EEG and iEEG "electrodes" and "coordsystem" files accept more entities than they should

[sappelhoff]

crossref:

• Add regexps for space entity: EEG and iEEG #1190 (comment)
• task entity for electrodes in eeg_face13? bids-examples#244

According to the spec, electrodes and coordsystem files should accept:

• sub
• ses
• acq
• space

see https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/03-electroencephalography.html#electrodes-description-_electrodestsv

But they accept many more.

See here:

bids-validator/bids-validator/bids_validator/rules/file_level_rules.json

Lines 358 to 498 in 5d3835b

	"eeg": {
	"regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?eeg[\\/\\\\]\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_split-[0-9]+)?(?:_space-(@@@_eeg_space_@@@))?((_eeg\\.(@@@_eeg_type_@@@)|(@@@_eeg_ext_@@@))|(?:_recording-[a-zA-Z0-9]+)?(?:@@@_cont_ext_@@@))$",
	"tokens": {
	"@@@_eeg_space_@@@": [
	"Other",
	"CapTrak",
	"CTF",
	"ElektaNeuromag",
	"4DBti",
	"KitYokogawa",
	"ChietiItab",
	"ICBM452AirSpace",
	"ICBM452Warp5Space",
	"IXI549Space",
	"fsaverage",
	"fsaverageSym",
	"fsLR",
	"MNIColin27",
	"MNI152Lin",
	"MNI152NLin2009aSym",
	"MNI152NLin2009bSym",
	"MNI152NLin2009cSym",
	"MNI152NLin2009aAsym",
	"MNI152NLin2009bAsym",
	"MNI152NLin2009cAsym",
	"MNI152NLin6Sym",
	"MNI152NLin6ASym",
	"MNI305",
	"NIHPD",
	"OASIS30AntsOASISAnts",
	"OASIS30Atropos",
	"Talairach",
	"UNCInfant",
	"fsaverage3",
	"fsaverage4",
	"fsaverage5",
	"fsaverage6",
	"fsaveragesym",
	"UNCInfant0V21",
	"UNCInfant1V21",
	"UNCInfant2V21",
	"UNCInfant0V22",
	"UNCInfant1V22",
	"UNCInfant2V22",
	"UNCInfant0V23",
	"UNCInfant1V23",
	"UNCInfant2V23"
	],
	"@@@_eeg_type_@@@": ["vhdr", "vmrk", "eeg", "edf", "bdf", "set", "fdt"],
	"@@@_eeg_ext_@@@": [
	"_events\\.json",
	"_events\\.tsv",
	"_electrodes\\.json",
	"_electrodes\\.tsv",
	"_channels\\.json",
	"_channels\\.tsv",
	"_eeg\\.json",
	"_coordsystem\\.json",
	"_photo\\.jpg"
	],
	"@@@_cont_ext_@@@": [
	"_physio\\.tsv\\.gz",
	"_stim\\.tsv\\.gz",
	"_physio\\.json",
	"_stim\\.json"
	]
	}
	},
	"ieeg": {
	"regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?ieeg[\\/\\\\]\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_split-[0-9]+)?(?:_space-(@@@_ieeg_space_@@@))?((_ieeg\\.(@@@_ieeg_type_@@@)|(@@@_ieeg_ext_@@@))|(?:_recording-[a-zA-Z0-9]+)?(?:@@@_cont_ext_@@@))$",
	"tokens": {
	"@@@_ieeg_space_@@@": [
	"Other",
	"Pixels",
	"ACPC",
	"ICBM452AirSpace",
	"ICBM452Warp5Space",
	"IXI549Space",
	"fsaverage",
	"fsaverageSym",
	"fsLR",
	"MNIColin27",
	"MNI152Lin",
	"MNI152NLin2009aSym",
	"MNI152NLin2009bSym",
	"MNI152NLin2009cSym",
	"MNI152NLin2009aAsym",
	"MNI152NLin2009bAsym",
	"MNI152NLin2009cAsym",
	"MNI152NLin6Sym",
	"MNI152NLin6ASym",
	"MNI305",
	"NIHPD",
	"OASIS30AntsOASISAnts",
	"OASIS30Atropos",
	"Talairach",
	"UNCInfant",
	"fsaverage3",
	"fsaverage4",
	"fsaverage5",
	"fsaverage6",
	"fsaveragesym",
	"UNCInfant0V21",
	"UNCInfant1V21",
	"UNCInfant2V21",
	"UNCInfant0V22",
	"UNCInfant1V22",
	"UNCInfant2V22",
	"UNCInfant0V23",
	"UNCInfant1V23",
	"UNCInfant2V23"
	],
	"@@@_ieeg_type_@@@": [
	"edf",
	"vhdr",
	"vmrk",
	"eeg",
	"set",
	"fdt",
	"nwb",
	"mefd[\\/\\\\].*"
	],
	"@@@_ieeg_ext_@@@": [
	"_events\\.json",
	"_events\\.tsv",
	"_electrodes\\.json",
	"_electrodes\\.tsv",
	"_channels\\.json",
	"_channels\\.tsv",
	"_ieeg\\.json",
	"_coordsystem\\.json",
	"_photo\\.jpg"
	],
	"@@@_cont_ext_@@@": [
	"_physio\\.tsv\\.gz",
	"_stim\\.tsv\\.gz",
	"_physio\\.json",
	"_stim\\.json"
	]
	}
	},

bids-validator/bids-validator/bids_validator/rules/session_level_rules.json

Lines 78 to 195 in 5d3835b

	"eeg_ses": {
	"regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_space-(@@@_eeg_space_@@@))?(@@@_eeg_ses_type_@@@)$",
	"tokens": {
	"@@@_eeg_ses_type_@@@": [
	"_events.tsv",
	"_channels.tsv",
	"_channels.json",
	"_electrodes.tsv",
	"_electrodes.json",
	"_eeg.json",
	"_coordsystem.json",
	"_photo.jpg"
	],
	"@@@_eeg_space_@@@": [
	"Other",
	"CapTrak",
	"CTF",
	"ElektaNeuromag",
	"4DBti",
	"KitYokogawa",
	"ChietiItab",
	"ICBM452AirSpace",
	"ICBM452Warp5Space",
	"IXI549Space",
	"fsaverage",
	"fsaverageSym",
	"fsLR",
	"MNIColin27",
	"MNI152Lin",
	"MNI152NLin2009aSym",
	"MNI152NLin2009bSym",
	"MNI152NLin2009cSym",
	"MNI152NLin2009aAsym",
	"MNI152NLin2009bAsym",
	"MNI152NLin2009cAsym",
	"MNI152NLin6Sym",
	"MNI152NLin6ASym",
	"MNI305",
	"NIHPD",
	"OASIS30AntsOASISAnts",
	"OASIS30Atropos",
	"Talairach",
	"UNCInfant",
	"fsaverage3",
	"fsaverage4",
	"fsaverage5",
	"fsaverage6",
	"fsaveragesym",
	"UNCInfant0V21",
	"UNCInfant1V21",
	"UNCInfant2V21",
	"UNCInfant0V22",
	"UNCInfant1V22",
	"UNCInfant2V22",
	"UNCInfant0V23",
	"UNCInfant1V23",
	"UNCInfant2V23"
	]
	}
	},
	"ieeg_ses": {
	"regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_space-(@@@_ieeg_space_@@@))?(@@@_ieeg_ses_type_@@@)$",
	"tokens": {
	"@@@_ieeg_ses_type_@@@": [
	"_events.tsv",
	"_channels.tsv",
	"_channels.json",
	"_electrodes.tsv",
	"_electrodes.json",
	"_ieeg.json",
	"_coordsystem.json",
	"_photo.jpg"
	],
	"@@@_ieeg_space_@@@": [
	"Other",
	"Pixels",
	"ACPC",
	"ICBM452AirSpace",
	"ICBM452Warp5Space",
	"IXI549Space",
	"fsaverage",
	"fsaverageSym",
	"fsLR",
	"MNIColin27",
	"MNI152Lin",
	"MNI152NLin2009aSym",
	"MNI152NLin2009bSym",
	"MNI152NLin2009cSym",
	"MNI152NLin2009aAsym",
	"MNI152NLin2009bAsym",
	"MNI152NLin2009cAsym",
	"MNI152NLin6Sym",
	"MNI152NLin6ASym",
	"MNI305",
	"NIHPD",
	"OASIS30AntsOASISAnts",
	"OASIS30Atropos",
	"Talairach",
	"UNCInfant",
	"fsaverage3",
	"fsaverage4",
	"fsaverage5",
	"fsaverage6",
	"fsaveragesym",
	"UNCInfant0V21",
	"UNCInfant1V21",
	"UNCInfant2V21",
	"UNCInfant0V22",
	"UNCInfant1V22",
	"UNCInfant2V22",
	"UNCInfant0V23",
	"UNCInfant1V23",
	"UNCInfant2V23"
	]
	}
	}
	}

bids-validator/bids-validator/bids_validator/rules/top_level_rules.json

Lines 80 to 119 in 5d3835b

	"eeg_top": {
	"regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:@@@_eeg_top_ext_@@@)$",
	"tokens": {
	"@@@_eeg_top_ext_@@@": [
	"_eeg\\.json",
	"_channels\\.tsv",
	"_channels\\.json",
	"_electrodes\\.tsv",
	"_electrodes\\.json",
	"_photo\\.jpg",
	"_coordsystem\\.json"
	]
	}
	},
	"ieeg_top": {
	"regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:@@@_ieeg_top_ext_@@@)$",
	"tokens": {
	"@@@_ieeg_top_ext_@@@": [
	"_ieeg\\.json",
	"_channels\\.tsv",
	"_channels\\.json",
	"_electrodes\\.tsv",
	"_electrodes\\.json",
	"_photo\\.jpg",
	"_coordsystem\\.json"
	]
	}
	},
	"meg_top": {
	"regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:@@@_meg_top_ext_@@@)$",
	"tokens": {
	"@@@_meg_top_ext_@@@": [
	"_meg\\.json",
	"_channels\\.tsv",
	"_channels\\.json",
	"_photo\\.jpg",
	"_coordsystem\\.json"
	]
	}
	},

Overall the regexps are getting unwieldy ... we should move towards building the regexps from the BIDS schema

[Remi-Gau]

Landed on this while investigating an issue from bids matlab bids-standard/bids-matlab#542

Just to know: is it worth putting effort into creating regex that match the schema or wait for the validator to directly use the schema.

[sappelhoff]

Just to know: is it worth putting effort into creating regex that match the schema or wait for the validator to directly use the schema.

I think at this point we should wait for the schema based validator to take over and invest our time in effort in more urgent issues. However if you want to dive into this, it'd still be helpful.

[Remi-Gau]

if you want to dive into this

irony: on

oh yes!!!! I love writing complex regex to parse file names!!!

irony: off

OK let's wait then.