BIDS GUIs: Difference between revisions
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==On Biowulf== |
==On Biowulf== |
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Log into biowulf using NoMachine. Setup instructions here: https://hpc.nih.gov/docs/nx.html |
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Start a compute node from the terminal |
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On biowulf open a terminal and start a compute node using the commands below |
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module use --append /data/MEGmodules/modulefiles |
module use --append /data/MEGmodules/modulefiles |
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module load mne/dev1.5.1 |
module load mne/dev1.5.1 |
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==Create BIDS Dataset Using GUI== |
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https://megcore.nih.gov/MEG/BIDS_gui_080224_anon.pdf |
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make_meg_bids_gui.py |
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[[File:Make_meg_bids_gui_startup.png | 700px]] |
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Launch the QA gui |
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bids_qa_gui.py -bids_root <<PATH to BIDS dir>> |
bids_qa_gui.py -bids_root <<PATH to BIDS dir>> |
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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 <br> |
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[[Meg_plotting_options.png]] |
[[File:Meg_plotting_options.png | 700px]] |
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[[File:Plot_meg_all.png | 700px]] |
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Plot whole head - subset of meg channels representing the Left (top half) to Right (bottom half) display <br> |
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[[ |
[[File:Plot_meg_fullview.png | 700px]] |
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Plot Trigger Channels |
Plot Trigger Channels <br> |
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Note the auditory delay added to the triggerline pulse <br> |
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[[Plot_meg_trigview.png]] |
[[File:Plot_meg_trigview.png | 700px]] |
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Latest revision as of 11:25, 11 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
Log into biowulf using NoMachine. Setup instructions here: https://hpc.nih.gov/docs/nx.html
On biowulf open a terminal and start a compute node using the commands below
sinteractive --mem=16G --cpus-per-task=4 --gres=lscratch:50 #adjust mem and cpus accordingly
module use --append /data/MEGmodules/modulefiles module load mne/dev1.5.1
Create BIDS Dataset Using GUI
https://megcore.nih.gov/MEG/BIDS_gui_080224_anon.pdf
make_meg_bids_gui.py
QA GUI Overview
Launch the QA gui
bids_qa_gui.py -bids_root <<PATH to BIDS dir>>
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
Plot All MEG channels (unorganized view of All channels)
Plot whole head - subset of meg channels representing the Left (top half) to Right (bottom half) display
Plot Trigger Channels
Note the auditory delay added to the triggerline pulse
