Bids Python Packages

bidsschematools

Brain Imaging Data Structure (BIDS) Specification

mne-bids

MNE-BIDS is a Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python.

pybids

Python tools for querying and manipulating BIDS datasets.

bids-validator

Validator for the Brain Imaging Data Structure

bids-validator-deno

Validator for the Brain Imaging Data Structure

pydra-bids

Pydra tasks for BIDS I/O

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.

scitex-dataset

Multi-domain scientific dataset fetcher — neuroscience, biology, pharmacology, medical. Part of SciTeX.

qsiprep

Preprocessing of diffusion MRI

bids2table

Index BIDS datasets fast, locally or in the cloud

rshrf

Resting state HRF estimation from BOLD-fMRI signal

dcm2bids

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

pypet2bids

PET2BIDS helps you convert your PET data into BIDS! raw PET scanner files (e.g. ecat, dicom) and additional side files like .e.g excel sheets -- paper @JOSS https://doi.org/10.21105/joss.06067

mne-bids-pipeline

Automatically process entire electrophysiological datasets using MNE-Python.

snakebids

Snakemake + BIDS

qsiprep-container

Preprocessing of diffusion MRI

bidscoin

BIDScoin converts your source-level neuroimaging data to BIDS

multiecho

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

phys2bids

Python3 library to format physiological files in BIDS. At the moment, it supports Acqknowledge and Labchart. BrainHack participants, check the issues with the BrainHack labels!

brainvision

Python implementation to read and write EEG data in the BrainVision Core data format

snirf2bids

Python package for generating BIDS-fNIRS files from SNIRF files

d2b

Organize data in the Brain Imaging Data Structure (BIDS) specification format — dcm2bids alternative

bruker

A modular toolkit for Bruker MRI raw-data handling.