Bids Python Packages

bidsschematools

Brain Imaging Data Structure (BIDS) Specification

pybids

Python tools for querying and manipulating BIDS datasets.

mne-bids

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

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

scitex-dataset

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

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.

qsiprep

Preprocessing of diffusion MRI

dcm2bids

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

bids2table

Index BIDS datasets fast, locally or in the cloud

pypet2bids

A python library for converting PET imaging and blood data to BIDS.

bidscoin

BIDScoin converts your source-level neuroimaging data to BIDS

snakebids

Snakemake + BIDS

rshrf

Resting state HRF estimation from BOLD-fMRI signal

mne-bids-pipeline

A full-flegded processing pipeline for your MEG and EEG data

brainvision

Read and write EEG data in the BrainVision Core data format

multiecho

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

qsiprep-container

qsiprep is a non-DTI diffusion-weighted image pre-processing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to differences in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

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!

bruker

A modular toolkit for Bruker MRI raw-data handling.

table-remodeler

Tabular files remodeling and reorganizing tools

snirf2bids

Python package for generating BIDS-fNIRS files from SNIRF files