BIDS GUIs

What is BIDS

https://bids-specification.readthedocs.io/en/stable/

BIDS is a standard specification for neuroimaging/physiology data. This currently includes at least: MRI, fMRI, DTI, EEG, MEG, fNIRS (and possibly ECOG/sEEG). BIDS typically describes how RAW data is organized - and processed data is located in the bids_dir/derivatives/{AnalysisPackage}/{SUBJECT}/... The main advantage is that common code can be generated to process data organized in a standard format. Therefore, you should be able to import the bids data into any number of neurophysiological packages (MNE, Brainstorm, SPM, Fieldtrip, ...). Additionally, standardized processing packages known as BIDS apps can be used to process the data in the same way as long as the data is organized in BIDS.

On Biowulf

Start a compute node from the terminal

sinteractive --mem=12G --cpus-per-task=4 --gres=lscratch:50  #adjust mem and cpus accordingly

module use --append /data/MEGmodules/modulefiles
module load mne/dev1.5.1

bids_qa_gui.py -bids_root <<PATH to BIDS dir>>

GUI Overview

Project Panel

Subject Panel

Task Switcher

Changing the task - shows the number of epochs in the selected task

MRI Viewing

MEG Plotting

Dropdown with MEG plotting options Meg_plotting_options.png

Plot All MEG channels (unorganized view) Plot_meg_all.png

Plot Trigger Channels Plot_meg_trigview.png