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meeg-ml-benchmarks / brain-age-benchmark-paper

M/EEG brain age benchmark paper
https://meeg-ml-benchmarks.github.io/brain-age-benchmark-paper/
BSD 3-Clause "New" or "Revised" License
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Adding script to convert TUAB to BIDS #1

Closed hubertjb closed 3 years ago

hubertjb commented 3 years ago

@dengemann @agramfort Here's the script for converting TUAB to BIDS. I ran the bids-validator and got the following error, in case you are already familiar with it, otherwise I'll investigate more:

1: [ERR] Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder. (code: 1 - NOT_INCLUDED)
        ./sub-00000021/ses-001/eeg/sub-00000021_ses-001_task-_split-00_channels.tsv
            Evidence: sub-00000021_ses-001_task-_split-00_channels.tsv
        ./sub-00000021/ses-001/eeg/sub-00000021_ses-001_task-_split-00_eeg.edf
            Evidence: sub-00000021_ses-001_task-_split-00_eeg.edf
        ./sub-00000021/ses-001/eeg/sub-00000021_ses-001_task-_split-00_eeg.json
            Evidence: sub-00000021_ses-001_task-_split-00_eeg.json
        ./sub-00000039/ses-001/eeg/sub-00000039_ses-001_task-_split-00_channels.tsv
            Evidence: sub-00000039_ses-001_task-_split-00_channels.tsv
        ./sub-00000039/ses-001/eeg/sub-00000039_ses-001_task-_split-00_eeg.edf
            Evidence: sub-00000039_ses-001_task-_split-00_eeg.edf
        ./sub-00000039/ses-001/eeg/sub-00000039_ses-001_task-_split-00_eeg.json
            Evidence: sub-00000039_ses-001_task-_split-00_eeg.json
        ./sub-00000135/ses-001/eeg/sub-00000135_ses-001_task-_split-00_channels.tsv
            Evidence: sub-00000135_ses-001_task-_split-00_channels.tsv
        ./sub-00000135/ses-001/eeg/sub-00000135_ses-001_task-_split-00_eeg.edf
            Evidence: sub-00000135_ses-001_task-_split-00_eeg.edf
        ./sub-00000135/ses-001/eeg/sub-00000135_ses-001_task-_split-00_eeg.json
            Evidence: sub-00000135_ses-001_task-_split-00_eeg.json
        ./sub-00000296/ses-001/eeg/sub-00000296_ses-001_task-_split-00_channels.tsv
            Evidence: sub-00000296_ses-001_task-_split-00_channels.tsv
        ... and 4553 more files having this issue (Use --verbose to see them all).

    Please visit https://neurostars.org/search?q=NOT_INCLUDED for existing conversations about this issue.

The converted data is under /storage/store2/data/TUAB-healthy-bids.