BIDS GUIs: Difference between revisions

From MEG Core
Jump to navigation Jump to search
Content added Content deleted
No edit summary
Line 13: Line 13:
bids_qa_gui.py -bids_root <<PATH to BIDS dir>>
bids_qa_gui.py -bids_root <<PATH to BIDS dir>>


==GUI Overview==
=GUI Overview=
==Project Panel==
[[File:Project_panel_view.png]]

==Subject Panel==
[[File:Gui_subject_panel.png]]

==Task Switcher==
Changing the task - shows the number of epochs in the selected task
[[File:Subject_panel_switch_task_epochs.png]]

==MRI Viewing==
[[File:Plot_mri_views.png]]

Revision as of 16:13, 3 December 2024

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