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

dcm2bids

Reorganising NIfTI files from dcm2niix into 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.

bids-manager

GUI and CLI tool for raw-to-BIDS conversion, curation, metadata editing, and validation for MRI, EEG, MEG, and physiological recordings.

scitex-dataset

Multi-domain scientific dataset fetcher (neuroscience, biology, medical)

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.

bids2table

Index BIDS datasets fast, locally or in the cloud

qsiprep

Preprocessing of diffusion MRI

bidscoin

BIDScoin converts your source-level neuroimaging data to BIDS

table-remodeler

Tabular files remodeling and reorganizing tools

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

rshrf

Resting state HRF estimation from BOLD-fMRI signal

mne-bids-pipeline

Automatically process entire electrophysiological datasets using MNE-Python.

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!

remodnav

Robust Eye Movement Detection for Natural Viewing

snakebids

Snakemake + BIDS

multiecho

Combine multiple-echoes from a multi-echo BOLD 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.

brainvision

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