A practical workflow for organizing clinical intraoperative and long-term iEEG data in BIDS
Authors: Demuru Matteo , van Blooijs Dorien , Zweiphenning Willemiek , Hermes Dora , Leijten Frans , Zijlmans Maeike 
Published: December 2020

The neuroscience community increasingly uses the Brain Imaging Data Structure (BIDS) to organize data, extending from MRI to electrophysiology data. While automated tools and workflows are developed that help organize MRI data from the scanner to BIDS, these workflows are lacking for clinical intracranial EEG (iEEG data). We present a practical guideline on how to organize full clinical iEEG epilepsy data into BIDS. We present electrophysiological datasets recorded from twelve subjects who underwent intracranial monitoring followed by resective epilepsy surgery at the University Medical Center Utrecht, the Netherlands, and became seizure-free after surgery. These data include intraoperative electrocorticography recordings from six patients, long-term electrocorticography recordings from three patients and stereo-encephalography recordings from three patients. We describe the 6 steps in the pipeline that are essential to structure the data from these clinical iEEG recordings into BIDS and the challenges during this process. These guidelines enable centers performing clinical iEEG recordings to structure their data to improve accessibility, reusability and interoperability of clinical data.

Background & Summary

Today’s era of big data and open science has highlighted the importance of organizing and storing data in keeping with the FAIR Data Principles of Findable, Accessible, Interoperable and Reusable Data to the neuroscientific community1,2. Over the past five years, a community-driven effort to develop a simple standardized method of organizing, annotating and describing neuroimaging data has resulted in the Brain Imaging Data Structure (BIDS). BIDS was originally developed for magnetic resonance imaging data (MRI3), but now also has extensions for magnetoencephalography (MEG4), electroencephalography (EEG5), and intracranial encephalography (iEEG6). BIDS prescribes rules about the organization of the data itself, with a formalized file/folder structure and naming conventions, and provides standardized templates to store associated metadata in human and machine readable, text-based, JSON and TSV file formats. Software packages analyzing neuroimaging data increasingly support data organized using the BIDS format (https://bids-apps.neuroimaging.io/apps/). However, a major challenge in the use of BIDS is to curate the data from their source format into a BIDS validated set. Several tools exist to convert MRI source data into BIDS datasets7–11, but to our knowledge, there is currently no tool or protocol for iEEG.

The University Medical Center in Utrecht, the Netherlands, is a tertiary referral center performing around 150 epilepsy surgeries per year. The success of surgery for treating focal epilepsy depends on accurate prediction of brain tissue that needs to be removed or disconnected to yield full seizure control. People referred for epilepsy surgery undergo an extensive presurgical work-up, starting with MRI and video-EEG and, if needed, PET or ictal SPECT. This noninvasive phase is followed directly by a resection, possibly guided by intraoperative ECoG, or by long-term electrocorticography (ECoG) or stereo-encephalography (SEEG) with electrodes placed on or implanted in the brain12. From January 2008 until December 2019, 560 of the epilepsy surgeries in our center were guided by intraoperative ECoG; 163 surgeries followed after long-term ECoG or SEEG investigation. These iEEG data offer a unique combination of high spatial and temporal resolution measurements of the living human brain and it is important to curate these data in a way such that they can be used by many people in the future to study epilepsy and typical brain dynamics.

As part of RESPect (Registry for Epilepsy Surgery Patients, ethical committee approval (18-109)), we started to retrospectively convert raw, unprocessed, clinical iEEG data of patients that underwent epilepsy surgery from January 2008 onwards, to the iEEG-BIDS format and identified 6 critical steps in this process. With this paper, we give a practical workflow of how we collected iEEG data in the UMC Utrecht and converted these data to BIDS. We share our entire pipeline and provide practical examples of six patients with intraoperative ECoG, three patients with long-term ECoG and three patients with SEEG data, demonstrating how BIDS can be used for intraoperative as well as long-term recordings.