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bids-apps / MRtrix3_connectome

Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalisation, using the MRtrix3 software package.
http://www.mrtrix.org/
Apache License 2.0
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Running the BIDS_validator on the subjects given in --participant_label only #95

Open civier opened 3 years ago

civier commented 3 years ago

Otherwise, the validity test can take a very long time (if the BIDS dataset has hundreds of subjects or more) If it's not supported downstream in the BIDS validator, maybe can make a temporary BIDS directory consisting of only the desired subjects using symbolic links, and run the BIDS validator there.

Lestropie commented 3 years ago

The latter suggestion would be quite the hack, given the concern would be equally applicable to all BIDS Apps. There is surely a neater way of doing this; and if there isn't, it's probably worth escalating up the chain.

I'm not very familiar with the validator, but looking at their latest README, I see a couple of options:

  1. Following parsing of the desired participant / subject labels, auto-generate a config file that excludes all data outside of the user's selection for processing, and pass that to the validator when invoking.

  2. Over time, hopefully the Python capabilities will extend beyond just checking compatibility of file extensions to running validation on subsets of a dataset.