BIDS GUIs: Difference between revisions
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==On Biowulf== |
==On Biowulf== |
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Start a compute node from the terminal |
Start a compute node from the terminal |
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sinteractive --mem=12G --cpus-per-task=4 --gres=lscratch:50 #adjust mem and cpus accordingly |
sinteractive --mem=12G --cpus-per-task=4 --gres=lscratch:50 #adjust mem and cpus accordingly |
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module use --append /data/MEGmodules/modulefiles |
module use --append /data/MEGmodules/modulefiles |
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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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==GUI Overview== |
Revision as of 14:58, 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>>