bids-specification/src/schema/rules/checks/mri.yaml at 0104732131d1ea1d95d4df451d1a44557b8c3be9 · bids-standard/bids-specification · GitHub

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---
PhasePartUnits:
  issue:
    code: PHASE_UNITS
    message: |
      Phase images (with the `part-phase` entity) must have units "rad" or "arbitrary".
    level: error
  selectors:
    - modality == "mri"
    - entities.part == "phase"
    - '"Units" in sidecar'
  checks:
    - intersects([sidecar.Units], ["rad", "arbitrary"])

# 3
EchoTimeGreaterThan:
  issue:
    code: ECHO_TIME_GREATER_THAN
    message: |
      'EchoTime' is greater than 1. Are you sure it's expressed in seconds?
    level: warning
  selectors:
    - modality == "mri"
    - sidecar.EchoTime
  checks:
    - max(sidecar.EchoTime) <= 1

# 5
TotalReadoutTimeGreaterThan:
  issue:
    code: TOTAL_READOUT_TIME_GREATER_THAN
    message: |
      'TotalReadoutTime' is greater than 10. Are you sure it's expressed in seconds?
    level: warning
  selectors:
    - modality == "mri"
    - sidecar.TotalReadoutTime
  checks:
    - sidecar.TotalReadoutTime <= 10

# 76
EffectiveEchoSpacingTooLarge:
  issue:
    code: EFFECTIVEECHOSPACING_TOO_LARGE
    message: |
      Abnormally high value of 'EffectiveEchoSpacing'.
    level: error
  selectors:
    - modality == "mri"
    - type(sidecar.RepetitionTime) != "null"
    - type(sidecar.EffectiveEchoSpacing) != "null"
    - type(sidecar.PhaseEncodingDirection) != "null"
    - type(nifti_header) != "null"
  checks:
    - |
      sidecar.RepetitionTime >= (
        sidecar.EffectiveEchoSpacing
        * nifti_header.dim[index(["i", "j", "k"], sidecar.PhaseEncodingDirection[0])]
      )

# 87
SliceTimingElements:
  issue:
    code: SLICETIMING_ELEMENTS
    message: |
      The number of elements in the 'SliceTiming' array should match the 'k'
      dimension of the corresponding NIfTI volume.
    level: warning
  selectors:
    - modality == "mri"
    - type(sidecar.SliceTiming) != "null"
    - type(nifti_header) != "null"
    - type(sidecar.SliceEncodingDirection) == 'null'
  checks:
    - length(sidecar.SliceTiming) == nifti_header.dim[3]

SliceTimingElementsWithDirection:
  issue:
    code: SLICETIMING_ELEMENTS
    message: |
      The number of elements in the 'SliceTiming' array should match the dimension
      of the corresponding NIfTI volume matching `SliceEncodingDirection`
    level: warning
  selectors:
    - modality == "mri"
    - type(sidecar.SliceTiming) != "null"
    - type(nifti_header) != "null"
    - sidecar.SliceEncodingDirection
  checks:
    - sidecar.SliceEncodingDirection[0] != "i" || length(sidecar.SliceTiming) == nifti_header.dim[1]
    - sidecar.SliceEncodingDirection[0] != "j" || length(sidecar.SliceTiming) == nifti_header.dim[2]
    - sidecar.SliceEncodingDirection[0] != "k" || length(sidecar.SliceTiming) == nifti_header.dim[3]

# 93
EESGreaterThanTRT:
  issue:
    code: EFFECTIVEECHOSPACING_LARGER_THAN_TOTALREADOUTTIME
    message: |
      'EffectiveEchoSpacing' should always be smaller than 'TotalReadoutTime'.
    level: error
  selectors:
    - modality == "mri"
    - sidecar.EffectiveEchoSpacing != null
    - sidecar.TotalReadoutTime != null
  checks:
    - sidecar.EffectiveEchoSpacing < sidecar.TotalReadoutTime

# 188
VolumeTimingNotMonotonicallyIncreasing:
  issue:
    code: VOLUME_TIMING_NOT_MONOTONICALLY_INCREASING
    message: |
      'VolumeTiming' is not monotonically increasing.
    level: error
  selectors:
    - modality == "mri"
    - sidecar.VolumeTiming != null
  checks:
    - allequal(sorted(sidecar.VolumeTiming), sidecar.VolumeTiming)

# 192
BolusCutOffDelayTimeNotMonotonicallyIncreasing:
  issue:
    code: BOLUS_CUT_OFF_DELAY_TIME_NOT_MONOTONICALLY_INCREASING
    message: |
      'BolusCutOffDelayTime' is not monotonically increasing.
    level: error
  selectors:
    - modality == "mri"
    - type(sidecar.BolusCutOffDelayTime) == 'array'
  checks:
    - allequal(sorted(sidecar.BolusCutOffDelayTime), sidecar.BolusCutOffDelayTime)

# 201
RepetitionTimePreparationNotConsistent:
  issue:
    code: REPETITIONTIME_PREPARATION_NOT_CONSISTENT
    message: |
      The number of values for 'RepetitionTimePreparation' for this file does
      not match the 4th dimension of the NIfTI header.
    level: error
  selectors:
    - modality == "mri"
    - type(sidecar.RepetitionTimePreparation) == "array"
    - type(nifti_header) != "null"
  checks:
    - length(sidecar.RepetitionTimePreparation) == nifti_header.dim[4]

BigDeltaNotConsistent:
  issue:
    code: BIGDELTA_NOT_CONSISTENT
    message: |
      The number of values for 'BigDelta' for this file does
      not match the 4th dimension of the NIfTI header.
    level: error
  selectors:
    - suffix == "dwi"
    - type(sidecar.BigDelta) == "array"
    - type(nifti_header) != "null"
  checks:
    - length(sidecar.BigDelta) == nifti_header.dim[4]

SmallDeltaNotConsistent:
  issue:
    code: SMALLDELTA_NOT_CONSISTENT
    message: |
      The number of values for 'SmallDelta' for this file does
      not match the 4th dimension of the NIfTI header.
    level: error
  selectors:
    - suffix == "dwi"
    - type(sidecar.SmallDelta) == "array"
    - type(nifti_header) != "null"
  checks:
    - length(sidecar.SmallDelta) == nifti_header.dim[4]