fNIRS example dataset (BEP030) #305
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FYI @rwblair The tests are failing as the validator is not ready/merged yet. |
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@rob-luke you can temporarily "switch on" fNIRS validation by changing this line in the CI workflow to use your validator branch:
should be this then:
git clone --depth 1 https://github.com/rob-luke/bids-validator --branch nirs
(Also, it'd be good if you could update your branch to be in line with master, it's currently 99 commits behind :-) )
Before merging this PR (or when the validator PR is merged), we would then revert this change, so make sure to do this as an individual commit, so that later we can easily git revert it :-)
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Thanks @sappelhoff that seems to have worked. The master branch is now going green. |
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Co-authored-by: Stefan Appelhoff <[email protected]>
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@rob-luke should we also add the NIRS dataset that was prepared by @helenacockx to this pull request and the test? |
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@robertoostenveld I would prefer if you could add that in a separate PR to the |
Thank you both very much! |
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Thank you Robert for adding that example! I've recently found out that the 'type'-column for the optodes.tsv file was missing and the optode_layout was in the wrong folder. I will update that in the near future! |
I have used the CHANGES file in my branch (see "files changed" and then "v1.1.3-emptyfiles") to document all json/tsv changes that were needed to get the data past the validator with the NIRS extensions that Rob has been working on. We can discuss these in detail later when you are back, and also apply them to the full dataset that you are about to share. |
Please be critical when incorporating feedback from the validator. The validator may have errors and/or the spec may be ambiguous. Now is the time to catch any of these small issues. Thanks for contributing a dataset here too. |
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Thanks @rob-luke |
* fNIRS example dataset (BEP030) (#305) * Add fNIRS example dataset * Use nirs branch for validator * Update fnirs_tapping/dataset_description.json Co-authored-by: Stefan Appelhoff <[email protected]> * Fix spacing in name * revert link change validator Co-authored-by: Stefan Appelhoff <[email protected]> * [ENH] New fNIRS example dataset: (non-)auto finger/foot tapping (#323) * added another example dataset for fNIRS, see #317 * use the nirs branch of the validator from rob-luke/bids-validator * replaced "large" PDF file with a zero-byte version * updated fNIRRS example dataset to pass the validator - fixed AnatomicalLandmarkCoordinateSy_t_em - fixed NIRSCoordinateUnit_e_s - removed txt from CHANGES - added stimulus MATLAB m-files to bidsignore - added sub-95 with n/a to practicelogbook.tsv - use n/a for empty cells in practicelogbook.tsv - added practicelogbook.tsv to bidsignore - HACK - removed sub-77 json files from sub-75/nirs directory - replaced 0-byte (empty) snirf files with 1-byte (still empty) snirf files - HACK - use forward slashes in scans.tsv - inserted "type" column in all optodes.tsv files - reordered the columns of channels.tsv * renamed stim to stimuli * added SourceType back to a JSON file where I accidentally deleted it * revert validator branch change, add entry to README Co-authored-by: Stefan Appelhoff <[email protected]> Co-authored-by: Rob Luke <[email protected]> Co-authored-by: Robert Oostenveld <[email protected]>
Dataset with functional near-infrared spectroscopy measurements in BIDS format.
Complete dataset (without zeroed data) can be found at https://github.com/rob-luke/BIDS-NIRS-Tapping