From 5e29bc6413963b0cbd0469c4ab64f15085d7e455 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 29 Aug 2022 23:29:56 -0400 Subject: [PATCH 1/2] Tracking error codes in unused format --- src/schema/errors.csv | 104 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 104 insertions(+) create mode 100644 src/schema/errors.csv diff --git a/src/schema/errors.csv b/src/schema/errors.csv new file mode 100644 index 0000000000..ea37abfc7d --- /dev/null +++ b/src/schema/errors.csv @@ -0,0 +1,104 @@ +,A,B,,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,AB,AC +1,Issue,Key,,Severity,Scope,"Coded in",Sources,Reason,Task,Status,PR,OriginalValidatorLink,SchemaLink,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +2,113,NO_AUTHORS,,warning,file,schema-query,"BIDS metadata","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.","dataset_description task",MERGED,1064,linked,https://github.com/bids-standard/bids-specification/blob/b59550c3d934c788f0a4829293bf19e583e2b109/src/schema/rules/dataset_metadata.yaml#L13,,,,,,,,,,,,,,,,, +3,128,NO_GENETIC_DATABASE,,error,file,schema-query,"BIDS metadata","A genetic_info.json file is present but no Database field present in Genetics object in dataset_description.json.","dataset_description task",MERGED,1064,,https://github.com/bids-standard/bids-specification/blob/b59550c3d934c788f0a4829293bf19e583e2b109/src/schema/rules/dataset_metadata.yaml#L50,,,,,,,,,,,,,,,,, +4,149,PASL_BOLUS_CUT_OFF_DELAY_TIME,,error,file,schema-query,"BIDS metadata","It is required to define 'BolusCutOffDelayTime' for this file, when 'BolusCutOffFlag' is set to true. 'BolusCutOffDelayTime' is the duration between the end of the labeling and the start of the bolus cut-off saturation pulse(s), in seconds. This can be a number or array of numbers, of which the values must be non-negative and monotonically increasing, depending on the number of bolus cut-off saturation pulses. For Q2TIPS, only the values for the first and last bolus cut-off saturation pulses are provided. Based on DICOM Tag 0018,925F ASL Bolus Cut-off Delay Time.","defined in src/schema/rules/sidecars/asl.yaml",MERGED,,,https://github.com/bids-standard/bids-specification/blob/8d4549dc6dada4d89b7029cb2959f1d9325133d4/src/schema/rules/sidecars/asl.yaml#L214,,,,,,,,,,,,,,,,, +5,150,PASL_BOLUS_CUT_OFF_TECHNIQUE,,error,file,schema-query,"BIDS metadata","It is required to define 'BolusCutOffTechnique' for this file, when 'BolusCutOffFlag' is set to true. 'BolusCutOffTechnique' is the name of the technique used (e.g. Q2TIPS, QUIPSS, QUIPSSII). Corresponds to DICOM Tag 0018,925E ASL Bolus Cut-off Technique.","defined in src/schema/rules/sidecars/asl.yaml",MERGED,,,https://github.com/bids-standard/bids-specification/blob/8d4549dc6dada4d89b7029cb2959f1d9325133d4/src/schema/rules/sidecars/asl.yaml#L228,,,,,,,,,,,,,,,,, +6,166,LOOK_LOCKER_FLIP_ANGLE_MISSING,,error,file,schema-query,"BIDS metadata","You should define 'FlipAngle' for this file, in case of a LookLocker acquisition. 'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees. Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`. The data type number may apply to files from any MRI modality concerned with a single value for this field, or to the files in a file collection where the value of this field is iterated using the flip entity. The data type array provides a value for each volume in a 4D dataset and should only be used when the volume timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.","defined in src/schema/rules/sidecars/asl.yaml",MERGED,,,https://github.com/bids-standard/bids-specification/blob/8d4549dc6dada4d89b7029cb2959f1d9325133d4/src/schema/rules/sidecars/asl.yaml#L54,,,,,,,,,,,,,,,,, +7,183,SLICE_TIMING_NOT_DEFINED_2D_ASL,,error,file,schema-query,"BIDS metadata","You should define SliceTiming', in case 'SequenceType' is set to a 2D sequence. 'SliceTiming' is the time at which each slice was acquired within each volume (frame) of the acquisition. Slice timing is not slice order -- rather, it is a list of times containing the time (in seconds) of each slice acquisition in relation to the beginning of volume acquisition. The list goes through the slices along the slice axis in the slice encoding dimension (see below). Note that to ensure the proper interpretation of the `SliceTiming` field, it is important to check if the OPTIONAL `SliceEncodingDirection` exists. In particular, if `SliceEncodingDirection` is negative, the entries in `SliceTiming` are defined in reverse order with respect to the slice axis, such that the final entry in the `SliceTiming` list is the time of acquisition of slice 0. Without this parameter slice time correction will not be possible.","defined in src/schema/rules/sidecars/asl.yaml",MERGED,,,https://github.com/bids-standard/bids-specification/blob/8d4549dc6dada4d89b7029cb2959f1d9325133d4/src/schema/rules/sidecars/asl.yaml#L33,,,,,,,,,,,,,,,,, +8,195,M0ESTIMATE_NOT_DEFINED,,error,file,schema-query,"BIDS metadata","You must define 'M0Estimate' for this file, in case 'M0Type' is defined as 'Estimate'. 'M0Estimate' is a single numerical whole-brain M0 value (referring to the M0 of blood), only if obtained externally (for example retrieved from CSF in a separate measurement).","defined in src/schema/rules/sidecars/asl.yaml",MERGED,,,https://github.com/bids-standard/bids-specification/blob/8d4549dc6dada4d89b7029cb2959f1d9325133d4/src/schema/rules/sidecars/asl.yaml#L111,,,,,,,,,,,,,,,,, +9,171,VOLUME_TIMING_MISSING_ACQUISITION_DURATION,,error,file,schema-query,"BIDS metadata","The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.","defined in src/schema/rules/sidecars/func.yaml",MERGED,,,https://github.com/bids-standard/bids-specification/blob/8d4549dc6dada4d89b7029cb2959f1d9325133d4/src/schema/rules/sidecars/func.yaml#L26,,,,,,,,,,,,,,,,, +10,8,EFFECTIVE_ECHO_SPACING_NOT_DEFINED,,warning,file,schema-query,"BIDS metadata","You should define 'EffectiveEchoSpacing' for this file. If you don't provide this information field map correction will not be possible.","defined in src/schema/rules/sidecars/mri.yaml",MERGED,,,https://github.com/bids-standard/bids-specification/blob/8d4549dc6dada4d89b7029cb2959f1d9325133d4/src/schema/rules/sidecars/mri.yaml#L130,,,,,,,,,,,,,,,,, +11,193,ECHO_TIME_NOT_DEFINED,,error,file,schema-query,"BIDS metadata","You must define 'EchoTime' for this file. 'EchoTime' is the echo time (TE) for the acquisition, specified in seconds. Corresponds to DICOM Tag 0018, 0081 Echo Time (please note that the DICOM term is in milliseconds not seconds). The data type number may apply to files from any MRI modality concerned with a single value for this field, or to the files in a file collection where the value of this field is iterated using the echo entity. The data type array provides a value for each volume in a 4D dataset and should only be used when the volume timing is critical for interpretation of the data, such as in ASL or variable echo time fMRI sequences.","defined in src/schema/rules/sidecars/mri.yaml",MERGED,,,https://github.com/bids-standard/bids-specification/blob/8d4549dc6dada4d89b7029cb2959f1d9325133d4/src/schema/rules/sidecars/mri.yaml#L157,,,,,,,,,,,,,,,,, +12,25,EVENTS_TSV_MISSING,,warning,file,,,"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"".","Associated files task",MERGED,,,https://github.com/bids-standard/bids-specification/blob/b59550c3d934c788f0a4829293bf19e583e2b109/src/schema/rules/checks/events.yaml#L5,,,,,,,,,,,,,,,,, +13,29,VOLUME_COUNT_MISMATCH,,error,,schema-query,"header of data file, associated file","The number of volumes in this scan does not match the number of volumes in the corresponding .bvec and .bval files.","Associated files task",MERGED,,,https://github.com/bids-standard/bids-specification/blob/b59550c3d934c788f0a4829293bf19e583e2b109/src/schema/rules/checks/dwi.yaml#L5,,,,,,,,,,,,,,,,, +14,32,DWI_MISSING_BVEC,,error,file,schema-query,"associated file","DWI scans should have a corresponding .bvec file.","Associated files task",MERGED,,,https://github.com/bids-standard/bids-specification/blob/b59550c3d934c788f0a4829293bf19e583e2b109/src/schema/rules/checks/dwi.yaml#L42,,,,,,,,,,,,,,,,, +15,33,DWI_MISSING_BVAL,,error,file,schema-query,"associated file","DWI scans should have a corresponding .bval file.","Associated files task",MERGED,,,https://github.com/bids-standard/bids-specification/blob/b59550c3d934c788f0a4829293bf19e583e2b109/src/schema/rules/checks/dwi.yaml#L53,,,,,,,,,,,,,,,,, +16,91,_FIELDMAP_WITHOUT_MAGNITUDE_FILE,,error,file,schema-query,"associated data","_fieldmap.nii[.gz] file does not have accompanying _magnitude.nii[.gz] file.","Associated files task",MERGED,,,https://github.com/bids-standard/bids-specification/blob/b59550c3d934c788f0a4829293bf19e583e2b109/src/schema/rules/checks/fmap.yaml#L5,,,,,,,,,,,,,,,,, +17,92,MISSING_MAGNITUDE1_FILE,,warning,file,schema-query,"associated data","Each _phasediff.nii[.gz] file should be associated with a _magnitude1.nii[.gz] file.","Associated files task",MERGED,,,https://github.com/bids-standard/bids-specification/blob/b59550c3d934c788f0a4829293bf19e583e2b109/src/schema/rules/checks/fmap.yaml#L17,,,,,,,,,,,,,,,,, +18,172,FLIP_ANGLE_NOT_MATCHING_ASLCONTEXT_TSV,,error,file,schema-query,"BIDS metadata, header of data file","The number of values for 'FlipAngle' for this file does not match the number of volumes in the 'sub-