singularity commands for simpler NiBabies usage

nibabies

fMRIPrep Lifespan - A robust, transparent workflow tailored for neonate and infant MRI

frat-brain

An analysis tool that uses per-voxel statistical maps in conjunction with FSL atlases to create per-region statistical maps. Current usage includes the creation of regional maps of temporal signal to noise ratio.

phys2cvr

python module to compute cerebrovascular reactivity mapping and other related maps

actflow

The Brain Activity Flow (Actflow) Toolbox. Tools to quantify the relationship between connectivity and task activity through network simulations and machine learning prediction. Helps determine how connections contribute to specific brain functions.

pyspfm

Sparse hemodynamic deconvolution of fMRI data with scikit-learn compatible estimators.

nichord

Creates chord diagrams for connectivity/graph data

fmri-volumetric-renderer

A volumetric fMRI renderer for Jupyter Notebook

hcp-utils

Utilities to use HCP and HCP-like data with nilearn and other Python tools

archepy

Multi-Subject Archetypal Analysis (MS-AA) for fMRI data, in Python.