Brain Imaging Data Structure - BIDS#

BIDS is an attempt to define some simple ways of organizing our data from different neuroimaging modalities so that it can be shared.

Meta data#

Language-agnostic files with relevant information.https://bids-standard.github.io/bids-starter-kit/folders_and_files/metadata.html. Two types of files are proposed

.json Java Script Object Notation. Human-readable text to store metadata. JSON online editor: https://jsoneditoronline.org/

{
  "key": "value",
  "key2": "value2",
  "key3": {
      "subkey1": "subvalue1"
  }
}

Read in Python

import json
with open('myfile.json', 'r') as ff:
    data = json.load(ff)

Write in Python

import json
data = {'field1': 'value1', 'field2': 3, 'field3': 'field3'}
with open('my_output_file.json', 'w') as ff:
   json.dump(data, ff)

.tsv Tab-delimited files For example , they can contain events, channel locations, etc.

Read in Python

import pandas as pd
pd.read_csv('./ds001/participants.tsv', delimiter='\t')

Write in Python

df.to_csv('my_new_file.tsv', sep='\t')

An open, fully automated EEG pipeline for biomarker discovery in clinical neuroscience https://www.biorxiv.org/content/10.1101/2023.01.20.524897v1