BIDS GUIs: Difference between revisions
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=GUI Overview= |
=GUI Overview= |
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==Project Panel== |
==Project Panel== |
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[[File:Project_panel_view.png]] |
[[File:Project_panel_view.png | 700px]] |
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==Subject Panel== |
==Subject Panel== |
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[[File:Gui_subject_panel.png]] |
[[File:Gui_subject_panel.png | 700px]] |
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==Task Switcher== |
==Task Switcher== |
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Changing the task - shows the number of epochs in the selected task |
Changing the task - shows the number of epochs in the selected task <br> |
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[[File:Subject_panel_switch_task_epochs.png]] |
[[File:Subject_panel_switch_task_epochs.png | 700px]] |
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==MRI Viewing== |
==MRI Viewing== |
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[[File:Plot_mri_views.png]] |
[[File:Plot_mri_views.png | 700px ]] |
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==MEG Plotting== |
==MEG Plotting== |
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Dropdown with MEG plotting options |
Dropdown with MEG plotting options |
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[[Meg_plotting_options.png]] |
[[Meg_plotting_options.png | 700px]] |
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Plot All MEG channels (unorganized view) |
Plot All MEG channels (unorganized view) |
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[[Plot_meg_all.png]] |
[[Plot_meg_all.png | 700px]] |
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Plot Trigger Channels |
Plot Trigger Channels |
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[[Plot_meg_trigview.png]] |
[[Plot_meg_trigview.png | 700px]] |
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Revision as of 15:26, 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
MEG Plotting
Dropdown with MEG plotting options 700px
Plot All MEG channels (unorganized view) 700px
Plot Trigger Channels 700px
