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list.js
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/**
* Issues
*
* A list of all possible issues organized by
* issue code and including severity and reason
* agnostic to file specifics.
*/
export default {
0: {
key: 'INTERNAL ERROR',
severity: 'error',
reason: 'Internal error. SOME VALIDATION STEPS MAY NOT HAVE OCCURRED',
},
1: {
key: 'NOT_INCLUDED',
severity: 'error',
reason:
'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.',
},
2: {
key: 'REPETITION_TIME_GREATER_THAN',
severity: 'warning',
reason:
"'RepetitionTime' is greater than 100 are you sure it's expressed in seconds?",
},
3: {
key: 'ECHO_TIME_GREATER_THAN',
severity: 'warning',
reason:
"'EchoTime' is greater than 1 are you sure it's expressed in seconds?",
},
4: {
key: 'ECHO_TIME_DIFFERENCE_GREATER_THAN',
severity: 'warning',
reason:
"'EchoTimeDifference' is greater than 1 are you sure it's expressed in seconds?",
},
5: {
key: 'TOTAL_READOUT_TIME_GREATER_THAN',
severity: 'warning',
reason:
"'TotalReadoutTime' is greater than 10 are you sure it's expressed in seconds?",
},
6: {
key: 'ECHO_TIME_NOT_DEFINED',
severity: 'warning',
reason:
"You should define 'EchoTime' for this file. If you don't provide this information field map correction will not be possible.",
},
7: {
key: 'PHASE_ENCODING_DIRECTION_NOT_DEFINED',
severity: 'warning',
reason:
"You should define 'PhaseEncodingDirection' for this file. If you don't provide this information field map correction will not be possible.",
},
8: {
key: 'EFFECTIVE_ECHO_SPACING_NOT_DEFINED',
severity: 'warning',
reason:
"You should define 'EffectiveEchoSpacing' for this file. If you don't provide this information field map correction will not be possible.",
},
9: {
key: 'TOTAL_READOUT_TIME_NOT_DEFINED',
severity: 'warning',
reason:
"You should define 'TotalReadoutTime' for this file. If you don't provide this information field map correction using TOPUP might not be possible.",
},
10: {
key: 'REPETITION_TIME_MUST_DEFINE',
severity: 'error',
reason: "You have to define 'RepetitionTime' for this file.",
},
11: {
key: 'REPETITION_TIME_UNITS',
severity: 'error',
reason:
"Repetition time was not defined in seconds, milliseconds or microseconds in the scan's header.",
},
12: {
key: 'REPETITION_TIME_MISMATCH',
severity: 'error',
reason:
"Repetition time did not match between the scan's header and the associated JSON metadata file.",
},
13: {
key: 'SLICE_TIMING_NOT_DEFINED',
severity: 'warning',
reason:
"You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible.",
},
15: {
key: 'ECHO_TIME1-2_NOT_DEFINED',
severity: 'error',
reason: "You have to define 'EchoTime1' and 'EchoTime2' for this file.",
},
16: {
key: 'ECHO_TIME_MUST_DEFINE',
severity: 'error',
reason: "You have to define 'EchoTime' for this file.",
},
17: {
key: 'UNITS_MUST_DEFINE',
severity: 'error',
reason: "You have to define 'Units' for this file.",
},
18: {
key: 'PHASE_ENCODING_DIRECTION_MUST_DEFINE',
severity: 'error',
reason: "You have to define 'PhaseEncodingDirection' for this file.",
},
19: {
key: 'TOTAL_READOUT_TIME_MUST_DEFINE',
severity: 'error',
reason: "You have to define 'TotalReadoutTime' for this file.",
},
20: {
key: 'EVENTS_COLUMN_ONSET',
severity: 'error',
reason: "First column of the events file must be named 'onset'",
},
21: {
key: 'EVENTS_COLUMN_DURATION',
severity: 'error',
reason: "Second column of the events file must be named 'duration'",
},
22: {
key: 'TSV_EQUAL_ROWS',
severity: 'error',
reason:
'All rows must have the same number of columns as there are headers.',
},
23: {
key: 'TSV_EMPTY_CELL',
severity: 'error',
reason:
'Empty cell in TSV file detected: The proper way of labeling missing values is "n/a".',
},
24: {
key: 'TSV_IMPROPER_NA',
severity: 'warning',
reason: 'A proper way of labeling missing values is "n/a".',
},
25: {
key: 'EVENTS_TSV_MISSING',
severity: 'warning',
reason:
'Task scans should have a corresponding events.tsv file. If this is a resting state scan you can ignore this warning or rename the task to include the word "rest".',
},
26: {
key: 'NIFTI_HEADER_UNREADABLE',
severity: 'error',
reason:
'We were unable to parse header data from this NIfTI file. Please ensure it is not corrupted or mislabeled.',
},
27: {
key: 'JSON_INVALID',
severity: 'error',
reason: 'Not a valid JSON file.',
},
28: {
key: 'GZ_NOT_GZIPPED',
severity: 'error',
reason: 'This file ends in the .gz extension but is not actually gzipped.',
},
29: {
key: 'VOLUME_COUNT_MISMATCH',
severity: 'error',
reason:
'The number of volumes in this scan does not match the number of volumes in the corresponding .bvec and .bval files.',
},
30: {
key: 'BVAL_MULTIPLE_ROWS',
severity: 'error',
reason: '.bval files should contain exactly one row of volumes.',
},
31: {
key: 'BVEC_NUMBER_ROWS',
severity: 'error',
reason: '.bvec files should contain exactly three rows of volumes.',
},
32: {
key: 'DWI_MISSING_BVEC',
severity: 'error',
reason: 'DWI scans should have a corresponding .bvec file.',
},
33: {
key: 'DWI_MISSING_BVAL',
severity: 'error',
reason: 'DWI scans should have a corresponding .bval file.',
},
36: {
key: 'NIFTI_TOO_SMALL',
severity: 'error',
reason: 'This file is too small to contain the minimal NIfTI header.',
},
37: {
key: 'INTENDED_FOR',
severity: 'error',
reason: "'IntendedFor' field needs to point to an existing file.",
},
38: {
key: 'INCONSISTENT_SUBJECTS',
severity: 'warning',
reason:
'Not all subjects contain the same files. Each subject should contain the same number of files with ' +
'the same naming unless some files are known to be missing.',
},
39: {
key: 'INCONSISTENT_PARAMETERS',
severity: 'warning',
reason: 'Not all subjects/sessions/runs have the same scanning parameters.',
},
40: {
key: 'NIFTI_DIMENSION',
severity: 'warning',
reason:
"NIfTI file's header field for dimension information blank or too short.",
},
41: {
key: 'NIFTI_UNIT',
severity: 'warning',
reason:
"NIfTI file's header field for unit information for x, y, z, and t dimensions empty or too short",
},
42: {
key: 'NIFTI_PIXDIM',
severity: 'warning',
reason:
"NIfTI file's header field for pixel dimension information empty or too short.",
},
43: {
key: 'ORPHANED_SYMLINK',
severity: 'error',
reason:
'This file appears to be an orphaned symlink. Make sure it correctly points to its referent.',
},
44: {
key: 'FILE_READ',
severity: 'error',
reason:
'We were unable to read this file. Make sure it contains data (file size > 0 kB) and is not corrupted, incorrectly named, or incorrectly symlinked.',
},
45: {
key: 'SUBJECT_FOLDERS',
severity: 'error',
reason:
'There are no subject folders (labeled "sub-*") in the root of this dataset.',
},
46: {
key: 'BVEC_ROW_LENGTH',
severity: 'error',
reason:
'Each row in a .bvec file should contain the same number of values.',
},
47: {
key: 'B_FILE',
severity: 'error',
reason:
'.bval and .bvec files must be single space delimited and contain only numerical values.',
},
48: {
key: 'PARTICIPANT_ID_COLUMN',
severity: 'error',
reason:
"Participants and phenotype .tsv files must have a 'participant_id' column.",
},
49: {
key: 'PARTICIPANT_ID_MISMATCH',
severity: 'error',
reason:
'Participant labels found in this dataset did not match the values in participant_id column found in the participants.tsv file.',
},
50: {
key: 'TASK_NAME_MUST_DEFINE',
severity: 'error',
reason: "You have to define 'TaskName' for this file.",
},
51: {
key: 'PHENOTYPE_SUBJECTS_MISSING',
severity: 'error',
reason:
'A phenotype/ .tsv file lists subjects that were not found in the dataset.',
},
52: {
key: 'STIMULUS_FILE_MISSING',
severity: 'error',
reason: 'A stimulus file was declared but not found in the dataset.',
},
53: {
key: 'NO_T1W',
severity: 'ignore',
reason: 'Dataset does not contain any T1w scans.',
},
54: {
key: 'BOLD_NOT_4D',
severity: 'error',
reason: 'Bold scans must be 4 dimensional.',
},
55: {
key: 'JSON_SCHEMA_VALIDATION_ERROR',
severity: 'error',
reason:
'Invalid JSON file. The file is not formatted according the schema.',
},
56: {
key: 'Participants age 89 or higher',
severity: 'warning',
reason:
'As per section 164.514(C) of "The De-identification Standard" under HIPAA guidelines, participants with age 89 or higher should be tagged as 89+. More information can be found at https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/#standard',
},
57: {
key: 'DATASET_DESCRIPTION_JSON_MISSING',
severity: 'error',
reason:
'The compulsory file /dataset_description.json is missing. See Section 03 (Modality agnostic files) of the BIDS specification.',
},
58: {
key: 'TASK_NAME_CONTAIN_ILLEGAL_CHARACTER',
severity: 'error',
reason:
'Task Name contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec.',
},
59: {
key: 'ACQ_NAME_CONTAIN_ILLEGAL_CHARACTER',
severity: 'error',
reason:
'acq Name contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec.',
},
60: {
key: 'SFORM_AND_QFORM_IN_IMAGE_HEADER_ARE_ZERO',
severity: 'error',
reason:
'sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.',
},
61: {
key: 'QUICK_VALIDATION_FAILED',
severity: 'error',
reason:
'Quick validation failed - the general folder structure does not resemble a BIDS dataset. Have you chosen the right folder (with "sub-*/" subfolders)? Check for structural/naming issues and presence of at least one subject.',
},
62: {
key: 'SUBJECT_VALUE_CONTAINS_ILLEGAL_CHARACTER',
severity: 'error',
reason:
'Sub label contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec.',
},
63: {
key: 'SESSION_VALUE_CONTAINS_ILLEGAL_CHARACTER',
severity: 'error',
reason:
'Ses label contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec.',
},
64: {
key: 'SUBJECT_LABEL_IN_FILENAME_DOESNOT_MATCH_DIRECTORY',
severity: 'error',
reason:
"Subject label in the filename doesn't match with the path of the file. File seems to be saved in incorrect subject directory.",
},
65: {
key: 'SESSION_LABEL_IN_FILENAME_DOESNOT_MATCH_DIRECTORY',
severity: 'error',
reason:
"Session label in the filename doesn't match with the path of the file. File seems to be saved in incorrect session directory.",
},
66: {
key: 'SLICETIMING_VALUES_GREATOR_THAN_REPETITION_TIME',
severity: 'error',
reason:
'"SliceTiming" value/s contains invalid value as it is greater than RepetitionTime. SliceTiming values should be in seconds not milliseconds (common mistake).',
},
67: {
key: 'NO_VALID_DATA_FOUND_FOR_SUBJECT',
severity: 'error',
reason: 'No BIDS compatible data found for at least one subject.',
},
68: {
key: 'FILENAME_COLUMN',
severity: 'error',
reason: "_scans.tsv files must have a 'filename' column.",
},
70: {
key: 'WRONG_NEW_LINE',
severity: 'error',
reason:
"All TSV files must use Line Feed '\\n' characters to denote new lines. This files uses Carriage Return '\\r'.",
},
71: {
key: 'MISSING_TSV_COLUMN_CHANNELS',
severity: 'error',
reason:
"The column names of the channels file must begin with ['name', 'type', 'units']",
},
72: {
key: 'MISSING_TSV_COLUMN_IEEG_CHANNELS',
severity: 'error',
reason:
"The column names of the channels file must begin with ['name', 'type', 'units', 'low_cutoff', 'high_cutoff']",
},
73: {
key: 'MISSING_TSV_COLUMN_IEEG_ELECTRODES',
severity: 'error',
reason:
"The column names of the electrodes file must begin with ['name', 'x', 'y', 'z', 'size']",
},
74: {
key: 'DUPLICATE_NIFTI_FILES',
severity: 'error',
reason: "NIfTI file exist with both '.nii' and '.nii.gz' extensions.",
},
75: {
key: 'NIFTI_PIXDIM4',
severity: 'error',
reason: "NIfTI file's header is missing time dimension information.",
},
76: {
key: 'EFFECTIVEECHOSPACING_TOO_LARGE',
severity: 'error',
reason: "Abnormally high value of 'EffectiveEchoSpacing'.",
},
77: {
key: 'UNUSED_STIMULUS',
severity: 'warning',
reason:
'There are files in the /stimuli directory that are not utilized in any _events.tsv file.',
},
78: {
key: 'CHANNELS_COLUMN_SFREQ',
severity: 'error',
reason:
"Fourth column of the channels file must be named 'sampling_frequency'",
},
79: {
key: 'CHANNELS_COLUMN_LOWCUT',
severity: 'error',
reason: "Third column of the channels file must be named 'low_cutoff'",
},
80: {
key: 'CHANNELS_COLUMN_HIGHCUT',
severity: 'error',
reason: "Third column of the channels file must be named 'high_cutoff'",
},
81: {
key: 'CHANNELS_COLUMN_NOTCH',
severity: 'error',
reason: "Third column of the channels file must be named 'notch'",
},
82: {
key: 'CUSTOM_COLUMN_WITHOUT_DESCRIPTION',
severity: 'warning',
reason:
'Tabular file contains custom columns not described in a data dictionary',
},
83: {
key: 'ECHOTIME1_2_DIFFERENCE_UNREASONABLE',
severity: 'error',
reason:
'The value of (EchoTime2 - EchoTime1) should be within the range of 0.0001 - 0.01.',
},
84: {
key: 'ACQTIME_FMT',
severity: 'error',
reason:
'Entries in the "acq_time" column of _scans.tsv should be expressed in the following format YYYY-MM-DDTHH:mm:ss (year, month, day, hour (24h), minute, second; this is equivalent to the RFC3339 “date-time” format. ',
},
85: {
key: 'SUSPICIOUSLY_LONG_EVENT_DESIGN',
severity: 'warning',
reason:
'The onset of the last event is after the total duration of the corresponding scan. This design is suspiciously long. ',
},
86: {
key: 'SUSPICIOUSLY_SHORT_EVENT_DESIGN',
severity: 'warning',
reason:
'The onset of the last event is less than half the total duration of the corresponding scan. This design is suspiciously short. ',
},
87: {
key: 'SLICETIMING_ELEMENTS',
severity: 'warning',
reason:
"The number of elements in the SliceTiming array should match the 'k' dimension of the corresponding NIfTI volume.",
},
88: {
key: 'MALFORMED_BVEC',
severity: 'error',
reason:
'The contents of this .bvec file are undefined or severely malformed. ',
},
89: {
key: 'MALFORMED_BVAL',
severity: 'error',
reason:
'The contents of this .bval file are undefined or severely malformed. ',
},
90: {
key: 'SIDECAR_WITHOUT_DATAFILE',
severity: 'error',
reason: 'A json sidecar file was found without a corresponding data file',
},
91: {
key: '_FIELDMAP_WITHOUT_MAGNITUDE_FILE',
severity: 'error',
reason:
'_fieldmap.nii[.gz] file does not have accompanying _magnitude.nii[.gz] file. ',
},
92: {
key: 'MISSING_MAGNITUDE1_FILE',
severity: 'warning',
reason:
'Each _phasediff.nii[.gz] file should be associated with a _magnitude1.nii[.gz] file.',
},
93: {
key: 'EFFECTIVEECHOSPACING_LARGER_THAN_TOTALREADOUTTIME',
severity: 'error',
reason:
'EffectiveEchoSpacing should always be smaller than TotalReadoutTime. ',
},
94: {
key: 'MAGNITUDE_FILE_WITH_TOO_MANY_DIMENSIONS',
severity: 'error',
reason:
'_magnitude1.nii[.gz] and _magnitude2.nii[.gz] files must have exactly three dimensions. ',
},
95: {
key: 'T1W_FILE_WITH_TOO_MANY_DIMENSIONS',
severity: 'error',
reason: '_T1w.nii[.gz] files must have exactly three dimensions. ',
},
96: {
key: 'MISSING_TSV_COLUMN_EEG_ELECTRODES',
severity: 'error',
reason:
"The column names of the electrodes file must begin with ['name', 'x', 'y', 'z']",
},
97: {
key: 'MISSING_SESSION',
severity: 'warning',
reason: 'Not all subjects contain the same sessions.',
},
98: {
key: 'INACCESSIBLE_REMOTE_FILE',
severity: 'error',
reason:
'This file appears to be a symlink to a remote annexed file but could not be accessed from any of the configured remotes.',
},
99: {
key: 'EMPTY_FILE',
severity: 'error',
reason: 'Empty files not allowed.',
},
100: {
key: 'BRAINVISION_LINKS_BROKEN',
severity: 'error',
reason:
'Internal file pointers in BrainVision file triplet (*.eeg, *.vhdr, and *.vmrk) are broken or some files do not exist.',
},
101: {
key: 'README_FILE_MISSING',
severity: 'warning',
reason:
'The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification.',
},
102: {
key: 'TOO_FEW_AUTHORS',
severity: 'warning',
reason:
'The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered based on the presence of only one author field. Please ignore if all contributors are already properly listed.',
},
103: {
key: 'MULTIPLE_COMMAS_IN_AUTHOR_FIELD',
severity: 'error',
reason:
'The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered based on the presence of multiple commas in a single author field. Please ensure your authors are properly formatted.',
},
104: {
key: 'HED_GENERIC_ERROR',
severity: 'error',
reason: 'The validation on this HED string returned an error.',
},
105: {
key: 'HED_GENERIC_WARNING',
severity: 'warning',
reason: 'The validation on this HED string returned a warning.',
},
106: {
key: 'HED_ILLEGAL_CHARACTER',
severity: 'error',
reason: 'This HED string contains an illegal character.',
},
107: {
key: 'HED_PARENTHESES_MISMATCH',
severity: 'error',
reason: 'This HED string contains mismatched parentheses.',
},
108: {
key: 'HED_MISSING_COMMA_AFTER_TAG',
severity: 'error',
reason: 'This HED string is missing a required comma after a HED tag.',
},
109: {
key: 'HED_CAPITALIZATION',
severity: 'warning',
reason:
'This HED string is not properly capitalized. HED tags should start with a capital letter or be in CamelCase.',
},
110: {
key: 'HED_DUPLICATE_TAG_IN_SAME_GROUP_OR_TOP_LEVEL',
severity: 'error',
reason:
'This HED string contains duplicate HED tags in the same group or at the top level.',
},
111: {
key: 'HED_TOO_MANY_TILDES',
severity: 'error',
reason: 'This HED string has more than 2 tildes in the same tag group.',
},
112: {
key: 'HED_MISSING_VALUE_IN_SIDECAR',
severity: 'warning',
reason:
'The json sidecar does not contain this column value as a possible key to a HED string.',
},
113: {
key: 'NO_AUTHORS',
severity: 'warning',
reason:
'The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered because there are no authors, which will make DOI registration from dataset metadata impossible.',
},
114: {
key: 'INCOMPLETE_DATASET',
severity: 'error',
reason:
'This dataset contains remote files. If you would like to validate with remote files, use the --remoteFiles option.',
},
115: {
key: 'HED_EXTRA_DELIMITER',
severity: 'error',
reason:
'This HED string contains an extra delimiter. There should be no consecutive delimiters or any delimiters at the start or end of the string.',
},
116: {
key: 'HED_INVALID_TAG',
severity: 'error',
reason:
"This HED string contains a tag that doesn't exist in the HED schema and isn't a legal extension of a valid tag.",
},
117: {
key: 'HED_MULTIPLE_UNIQUE_TAGS',
severity: 'error',
reason:
'This HED string contains multiple tags with a prefix defined as unique by the HED schema.',
},
118: {
key: 'HED_CHILD_REQUIRED',
severity: 'error',
reason:
"This HED string contains a tag which doesn't have a child, but is required to have one by the HED schema.",
},
119: {
key: 'HED_REQUIRED_PREFIX_MISSING',
severity: 'warning',
reason:
'This HED string is missing a tag with a prefix required by the HED schema.',
},
120: {
key: 'HED_UNIT_CLASS_DEFAULT_USED',
severity: 'warning',
reason:
"This HED string contains a tag with a missing unit. The default unit for that tag's unit class was used.",
},
121: {
key: 'HED_UNIT_CLASS_INVALID_UNIT',
severity: 'error',
reason:
'This HED string contains a tag with a unit that is not valid for its unit class.',
},
122: {
key: 'HED_EXTRA_COMMA_OR_INVALID',
severity: 'error',
reason:
'This HED string contains either a tag with an extra comma or an invalid tag.',
},
123: {
key: 'INVALID JSON ENCODING',
severity: 'error',
reason: 'JSON files must be valid utf-8.',
},
124: {
key: 'INVALID_TSV_UNITS',
severity: 'error',
reason:
'Units in .tsv files must be valid SI units as described in the BIDS spec Appendix V (https://bids-specification.readthedocs.io/en/stable/99-appendices/05-units.html).'
},
125: {
key: 'CHANNELS_COLUMN_STATUS',
severity: 'error',
reason:
'Status column in channels.tsv files must contain only one of two values: good or bad. Per the BIDS spec: (https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/04-intracranial-electroencephalography.html#channels-description-_channelstsv).'
},
128: {
key: 'NO_GENETIC_DATABASE',
severity: 'error',
reason:
'A genetic_info.json file is present but no Database field present in Genetics object in dataset_description.json.',
},
}