Mne bids pipeline: Difference between revisions
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https://mne.tools/mne-bids-pipeline/examples/ds000248.html |
https://mne.tools/mne-bids-pipeline/examples/ds000248.html |
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===Processing=== |
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All processing is defined in the config.py file. This has hundreds of options to define the processing. |
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Here are some of the typical options: https://mne.tools/mne-bids-pipeline/settings/general.html |
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Here is the full list of options: |
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https://github.com/mne-tools/mne-bids-pipeline/blob/main/config.py |
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==Use on biowulf== |
==Use on biowulf== |
Revision as of 09:51, 3 May 2022
Intro
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.
BIDS (formal specs) >> MNE_BIDS (python neurophysiological BIDS) >> MNE_BIDS_PIPELINE (structured processing in MNE python according to BIDS definition)
BIDS website
https://bids-specification.readthedocs.io/en/stable/
MNE Bids
MNE bids is a python tool to make and access neurophysiological data. This tool is a branch of the MNE tools for neurophysiological analysis.
MNE Bids website
https://mne.tools/mne-bids/stable/index.html
MNE bids pipeline background
Mne bids pipeline website:
https://mne.tools/mne-bids-pipeline/
Full example:
https://mne.tools/mne-bids-pipeline/examples/ds000248.html
Processing
All processing is defined in the config.py file. This has hundreds of options to define the processing.
Here are some of the typical options: https://mne.tools/mne-bids-pipeline/settings/general.html
Here is the full list of options:
https://github.com/mne-tools/mne-bids-pipeline/blob/main/config.py
Use on biowulf
module load mne_bids_pipeline