From 341a73bec9ef1d114e0b8508ca9125d8c96e9117 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 12 Apr 2022 14:25:41 -0400
Subject: [PATCH 01/16] Draft ASL validation file.

---
 src/schema/rules/sidecars/asl_validation.yaml | 178 ++++++++++++++++++
 1 file changed, 178 insertions(+)
 create mode 100644 src/schema/rules/sidecars/asl_validation.yaml

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
new file mode 100644
index 0000000000..3319d3041d
--- /dev/null
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -0,0 +1,178 @@
+# Rules for ASL data that are not defined in tables.
+---
+ASLPostLabelingDelayASLContextLength:
+    code: POST_LABELING_DELAY_NOT_MATCHING_ASLCONTEXT_TSV
+    description: |
+        The number of values for 'PostLabelingDelay' for this file does not match the number of volumes
+        in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or
+        middle of the labeling pulse (for PASL) until the middle of the excitation pulse applied to
+        the imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
+        Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
+        In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
+        in the acquisition order.
+        Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a zero.
+        Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
+    level: error
+    selectors:
+    - sidecar contains "PostLabelingDelay"
+    - type(sidecar.PostLabelingDelay) == "array"
+    - suffix == "asl"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.PostLabelingDelay.size
+
+ASLLabelingDurationASLContextLength:
+    code: LABELLING_DURATION_NOT_MATCHING_ASLCONTEXT_TSV
+    description: |
+        The number of values for 'LabelingDuration' for this file does not match the number of volumes
+        in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
+        corresponding to the temporal width of the labeling bolus for `(P)CASL`.
+        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`,
+        a scalar must be specified.
+        In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
+        an array of numbers must be specified, for which any `m0scan` in the timeseries has a
+        `LabelingDuration` of zero.
+        In case an array of numbers is provided, its length should be equal to the number of volumes
+        specified in `*_aslcontext.tsv`.
+        Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
+    level: error
+    selectors:
+    - sidecar contains "LabelingDuration"
+    - type(sidecar.LabelingDuration) == "array"
+    - suffix == "asl"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.LabelingDuration.size
+
+ASLRepetitionTimePreparationASLContextLength:
+    code: REPETITIONTIMEPREPARATION_NOT_MATCHING_ASLCONTEXT_TSV
+    description: |
+        The number of values of 'RepetitionTimePreparation' for this file does not match the number of
+        volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'RepetitionTimePreparation' is the interval, in seconds, that it takes a preparation pulse block to
+        re-appear at the beginning of the succeeding (essentially identical) pulse sequence block.
+        The data type number may apply to files from any MRI modality concerned with a single value for this field.
+        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.
+    level: error
+    selectors:
+    - sidecar contains "RepetitionTimePreparation"
+    - type(sidecar.RepetitionTimePreparation) == "array"
+    - suffix == "asl"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.RepetitionTimePreparation.size
+
+ASLTotalAcquiredVolumesASLContextLength:
+    code: TOTAL_ACQUIRED_VOLUMES_NOT_CONSISTENT
+    description: |
+        The number of values for 'TotalAcquiredVolumes' for this file does not match number of
+        volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'TotalAcquiredVolumes' is the original number of 3D volumes acquired for each volume defined in the
+        'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+    level: error
+    selectors:
+    - sidecar contains "TotalAcquiredVolumes"
+    - suffix == "asl"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.TotalAcquiredVolumes
+
+ASLFlipAngleASLContextLength:
+    code: FLIP_ANGLE_NOT_MATCHING_ASLCONTEXT_TSV
+    description: |
+       The number of values for 'FlipAngle' for this file does not match the number of volumes in the
+       'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+       '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.
+    level: error
+    selectors:
+    - sidecar contains "FlipAngle"
+    - type(sidecar.FlipAngle) == "array"
+    - suffix == "asl"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.FlipAngle.size
+
+ASLFlipAngleNiftiLength:
+    code: FLIP_ANGLE_NOT_MATCHING_NIFTI
+    description: |
+        The number of values for 'FlipAngle' for this file does not match the 4th dimension of the NIfTI header.
+        '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.
+    level: error
+    selectors:
+    - sidecar contains "FlipAngle"
+    - type(sidecar.FlipAngle) == "array"
+    - suffix == "asl"
+    checks:
+    - data.shape[3] == sidecar.FlipAngle.size
+
+ASLPostLabelingDelayNiftiLength:
+    code: POST_LABELING_DELAY_NOT_MATCHING_NIFTI
+    description: |
+        The number of values for 'PostLabelingDelay' for this file does not match the 4th dimension of the NIfTI header.
+        'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or middle of the
+        labeling pulse (for PASL) until the middle of the excitation pulse applied to the imaging slab
+        (for 3D acquisition) or first slice (for 2D acquisition).
+        Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
+        In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
+        in the acquisition order. Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a zero.
+        Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
+    level: error
+    selectors:
+    - sidecar contains "PostLabelingDelay"
+    - type(sidecar.PostLabelingDelay) == "array"
+    - suffix == "asl"
+    checks:
+    - data.shape[3] == sidecar.PostLabelingDelay.size
+
+ASLContextConsistent:
+    code: ASLCONTEXT_TSV_NOT_CONSISTENT
+    description: |
+        The number of volumes in the '*_aslcontext.tsv' for this file does not match the number of
+        values in the NIfTI header.
+    level: error
+    selectors:
+    - suffix == "asl"
+    checks:
+    - data.shape[3] == associated["aslcontext"].shape[0]
+
+ASLBackgroundSuppressionNumberPulses:
+    code: BACKGROUND_SUPPRESSION_PULSE_NUMBER_NOT_CONSISTENT
+    description: |
+        The 'BackgroundSuppressionNumberPulses' field is not consistent with the length of 'BackgroundSuppressionPulseTime'.
+        'BackgroundSuppressionNumberPulses' is the number of background suppression pulses used.
+        Note that this excludes any effect of background suppression pulses applied before the labeling.
+    level: warning
+    selectors:
+    - sidecar contains "BackgroundSuppressionNumberPulses"
+    - sidecar contains "BackgroundSuppressionPulseTime"
+    - type(sidecar.BackgroundSuppressionPulseTime) == "array"
+    - suffix == "asl"
+    checks:
+    - sidecar.BackgroundSuppressionPulseTime.size == sidecar.BackgroundSuppressionNumberPulses
+
+ASLLabelingDurationNiftiLength:
+    code: LABELING_DURATION_LENGTH_NOT_MATCHING_NIFTI
+    description: |
+        The number of values for 'LabelingDuration' for this file does not match the 4th dimension of the NIfTI header.
+        'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
+        corresponding to the temporal width of the labeling bolus for `(P)CASL`.
+        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be specified.
+        In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
+        an array of numbers must be specified, for which any `m0scan` in the timeseries has a `LabelingDuration` of zero.
+        In case an array of numbers is provided, its length should be equal to the number of volumes specified in
+        `*_aslcontext.tsv`. Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
+    level: error
+    selectors:
+    - sidecar contains "LabelingDuration"
+    - type(sidecar.LabelingDuration) == "array"
+    - suffix == "asl"
+    checks:
+    - data.shape[3] == sidecar.LabelingDuration.size

From c57135839c4887021e488b6076ee303e8dabaf2b Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 12 Apr 2022 14:27:17 -0400
Subject: [PATCH 02/16] Fix level.

---
 src/schema/rules/sidecars/asl_validation.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 3319d3041d..dcd0764bda 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -69,7 +69,7 @@ ASLTotalAcquiredVolumesASLContextLength:
         volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
         'TotalAcquiredVolumes' is the original number of 3D volumes acquired for each volume defined in the
         'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-    level: error
+    level: warning
     selectors:
     - sidecar contains "TotalAcquiredVolumes"
     - suffix == "asl"

From a6b22c492fdefd53dd7d43634961e9e1f30fcadb Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 12 Apr 2022 15:25:19 -0400
Subject: [PATCH 03/16] Reorder based on code.

---
 src/schema/rules/sidecars/asl_validation.yaml | 191 +++++++++---------
 1 file changed, 101 insertions(+), 90 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index dcd0764bda..437a4d959f 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -1,81 +1,58 @@
 # Rules for ASL data that are not defined in tables.
 ---
-ASLPostLabelingDelayASLContextLength:
-    code: POST_LABELING_DELAY_NOT_MATCHING_ASLCONTEXT_TSV
-    description: |
-        The number of values for 'PostLabelingDelay' for this file does not match the number of volumes
-        in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-        'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or
-        middle of the labeling pulse (for PASL) until the middle of the excitation pulse applied to
-        the imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
-        Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
-        In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
-        in the acquisition order.
-        Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a zero.
-        Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
-    level: error
-    selectors:
-    - sidecar contains "PostLabelingDelay"
-    - type(sidecar.PostLabelingDelay) == "array"
-    - suffix == "asl"
-    checks:
-    - associated["aslcontext"].shape[0] == sidecar.PostLabelingDelay.size
 
-ASLLabelingDurationASLContextLength:
-    code: LABELLING_DURATION_NOT_MATCHING_ASLCONTEXT_TSV
+# 157
+ASLLabelingDurationNiftiLength:
+    code: LABELING_DURATION_LENGTH_NOT_MATCHING_NIFTI
     description: |
-        The number of values for 'LabelingDuration' for this file does not match the number of volumes
-        in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        The number of values for 'LabelingDuration' for this file does not match the 4th dimension of the NIfTI header.
         'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
         corresponding to the temporal width of the labeling bolus for `(P)CASL`.
-        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`,
-        a scalar must be specified.
+        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be specified.
         In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
-        an array of numbers must be specified, for which any `m0scan` in the timeseries has a
-        `LabelingDuration` of zero.
-        In case an array of numbers is provided, its length should be equal to the number of volumes
-        specified in `*_aslcontext.tsv`.
-        Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
+        an array of numbers must be specified, for which any `m0scan` in the timeseries has a `LabelingDuration` of zero.
+        In case an array of numbers is provided, its length should be equal to the number of volumes specified in
+        `*_aslcontext.tsv`. Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
     level: error
     selectors:
     - sidecar contains "LabelingDuration"
     - type(sidecar.LabelingDuration) == "array"
     - suffix == "asl"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.LabelingDuration.size
+    - data.shape[3] == sidecar.LabelingDuration.size
 
-ASLRepetitionTimePreparationASLContextLength:
-    code: REPETITIONTIMEPREPARATION_NOT_MATCHING_ASLCONTEXT_TSV
+# 165
+ASLContextConsistent:
+    code: ASLCONTEXT_TSV_NOT_CONSISTENT
     description: |
-        The number of values of 'RepetitionTimePreparation' for this file does not match the number of
-        volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-        'RepetitionTimePreparation' is the interval, in seconds, that it takes a preparation pulse block to
-        re-appear at the beginning of the succeeding (essentially identical) pulse sequence block.
-        The data type number may apply to files from any MRI modality concerned with a single value for this field.
-        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.
+        The number of volumes in the '*_aslcontext.tsv' for this file does not match the number of
+        values in the NIfTI header.
     level: error
     selectors:
-    - sidecar contains "RepetitionTimePreparation"
-    - type(sidecar.RepetitionTimePreparation) == "array"
     - suffix == "asl"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.RepetitionTimePreparation.size
+    - data.shape[3] == associated["aslcontext"].shape[0]
 
-ASLTotalAcquiredVolumesASLContextLength:
-    code: TOTAL_ACQUIRED_VOLUMES_NOT_CONSISTENT
+# 168
+ASLFlipAngleNiftiLength:
+    code: FLIP_ANGLE_NOT_MATCHING_NIFTI
     description: |
-        The number of values for 'TotalAcquiredVolumes' for this file does not match number of
-        volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-        'TotalAcquiredVolumes' is the original number of 3D volumes acquired for each volume defined in the
-        'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
-    level: warning
+        The number of values for 'FlipAngle' for this file does not match the 4th dimension of the NIfTI header.
+        '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.
+    level: error
     selectors:
-    - sidecar contains "TotalAcquiredVolumes"
+    - sidecar contains "FlipAngle"
+    - type(sidecar.FlipAngle) == "array"
     - suffix == "asl"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.TotalAcquiredVolumes
+    - data.shape[3] == sidecar.FlipAngle.size
 
+# 172
 ASLFlipAngleASLContextLength:
     code: FLIP_ANGLE_NOT_MATCHING_ASLCONTEXT_TSV
     description: |
@@ -95,24 +72,7 @@ ASLFlipAngleASLContextLength:
     checks:
     - associated["aslcontext"].shape[0] == sidecar.FlipAngle.size
 
-ASLFlipAngleNiftiLength:
-    code: FLIP_ANGLE_NOT_MATCHING_NIFTI
-    description: |
-        The number of values for 'FlipAngle' for this file does not match the 4th dimension of the NIfTI header.
-        '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.
-    level: error
-    selectors:
-    - sidecar contains "FlipAngle"
-    - type(sidecar.FlipAngle) == "array"
-    - suffix == "asl"
-    checks:
-    - data.shape[3] == sidecar.FlipAngle.size
-
+# 173
 ASLPostLabelingDelayNiftiLength:
     code: POST_LABELING_DELAY_NOT_MATCHING_NIFTI
     description: |
@@ -132,17 +92,72 @@ ASLPostLabelingDelayNiftiLength:
     checks:
     - data.shape[3] == sidecar.PostLabelingDelay.size
 
-ASLContextConsistent:
-    code: ASLCONTEXT_TSV_NOT_CONSISTENT
+# 174
+ASLPostLabelingDelayASLContextLength:
+    code: POST_LABELING_DELAY_NOT_MATCHING_ASLCONTEXT_TSV
     description: |
-        The number of volumes in the '*_aslcontext.tsv' for this file does not match the number of
-        values in the NIfTI header.
+        The number of values for 'PostLabelingDelay' for this file does not match the number of volumes
+        in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or
+        middle of the labeling pulse (for PASL) until the middle of the excitation pulse applied to
+        the imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
+        Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
+        In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
+        in the acquisition order.
+        Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a zero.
+        Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
     level: error
     selectors:
+    - sidecar contains "PostLabelingDelay"
+    - type(sidecar.PostLabelingDelay) == "array"
     - suffix == "asl"
     checks:
-    - data.shape[3] == associated["aslcontext"].shape[0]
+    - associated["aslcontext"].shape[0] == sidecar.PostLabelingDelay.size
+
+# 175
+ASLLabelingDurationASLContextLength:
+    code: LABELLING_DURATION_NOT_MATCHING_ASLCONTEXT_TSV
+    description: |
+        The number of values for 'LabelingDuration' for this file does not match the number of volumes
+        in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
+        corresponding to the temporal width of the labeling bolus for `(P)CASL`.
+        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`,
+        a scalar must be specified.
+        In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
+        an array of numbers must be specified, for which any `m0scan` in the timeseries has a
+        `LabelingDuration` of zero.
+        In case an array of numbers is provided, its length should be equal to the number of volumes
+        specified in `*_aslcontext.tsv`.
+        Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
+    level: error
+    selectors:
+    - sidecar contains "LabelingDuration"
+    - type(sidecar.LabelingDuration) == "array"
+    - suffix == "asl"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.LabelingDuration.size
 
+# 177
+ASLRepetitionTimePreparationASLContextLength:
+    code: REPETITIONTIMEPREPARATION_NOT_MATCHING_ASLCONTEXT_TSV
+    description: |
+        The number of values of 'RepetitionTimePreparation' for this file does not match the number of
+        volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'RepetitionTimePreparation' is the interval, in seconds, that it takes a preparation pulse block to
+        re-appear at the beginning of the succeeding (essentially identical) pulse sequence block.
+        The data type number may apply to files from any MRI modality concerned with a single value for this field.
+        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.
+    level: error
+    selectors:
+    - sidecar contains "RepetitionTimePreparation"
+    - type(sidecar.RepetitionTimePreparation) == "array"
+    - suffix == "asl"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.RepetitionTimePreparation.size
+
+# 180
 ASLBackgroundSuppressionNumberPulses:
     code: BACKGROUND_SUPPRESSION_PULSE_NUMBER_NOT_CONSISTENT
     description: |
@@ -158,21 +173,17 @@ ASLBackgroundSuppressionNumberPulses:
     checks:
     - sidecar.BackgroundSuppressionPulseTime.size == sidecar.BackgroundSuppressionNumberPulses
 
-ASLLabelingDurationNiftiLength:
-    code: LABELING_DURATION_LENGTH_NOT_MATCHING_NIFTI
+# 181
+ASLTotalAcquiredVolumesASLContextLength:
+    code: TOTAL_ACQUIRED_VOLUMES_NOT_CONSISTENT
     description: |
-        The number of values for 'LabelingDuration' for this file does not match the 4th dimension of the NIfTI header.
-        'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
-        corresponding to the temporal width of the labeling bolus for `(P)CASL`.
-        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be specified.
-        In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
-        an array of numbers must be specified, for which any `m0scan` in the timeseries has a `LabelingDuration` of zero.
-        In case an array of numbers is provided, its length should be equal to the number of volumes specified in
-        `*_aslcontext.tsv`. Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
-    level: error
+        The number of values for 'TotalAcquiredVolumes' for this file does not match number of
+        volumes in the 'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'TotalAcquiredVolumes' is the original number of 3D volumes acquired for each volume defined in the
+        'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+    level: warning
     selectors:
-    - sidecar contains "LabelingDuration"
-    - type(sidecar.LabelingDuration) == "array"
+    - sidecar contains "TotalAcquiredVolumes"
     - suffix == "asl"
     checks:
-    - data.shape[3] == sidecar.LabelingDuration.size
+    - associated["aslcontext"].shape[0] == sidecar.TotalAcquiredVolumes

From 60d1572c5a9dad1922665ab9b744b934416aa5ca Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 12 Apr 2022 15:34:06 -0400
Subject: [PATCH 04/16] Add 196 and reorder selectors.

---
 src/schema/rules/sidecars/asl_validation.yaml | 40 ++++++++++++++-----
 1 file changed, 31 insertions(+), 9 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 437a4d959f..fe340bc6d2 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -15,9 +15,9 @@ ASLLabelingDurationNiftiLength:
         `*_aslcontext.tsv`. Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
     level: error
     selectors:
+    - suffix == "asl"
     - sidecar contains "LabelingDuration"
     - type(sidecar.LabelingDuration) == "array"
-    - suffix == "asl"
     checks:
     - data.shape[3] == sidecar.LabelingDuration.size
 
@@ -30,6 +30,7 @@ ASLContextConsistent:
     level: error
     selectors:
     - suffix == "asl"
+    - associated contains "aslcontext"
     checks:
     - data.shape[3] == associated["aslcontext"].shape[0]
 
@@ -46,9 +47,9 @@ ASLFlipAngleNiftiLength:
         volume timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
     level: error
     selectors:
+    - suffix == "asl"
     - sidecar contains "FlipAngle"
     - type(sidecar.FlipAngle) == "array"
-    - suffix == "asl"
     checks:
     - data.shape[3] == sidecar.FlipAngle.size
 
@@ -66,9 +67,10 @@ ASLFlipAngleASLContextLength:
        timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.
     level: error
     selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
     - sidecar contains "FlipAngle"
     - type(sidecar.FlipAngle) == "array"
-    - suffix == "asl"
     checks:
     - associated["aslcontext"].shape[0] == sidecar.FlipAngle.size
 
@@ -86,9 +88,9 @@ ASLPostLabelingDelayNiftiLength:
         Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
     level: error
     selectors:
+    - suffix == "asl"
     - sidecar contains "PostLabelingDelay"
     - type(sidecar.PostLabelingDelay) == "array"
-    - suffix == "asl"
     checks:
     - data.shape[3] == sidecar.PostLabelingDelay.size
 
@@ -108,9 +110,10 @@ ASLPostLabelingDelayASLContextLength:
         Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
     level: error
     selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
     - sidecar contains "PostLabelingDelay"
     - type(sidecar.PostLabelingDelay) == "array"
-    - suffix == "asl"
     checks:
     - associated["aslcontext"].shape[0] == sidecar.PostLabelingDelay.size
 
@@ -132,9 +135,10 @@ ASLLabelingDurationASLContextLength:
         Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
     level: error
     selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
     - sidecar contains "LabelingDuration"
     - type(sidecar.LabelingDuration) == "array"
-    - suffix == "asl"
     checks:
     - associated["aslcontext"].shape[0] == sidecar.LabelingDuration.size
 
@@ -151,9 +155,10 @@ ASLRepetitionTimePreparationASLContextLength:
         volume timing is critical for interpretation of the data, such as in ASL.
     level: error
     selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
     - sidecar contains "RepetitionTimePreparation"
     - type(sidecar.RepetitionTimePreparation) == "array"
-    - suffix == "asl"
     checks:
     - associated["aslcontext"].shape[0] == sidecar.RepetitionTimePreparation.size
 
@@ -166,10 +171,10 @@ ASLBackgroundSuppressionNumberPulses:
         Note that this excludes any effect of background suppression pulses applied before the labeling.
     level: warning
     selectors:
+    - suffix == "asl"
     - sidecar contains "BackgroundSuppressionNumberPulses"
     - sidecar contains "BackgroundSuppressionPulseTime"
     - type(sidecar.BackgroundSuppressionPulseTime) == "array"
-    - suffix == "asl"
     checks:
     - sidecar.BackgroundSuppressionPulseTime.size == sidecar.BackgroundSuppressionNumberPulses
 
@@ -183,7 +188,24 @@ ASLTotalAcquiredVolumesASLContextLength:
         'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
     level: warning
     selectors:
-    - sidecar contains "TotalAcquiredVolumes"
     - suffix == "asl"
+    - associated contains "aslcontext"
+    - sidecar contains "TotalAcquiredVolumes"
     checks:
     - associated["aslcontext"].shape[0] == sidecar.TotalAcquiredVolumes
+
+# 196
+ASLEchoTimeASLContextLength:
+    code: ECHO_TIME_NOT_CONSISTENT
+    description: |
+        The number of values for 'EchoTime' for this file does not match number of volumes in the
+        'sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_aslcontext.tsv'.
+        'EchoTime' is the echo time (TE) for the acquisition, specified in seconds.
+    level: warning
+    selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
+    - sidecar contains "EchoTime"
+    - type(sidecar.EchoTime) == "array"
+    checks:
+    - associated["aslcontext"].shape[0] == sidecar.EchoTime.size

From f8214ba066b782506596430ca835258d5a7276fb Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 12 Apr 2022 15:47:29 -0400
Subject: [PATCH 05/16] Add a few DWI and events rules.

---
 src/schema/rules/sidecars/dwi_validation.yaml | 39 +++++++++++++++++++
 .../rules/sidecars/events_validation.yaml     | 16 ++++++++
 2 files changed, 55 insertions(+)
 create mode 100644 src/schema/rules/sidecars/dwi_validation.yaml
 create mode 100644 src/schema/rules/sidecars/events_validation.yaml

diff --git a/src/schema/rules/sidecars/dwi_validation.yaml b/src/schema/rules/sidecars/dwi_validation.yaml
new file mode 100644
index 0000000000..73f51ea883
--- /dev/null
+++ b/src/schema/rules/sidecars/dwi_validation.yaml
@@ -0,0 +1,39 @@
+# Rules for DWI data that are not defined in tables.
+---
+
+# 29
+DWIVolumeCount:
+    code: VOLUME_COUNT_MISMATCH
+    description: |
+        The number of volumes in this scan does not match the number of volumes in the
+        corresponding .bvec and .bval files.
+    level: error
+    selectors:
+    - suffix == "dwi"
+    - associated contains "bval"
+    - associated contains "bvec"
+    checks:
+    - associated["bval"].shape[0] == data.shape[3]
+    - associated["bvec"].shape[0] == data.shape[3]
+
+# 32
+DWIMissingBvec:
+    code: DWI_MISSING_BVEC
+    description: |
+        DWI scans must have a corresponding .bvec file.
+    level: error
+    selectors:
+    - suffix == "dwi"
+    checks:
+    - associated contains "bvec"
+
+# 33
+DWIMissingBval:
+    code: DWI_MISSING_BVAL
+    description: |
+        DWI scans must have a corresponding .bval file.
+    level: error
+    selectors:
+    - suffix == "dwi"
+    checks:
+    - associated contains "bval"
diff --git a/src/schema/rules/sidecars/events_validation.yaml b/src/schema/rules/sidecars/events_validation.yaml
new file mode 100644
index 0000000000..ff445ec4c0
--- /dev/null
+++ b/src/schema/rules/sidecars/events_validation.yaml
@@ -0,0 +1,16 @@
+# Rules for events data that are not defined in tables.
+---
+
+# 25
+EventsMissing:
+    code: EVENTS_TSV_MISSING
+    description: |
+        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".
+    level: warning  # could be an error with the proper selectors, I think
+    selectors:
+    - entities contains "task"
+    - entities.task != "rest"
+    - "rest" not in entities.task  # Alternative for including the word "rest"
+    checks:
+    - associated contains "events"

From a295fc270abb271e1a9e37f206784894b24c03b9 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 12 Apr 2022 16:09:52 -0400
Subject: [PATCH 06/16] Fix linter issues.

---
 src/schema/rules/sidecars/asl_validation.yaml    | 15 ++++++++++-----
 src/schema/rules/sidecars/events_validation.yaml |  2 +-
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index fe340bc6d2..e34f9b8ebd 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -8,9 +8,11 @@ ASLLabelingDurationNiftiLength:
         The number of values for 'LabelingDuration' for this file does not match the 4th dimension of the NIfTI header.
         'LabelingDuration' is the total duration of the labeling pulse train, in seconds,
         corresponding to the temporal width of the labeling bolus for `(P)CASL`.
-        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be specified.
+        In case all control-label volumes (or deltam or CBF) have the same `LabelingDuration`, a scalar must be
+        specified.
         In case the control-label volumes (or deltam or cbf) have a different `LabelingDuration`,
-        an array of numbers must be specified, for which any `m0scan` in the timeseries has a `LabelingDuration` of zero.
+        an array of numbers must be specified, for which any `m0scan` in the timeseries has a `LabelingDuration` of
+        zero.
         In case an array of numbers is provided, its length should be equal to the number of volumes specified in
         `*_aslcontext.tsv`. Corresponds to DICOM Tag 0018,9258 `ASL Pulse Train Duration`.
     level: error
@@ -78,13 +80,15 @@ ASLFlipAngleASLContextLength:
 ASLPostLabelingDelayNiftiLength:
     code: POST_LABELING_DELAY_NOT_MATCHING_NIFTI
     description: |
-        The number of values for 'PostLabelingDelay' for this file does not match the 4th dimension of the NIfTI header.
+        The number of values for 'PostLabelingDelay' for this file does not match the 4th dimension of the NIfTI
+        header.
         'PostLabelingDelay' is the time, in seconds, after the end of the labeling (for (P)CASL) or middle of the
         labeling pulse (for PASL) until the middle of the excitation pulse applied to the imaging slab
         (for 3D acquisition) or first slice (for 2D acquisition).
         Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker).
         In the latter case, the array of numbers contains the PLD of each volume (i.e. each 'control' and 'label')
-        in the acquisition order. Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a zero.
+        in the acquisition order. Any image within the time-series without a PLD (e.g. an 'm0scan') is indicated by a
+        zero.
         Based on DICOM Tags 0018,9079 Inversion Times and 0018,0082 InversionTime.
     level: error
     selectors:
@@ -166,7 +170,8 @@ ASLRepetitionTimePreparationASLContextLength:
 ASLBackgroundSuppressionNumberPulses:
     code: BACKGROUND_SUPPRESSION_PULSE_NUMBER_NOT_CONSISTENT
     description: |
-        The 'BackgroundSuppressionNumberPulses' field is not consistent with the length of 'BackgroundSuppressionPulseTime'.
+        The 'BackgroundSuppressionNumberPulses' field is not consistent with the length of
+        'BackgroundSuppressionPulseTime'.
         'BackgroundSuppressionNumberPulses' is the number of background suppression pulses used.
         Note that this excludes any effect of background suppression pulses applied before the labeling.
     level: warning
diff --git a/src/schema/rules/sidecars/events_validation.yaml b/src/schema/rules/sidecars/events_validation.yaml
index ff445ec4c0..e4e74e9adc 100644
--- a/src/schema/rules/sidecars/events_validation.yaml
+++ b/src/schema/rules/sidecars/events_validation.yaml
@@ -11,6 +11,6 @@ EventsMissing:
     selectors:
     - entities contains "task"
     - entities.task != "rest"
-    - "rest" not in entities.task  # Alternative for including the word "rest"
+    - entities.task not contains "rest"  # Alternative for including the word "rest"
     checks:
     - associated contains "events"

From 5d6f7cd66d6fc711c81b9c5614ea99f43480dd1f Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 12 Apr 2022 16:29:24 -0400
Subject: [PATCH 07/16] Add a few more rules.

---
 src/schema/rules/sidecars/asl_validation.yaml | 43 +++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index e34f9b8ebd..4e02f30f2e 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -214,3 +214,46 @@ ASLEchoTimeASLContextLength:
     - type(sidecar.EchoTime) == "array"
     checks:
     - associated["aslcontext"].shape[0] == sidecar.EchoTime.size
+
+# 198
+ASLM0TypeAbsentScan:
+    code: M0Type_SET_INCORRECTLY_TO_ABSENT
+    description: |
+        You defined M0Type as 'absent' while including a separate '*_m0scan.nii[.gz]' and
+        '*_m0scan.json', or defining the 'M0Estimate' field.
+        This is not allowed, please check that this field are filled correctly.
+    level: error
+    selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
+    - associated contains "m0scan"
+    checks:
+    - sidecar.M0Type != "absent"
+
+# 199
+ASLM0TypeAbsentASLContext:
+    code: M0Type_SET_INCORRECTLY_TO_ABSENT_IN_ASLCONTEXT
+    description: |
+        You defined M0Type as 'absent' while including an m0scan volume within the '*_aslcontext.tsv'.
+        This is not allowed, please check that this field are filled correctly.
+    level: error
+    selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
+    - associated["aslcontext"]["volume_type"] contains "m0scan"
+    checks:
+    - sidecar.M0Type != "absent"
+
+# 202
+ASLM0TypeIncorrect:
+    code: M0Type_SET_INCORRECTLY
+    description: |
+        M0Type was not defined correctly.
+        If 'M0Type' is equal to 'separate', the dataset should include a *_m0scan.nii[.gz] and *_m0scan.json file.
+    level: error
+    selectors:
+    - suffix == "asl"
+    - associated contains "aslcontext"
+    - sidecar.M0Type == "separate"
+    checks:
+    - associated contains "m0scan"

From 3bec3f8b56f65f4176c91f52d9df00528ac33958 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Wed, 13 Apr 2022 14:29:36 -0400
Subject: [PATCH 08/16] Add a few more rules.

---
 src/schema/rules/sidecars/dwi_validation.yaml | 22 +++++++++++++++++
 .../rules/sidecars/fmap_validation.yaml       | 24 +++++++++++++++++++
 2 files changed, 46 insertions(+)
 create mode 100644 src/schema/rules/sidecars/fmap_validation.yaml

diff --git a/src/schema/rules/sidecars/dwi_validation.yaml b/src/schema/rules/sidecars/dwi_validation.yaml
index 73f51ea883..2ed5401f6d 100644
--- a/src/schema/rules/sidecars/dwi_validation.yaml
+++ b/src/schema/rules/sidecars/dwi_validation.yaml
@@ -16,6 +16,28 @@ DWIVolumeCount:
     - associated["bval"].shape[0] == data.shape[3]
     - associated["bvec"].shape[0] == data.shape[3]
 
+# 30
+DWIBvalRows:
+    code: BVAL_MULTIPLE_ROWS
+    description: |
+        '.bval' files should contain exactly one row of volumes.
+    level: error
+    selectors:
+    - extension == "bval"
+    checks:
+    - data.n_rows == 1
+
+# 31
+DWIBvecRows:
+    code: BVEC_NUMBER_ROWS
+    description: |
+        '.bvec' files should contain exactly three rows of volumes.
+    level: error
+    selectors:
+    - extension == "bvec"
+    checks:
+    - data.n_rows == 3
+
 # 32
 DWIMissingBvec:
     code: DWI_MISSING_BVEC
diff --git a/src/schema/rules/sidecars/fmap_validation.yaml b/src/schema/rules/sidecars/fmap_validation.yaml
new file mode 100644
index 0000000000..b88bce11ef
--- /dev/null
+++ b/src/schema/rules/sidecars/fmap_validation.yaml
@@ -0,0 +1,24 @@
+# Rules for fieldmap data that are not defined in tables.
+---
+
+# 91
+FmapFieldmapWithoutMagnitude:
+    code: _FIELDMAP_WITHOUT_MAGNITUDE_FILE
+    description: |
+        '_fieldmap.nii[.gz]' file does not have accompanying '_magnitude.nii[.gz]' file.
+    level: error
+    selectors:
+    - suffix == "fieldmap"
+    checks:
+    - associated contains "magnitude"
+
+# 92
+FmapPhasediffWithoutMagnitude:
+    code: MISSING_MAGNITUDE1_FILE
+    description: |
+        Each '_phasediff.nii[.gz]' file should be associated with a '_magnitude1.nii[.gz]' file.
+    level: warning
+    selectors:
+    - suffix == "phasediff"
+    checks:
+    - associated contains "magnitude1"

From 8f4eec7c5eebef177ee9b26ba7e06671a39bae94 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 14 Apr 2022 14:14:05 -0400
Subject: [PATCH 09/16] Update src/schema/rules/sidecars/asl_validation.yaml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/schema/rules/sidecars/asl_validation.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 4e02f30f2e..02a824e10e 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -34,7 +34,7 @@ ASLContextConsistent:
     - suffix == "asl"
     - associated contains "aslcontext"
     checks:
-    - data.shape[3] == associated["aslcontext"].shape[0]
+    - nifti_header.pixdim[4] == aslcontext.n_rows
 
 # 168
 ASLFlipAngleNiftiLength:

From c040e0942a1fe95e10631c7207f6afc4398bdf95 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 14 Apr 2022 14:16:43 -0400
Subject: [PATCH 10/16] Switch to new context terms.

---
 src/schema/rules/sidecars/asl_validation.yaml | 18 +++++++++---------
 src/schema/rules/sidecars/dwi_validation.yaml |  4 ++--
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 02a824e10e..903cc81f50 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -21,7 +21,7 @@ ASLLabelingDurationNiftiLength:
     - sidecar contains "LabelingDuration"
     - type(sidecar.LabelingDuration) == "array"
     checks:
-    - data.shape[3] == sidecar.LabelingDuration.size
+    - nifti_header.pixdim[4] == sidecar.LabelingDuration.size
 
 # 165
 ASLContextConsistent:
@@ -53,7 +53,7 @@ ASLFlipAngleNiftiLength:
     - sidecar contains "FlipAngle"
     - type(sidecar.FlipAngle) == "array"
     checks:
-    - data.shape[3] == sidecar.FlipAngle.size
+    - nifti_header.pixdim[4] == sidecar.FlipAngle.size
 
 # 172
 ASLFlipAngleASLContextLength:
@@ -74,7 +74,7 @@ ASLFlipAngleASLContextLength:
     - sidecar contains "FlipAngle"
     - type(sidecar.FlipAngle) == "array"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.FlipAngle.size
+    - associated["aslcontext"].n_rows == sidecar.FlipAngle.size
 
 # 173
 ASLPostLabelingDelayNiftiLength:
@@ -96,7 +96,7 @@ ASLPostLabelingDelayNiftiLength:
     - sidecar contains "PostLabelingDelay"
     - type(sidecar.PostLabelingDelay) == "array"
     checks:
-    - data.shape[3] == sidecar.PostLabelingDelay.size
+    - nifti_header.pixdim[4] == sidecar.PostLabelingDelay.size
 
 # 174
 ASLPostLabelingDelayASLContextLength:
@@ -119,7 +119,7 @@ ASLPostLabelingDelayASLContextLength:
     - sidecar contains "PostLabelingDelay"
     - type(sidecar.PostLabelingDelay) == "array"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.PostLabelingDelay.size
+    - associated["aslcontext"].n_rows == sidecar.PostLabelingDelay.size
 
 # 175
 ASLLabelingDurationASLContextLength:
@@ -144,7 +144,7 @@ ASLLabelingDurationASLContextLength:
     - sidecar contains "LabelingDuration"
     - type(sidecar.LabelingDuration) == "array"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.LabelingDuration.size
+    - associated["aslcontext"].n_rows == sidecar.LabelingDuration.size
 
 # 177
 ASLRepetitionTimePreparationASLContextLength:
@@ -164,7 +164,7 @@ ASLRepetitionTimePreparationASLContextLength:
     - sidecar contains "RepetitionTimePreparation"
     - type(sidecar.RepetitionTimePreparation) == "array"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.RepetitionTimePreparation.size
+    - associated["aslcontext"].n_rows == sidecar.RepetitionTimePreparation.size
 
 # 180
 ASLBackgroundSuppressionNumberPulses:
@@ -197,7 +197,7 @@ ASLTotalAcquiredVolumesASLContextLength:
     - associated contains "aslcontext"
     - sidecar contains "TotalAcquiredVolumes"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.TotalAcquiredVolumes
+    - associated["aslcontext"].n_rows == sidecar.TotalAcquiredVolumes
 
 # 196
 ASLEchoTimeASLContextLength:
@@ -213,7 +213,7 @@ ASLEchoTimeASLContextLength:
     - sidecar contains "EchoTime"
     - type(sidecar.EchoTime) == "array"
     checks:
-    - associated["aslcontext"].shape[0] == sidecar.EchoTime.size
+    - associated["aslcontext"].n_rows == sidecar.EchoTime.size
 
 # 198
 ASLM0TypeAbsentScan:
diff --git a/src/schema/rules/sidecars/dwi_validation.yaml b/src/schema/rules/sidecars/dwi_validation.yaml
index 2ed5401f6d..0bc0970609 100644
--- a/src/schema/rules/sidecars/dwi_validation.yaml
+++ b/src/schema/rules/sidecars/dwi_validation.yaml
@@ -13,8 +13,8 @@ DWIVolumeCount:
     - associated contains "bval"
     - associated contains "bvec"
     checks:
-    - associated["bval"].shape[0] == data.shape[3]
-    - associated["bvec"].shape[0] == data.shape[3]
+    - associated["bval"].n_rows == nifti_header.pixdim[4]
+    - associated["bvec"].n_rows == nifti_header.pixdim[4]
 
 # 30
 DWIBvalRows:

From 3b40559695dd271378827d216d05fd64587eada9 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 14 Apr 2022 14:19:18 -0400
Subject: [PATCH 11/16] More.

---
 src/schema/rules/sidecars/asl_validation.yaml | 14 +++++++-------
 src/schema/rules/sidecars/dwi_validation.yaml |  4 ++--
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 903cc81f50..6546891a41 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -74,7 +74,7 @@ ASLFlipAngleASLContextLength:
     - sidecar contains "FlipAngle"
     - type(sidecar.FlipAngle) == "array"
     checks:
-    - associated["aslcontext"].n_rows == sidecar.FlipAngle.size
+    - aslcontext.n_rows == sidecar.FlipAngle.size
 
 # 173
 ASLPostLabelingDelayNiftiLength:
@@ -119,7 +119,7 @@ ASLPostLabelingDelayASLContextLength:
     - sidecar contains "PostLabelingDelay"
     - type(sidecar.PostLabelingDelay) == "array"
     checks:
-    - associated["aslcontext"].n_rows == sidecar.PostLabelingDelay.size
+    - aslcontext.n_rows == sidecar.PostLabelingDelay.size
 
 # 175
 ASLLabelingDurationASLContextLength:
@@ -144,7 +144,7 @@ ASLLabelingDurationASLContextLength:
     - sidecar contains "LabelingDuration"
     - type(sidecar.LabelingDuration) == "array"
     checks:
-    - associated["aslcontext"].n_rows == sidecar.LabelingDuration.size
+    - aslcontext.n_rows == sidecar.LabelingDuration.size
 
 # 177
 ASLRepetitionTimePreparationASLContextLength:
@@ -164,7 +164,7 @@ ASLRepetitionTimePreparationASLContextLength:
     - sidecar contains "RepetitionTimePreparation"
     - type(sidecar.RepetitionTimePreparation) == "array"
     checks:
-    - associated["aslcontext"].n_rows == sidecar.RepetitionTimePreparation.size
+    - aslcontext.n_rows == sidecar.RepetitionTimePreparation.size
 
 # 180
 ASLBackgroundSuppressionNumberPulses:
@@ -197,7 +197,7 @@ ASLTotalAcquiredVolumesASLContextLength:
     - associated contains "aslcontext"
     - sidecar contains "TotalAcquiredVolumes"
     checks:
-    - associated["aslcontext"].n_rows == sidecar.TotalAcquiredVolumes
+    - aslcontext.n_rows == sidecar.TotalAcquiredVolumes
 
 # 196
 ASLEchoTimeASLContextLength:
@@ -213,7 +213,7 @@ ASLEchoTimeASLContextLength:
     - sidecar contains "EchoTime"
     - type(sidecar.EchoTime) == "array"
     checks:
-    - associated["aslcontext"].n_rows == sidecar.EchoTime.size
+    - aslcontext.n_rows == sidecar.EchoTime.size
 
 # 198
 ASLM0TypeAbsentScan:
@@ -240,7 +240,7 @@ ASLM0TypeAbsentASLContext:
     selectors:
     - suffix == "asl"
     - associated contains "aslcontext"
-    - associated["aslcontext"]["volume_type"] contains "m0scan"
+    - aslcontext.volume_type contains "m0scan"
     checks:
     - sidecar.M0Type != "absent"
 
diff --git a/src/schema/rules/sidecars/dwi_validation.yaml b/src/schema/rules/sidecars/dwi_validation.yaml
index 0bc0970609..f8b3a31140 100644
--- a/src/schema/rules/sidecars/dwi_validation.yaml
+++ b/src/schema/rules/sidecars/dwi_validation.yaml
@@ -13,8 +13,8 @@ DWIVolumeCount:
     - associated contains "bval"
     - associated contains "bvec"
     checks:
-    - associated["bval"].n_rows == nifti_header.pixdim[4]
-    - associated["bvec"].n_rows == nifti_header.pixdim[4]
+    - bval.n_rows == nifti_header.pixdim[4]
+    - bvec.n_rows == nifti_header.pixdim[4]
 
 # 30
 DWIBvalRows:

From 6530002fcfab843e89092331bf18713c8ca5d9f2 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 14 Apr 2022 14:21:29 -0400
Subject: [PATCH 12/16] Use YAML schema types.

---
 src/schema/rules/sidecars/asl_validation.yaml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 6546891a41..9a629e9028 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -19,7 +19,7 @@ ASLLabelingDurationNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "LabelingDuration"
-    - type(sidecar.LabelingDuration) == "array"
+    - type(sidecar.LabelingDuration) == "seq"
     checks:
     - nifti_header.pixdim[4] == sidecar.LabelingDuration.size
 
@@ -51,7 +51,7 @@ ASLFlipAngleNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "FlipAngle"
-    - type(sidecar.FlipAngle) == "array"
+    - type(sidecar.FlipAngle) == "seq"
     checks:
     - nifti_header.pixdim[4] == sidecar.FlipAngle.size
 
@@ -72,7 +72,7 @@ ASLFlipAngleASLContextLength:
     - suffix == "asl"
     - associated contains "aslcontext"
     - sidecar contains "FlipAngle"
-    - type(sidecar.FlipAngle) == "array"
+    - type(sidecar.FlipAngle) == "seq"
     checks:
     - aslcontext.n_rows == sidecar.FlipAngle.size
 
@@ -94,7 +94,7 @@ ASLPostLabelingDelayNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "PostLabelingDelay"
-    - type(sidecar.PostLabelingDelay) == "array"
+    - type(sidecar.PostLabelingDelay) == "seq"
     checks:
     - nifti_header.pixdim[4] == sidecar.PostLabelingDelay.size
 
@@ -117,7 +117,7 @@ ASLPostLabelingDelayASLContextLength:
     - suffix == "asl"
     - associated contains "aslcontext"
     - sidecar contains "PostLabelingDelay"
-    - type(sidecar.PostLabelingDelay) == "array"
+    - type(sidecar.PostLabelingDelay) == "seq"
     checks:
     - aslcontext.n_rows == sidecar.PostLabelingDelay.size
 
@@ -142,7 +142,7 @@ ASLLabelingDurationASLContextLength:
     - suffix == "asl"
     - associated contains "aslcontext"
     - sidecar contains "LabelingDuration"
-    - type(sidecar.LabelingDuration) == "array"
+    - type(sidecar.LabelingDuration) == "seq"
     checks:
     - aslcontext.n_rows == sidecar.LabelingDuration.size
 
@@ -162,7 +162,7 @@ ASLRepetitionTimePreparationASLContextLength:
     - suffix == "asl"
     - associated contains "aslcontext"
     - sidecar contains "RepetitionTimePreparation"
-    - type(sidecar.RepetitionTimePreparation) == "array"
+    - type(sidecar.RepetitionTimePreparation) == "seq"
     checks:
     - aslcontext.n_rows == sidecar.RepetitionTimePreparation.size
 
@@ -179,7 +179,7 @@ ASLBackgroundSuppressionNumberPulses:
     - suffix == "asl"
     - sidecar contains "BackgroundSuppressionNumberPulses"
     - sidecar contains "BackgroundSuppressionPulseTime"
-    - type(sidecar.BackgroundSuppressionPulseTime) == "array"
+    - type(sidecar.BackgroundSuppressionPulseTime) == "seq"
     checks:
     - sidecar.BackgroundSuppressionPulseTime.size == sidecar.BackgroundSuppressionNumberPulses
 
@@ -211,7 +211,7 @@ ASLEchoTimeASLContextLength:
     - suffix == "asl"
     - associated contains "aslcontext"
     - sidecar contains "EchoTime"
-    - type(sidecar.EchoTime) == "array"
+    - type(sidecar.EchoTime) == "seq"
     checks:
     - aslcontext.n_rows == sidecar.EchoTime.size
 

From 9820ae752dd574a1a827e54550dd5df4b6c362e4 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 15 Apr 2022 10:31:59 -0400
Subject: [PATCH 13/16] Apply suggestions from code review

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/schema/rules/sidecars/asl_validation.yaml | 10 +++++-----
 src/schema/rules/sidecars/dwi_validation.yaml |  4 ++--
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 9a629e9028..d6f614d7a2 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -19,9 +19,9 @@ ASLLabelingDurationNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "LabelingDuration"
-    - type(sidecar.LabelingDuration) == "seq"
+    - type(sidecar.LabelingDuration) == "array"
     checks:
-    - nifti_header.pixdim[4] == sidecar.LabelingDuration.size
+    - nifti_header.dim[4] == len(sidecar.LabelingDuration)
 
 # 165
 ASLContextConsistent:
@@ -34,7 +34,7 @@ ASLContextConsistent:
     - suffix == "asl"
     - associated contains "aslcontext"
     checks:
-    - nifti_header.pixdim[4] == aslcontext.n_rows
+    - nifti_header.dim[4] == associations.aslcontext.n_rows
 
 # 168
 ASLFlipAngleNiftiLength:
@@ -51,9 +51,9 @@ ASLFlipAngleNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "FlipAngle"
-    - type(sidecar.FlipAngle) == "seq"
+    - type(sidecar.FlipAngle) == "array"
     checks:
-    - nifti_header.pixdim[4] == sidecar.FlipAngle.size
+    - nifti_header.dim[4] == len(sidecar.FlipAngle)
 
 # 172
 ASLFlipAngleASLContextLength:
diff --git a/src/schema/rules/sidecars/dwi_validation.yaml b/src/schema/rules/sidecars/dwi_validation.yaml
index f8b3a31140..68b6a8a61a 100644
--- a/src/schema/rules/sidecars/dwi_validation.yaml
+++ b/src/schema/rules/sidecars/dwi_validation.yaml
@@ -13,8 +13,8 @@ DWIVolumeCount:
     - associated contains "bval"
     - associated contains "bvec"
     checks:
-    - bval.n_rows == nifti_header.pixdim[4]
-    - bvec.n_rows == nifti_header.pixdim[4]
+    - associations.bval.n_cols == nifti_header.dim[4]
+    - associations.bvec.n_cols == nifti_header.dim[4]
 
 # 30
 DWIBvalRows:

From ebf3c23920cd9d3bca94b16b6a2e42de0c013e72 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 15 Apr 2022 10:33:30 -0400
Subject: [PATCH 14/16] associated --> associations

---
 src/schema/rules/sidecars/asl_validation.yaml | 24 +++++++++----------
 src/schema/rules/sidecars/dwi_validation.yaml |  8 +++----
 src/schema/rules/sidecars/eeg.yaml            |  2 +-
 .../rules/sidecars/events_validation.yaml     |  2 +-
 .../rules/sidecars/fmap_validation.yaml       |  6 ++---
 5 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 9a629e9028..47c4ed3fe4 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -32,7 +32,7 @@ ASLContextConsistent:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     checks:
     - nifti_header.pixdim[4] == aslcontext.n_rows
 
@@ -70,7 +70,7 @@ ASLFlipAngleASLContextLength:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - sidecar contains "FlipAngle"
     - type(sidecar.FlipAngle) == "seq"
     checks:
@@ -115,7 +115,7 @@ ASLPostLabelingDelayASLContextLength:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - sidecar contains "PostLabelingDelay"
     - type(sidecar.PostLabelingDelay) == "seq"
     checks:
@@ -140,7 +140,7 @@ ASLLabelingDurationASLContextLength:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - sidecar contains "LabelingDuration"
     - type(sidecar.LabelingDuration) == "seq"
     checks:
@@ -160,7 +160,7 @@ ASLRepetitionTimePreparationASLContextLength:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - sidecar contains "RepetitionTimePreparation"
     - type(sidecar.RepetitionTimePreparation) == "seq"
     checks:
@@ -194,7 +194,7 @@ ASLTotalAcquiredVolumesASLContextLength:
     level: warning
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - sidecar contains "TotalAcquiredVolumes"
     checks:
     - aslcontext.n_rows == sidecar.TotalAcquiredVolumes
@@ -209,7 +209,7 @@ ASLEchoTimeASLContextLength:
     level: warning
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - sidecar contains "EchoTime"
     - type(sidecar.EchoTime) == "seq"
     checks:
@@ -225,8 +225,8 @@ ASLM0TypeAbsentScan:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
-    - associated contains "m0scan"
+    - associations contains "aslcontext"
+    - associations contains "m0scan"
     checks:
     - sidecar.M0Type != "absent"
 
@@ -239,7 +239,7 @@ ASLM0TypeAbsentASLContext:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - aslcontext.volume_type contains "m0scan"
     checks:
     - sidecar.M0Type != "absent"
@@ -253,7 +253,7 @@ ASLM0TypeIncorrect:
     level: error
     selectors:
     - suffix == "asl"
-    - associated contains "aslcontext"
+    - associations contains "aslcontext"
     - sidecar.M0Type == "separate"
     checks:
-    - associated contains "m0scan"
+    - associations contains "m0scan"
diff --git a/src/schema/rules/sidecars/dwi_validation.yaml b/src/schema/rules/sidecars/dwi_validation.yaml
index f8b3a31140..9ebf597882 100644
--- a/src/schema/rules/sidecars/dwi_validation.yaml
+++ b/src/schema/rules/sidecars/dwi_validation.yaml
@@ -10,8 +10,8 @@ DWIVolumeCount:
     level: error
     selectors:
     - suffix == "dwi"
-    - associated contains "bval"
-    - associated contains "bvec"
+    - associations contains "bval"
+    - associations contains "bvec"
     checks:
     - bval.n_rows == nifti_header.pixdim[4]
     - bvec.n_rows == nifti_header.pixdim[4]
@@ -47,7 +47,7 @@ DWIMissingBvec:
     selectors:
     - suffix == "dwi"
     checks:
-    - associated contains "bvec"
+    - associations contains "bvec"
 
 # 33
 DWIMissingBval:
@@ -58,4 +58,4 @@ DWIMissingBval:
     selectors:
     - suffix == "dwi"
     checks:
-    - associated contains "bval"
+    - associations contains "bval"
diff --git a/src/schema/rules/sidecars/eeg.yaml b/src/schema/rules/sidecars/eeg.yaml
index 4b1902bd23..224558cc06 100644
--- a/src/schema/rules/sidecars/eeg.yaml
+++ b/src/schema/rules/sidecars/eeg.yaml
@@ -89,7 +89,7 @@ EEGCoordsystemGeneral:
         IntendedFor:
             level: OPTIONAL
             addendum: |
-                This identifies the MRI or CT scan associated with the electrodes,
+                This identifies the MRI or CT scan associations with the electrodes,
                 landmarks, and fiducials.
 
 # Fields relating to the EEG electrode positions
diff --git a/src/schema/rules/sidecars/events_validation.yaml b/src/schema/rules/sidecars/events_validation.yaml
index e4e74e9adc..4e735a38e0 100644
--- a/src/schema/rules/sidecars/events_validation.yaml
+++ b/src/schema/rules/sidecars/events_validation.yaml
@@ -13,4 +13,4 @@ EventsMissing:
     - entities.task != "rest"
     - entities.task not contains "rest"  # Alternative for including the word "rest"
     checks:
-    - associated contains "events"
+    - associations contains "events"
diff --git a/src/schema/rules/sidecars/fmap_validation.yaml b/src/schema/rules/sidecars/fmap_validation.yaml
index b88bce11ef..53c231d89e 100644
--- a/src/schema/rules/sidecars/fmap_validation.yaml
+++ b/src/schema/rules/sidecars/fmap_validation.yaml
@@ -10,15 +10,15 @@ FmapFieldmapWithoutMagnitude:
     selectors:
     - suffix == "fieldmap"
     checks:
-    - associated contains "magnitude"
+    - associations contains "magnitude"
 
 # 92
 FmapPhasediffWithoutMagnitude:
     code: MISSING_MAGNITUDE1_FILE
     description: |
-        Each '_phasediff.nii[.gz]' file should be associated with a '_magnitude1.nii[.gz]' file.
+        Each '_phasediff.nii[.gz]' file should be associations with a '_magnitude1.nii[.gz]' file.
     level: warning
     selectors:
     - suffix == "phasediff"
     checks:
-    - associated contains "magnitude1"
+    - associations contains "magnitude1"

From fd046c4e8a48ddcee253f0f4121fa40ba9a3967a Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 15 Apr 2022 10:34:28 -0400
Subject: [PATCH 15/16] seq --> array

---
 src/schema/rules/sidecars/asl_validation.yaml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/schema/rules/sidecars/asl_validation.yaml b/src/schema/rules/sidecars/asl_validation.yaml
index 47c4ed3fe4..a6f5c67734 100644
--- a/src/schema/rules/sidecars/asl_validation.yaml
+++ b/src/schema/rules/sidecars/asl_validation.yaml
@@ -19,7 +19,7 @@ ASLLabelingDurationNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "LabelingDuration"
-    - type(sidecar.LabelingDuration) == "seq"
+    - type(sidecar.LabelingDuration) == "array"
     checks:
     - nifti_header.pixdim[4] == sidecar.LabelingDuration.size
 
@@ -51,7 +51,7 @@ ASLFlipAngleNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "FlipAngle"
-    - type(sidecar.FlipAngle) == "seq"
+    - type(sidecar.FlipAngle) == "array"
     checks:
     - nifti_header.pixdim[4] == sidecar.FlipAngle.size
 
@@ -72,7 +72,7 @@ ASLFlipAngleASLContextLength:
     - suffix == "asl"
     - associations contains "aslcontext"
     - sidecar contains "FlipAngle"
-    - type(sidecar.FlipAngle) == "seq"
+    - type(sidecar.FlipAngle) == "array"
     checks:
     - aslcontext.n_rows == sidecar.FlipAngle.size
 
@@ -94,7 +94,7 @@ ASLPostLabelingDelayNiftiLength:
     selectors:
     - suffix == "asl"
     - sidecar contains "PostLabelingDelay"
-    - type(sidecar.PostLabelingDelay) == "seq"
+    - type(sidecar.PostLabelingDelay) == "array"
     checks:
     - nifti_header.pixdim[4] == sidecar.PostLabelingDelay.size
 
@@ -117,7 +117,7 @@ ASLPostLabelingDelayASLContextLength:
     - suffix == "asl"
     - associations contains "aslcontext"
     - sidecar contains "PostLabelingDelay"
-    - type(sidecar.PostLabelingDelay) == "seq"
+    - type(sidecar.PostLabelingDelay) == "array"
     checks:
     - aslcontext.n_rows == sidecar.PostLabelingDelay.size
 
@@ -142,7 +142,7 @@ ASLLabelingDurationASLContextLength:
     - suffix == "asl"
     - associations contains "aslcontext"
     - sidecar contains "LabelingDuration"
-    - type(sidecar.LabelingDuration) == "seq"
+    - type(sidecar.LabelingDuration) == "array"
     checks:
     - aslcontext.n_rows == sidecar.LabelingDuration.size
 
@@ -162,7 +162,7 @@ ASLRepetitionTimePreparationASLContextLength:
     - suffix == "asl"
     - associations contains "aslcontext"
     - sidecar contains "RepetitionTimePreparation"
-    - type(sidecar.RepetitionTimePreparation) == "seq"
+    - type(sidecar.RepetitionTimePreparation) == "array"
     checks:
     - aslcontext.n_rows == sidecar.RepetitionTimePreparation.size
 
@@ -179,7 +179,7 @@ ASLBackgroundSuppressionNumberPulses:
     - suffix == "asl"
     - sidecar contains "BackgroundSuppressionNumberPulses"
     - sidecar contains "BackgroundSuppressionPulseTime"
-    - type(sidecar.BackgroundSuppressionPulseTime) == "seq"
+    - type(sidecar.BackgroundSuppressionPulseTime) == "array"
     checks:
     - sidecar.BackgroundSuppressionPulseTime.size == sidecar.BackgroundSuppressionNumberPulses
 
@@ -211,7 +211,7 @@ ASLEchoTimeASLContextLength:
     - suffix == "asl"
     - associations contains "aslcontext"
     - sidecar contains "EchoTime"
-    - type(sidecar.EchoTime) == "seq"
+    - type(sidecar.EchoTime) == "array"
     checks:
     - aslcontext.n_rows == sidecar.EchoTime.size
 

From 4e9b98077c695e902b620dc08d9128419eac2093 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 15 Apr 2022 10:35:29 -0400
Subject: [PATCH 16/16] Revert extra change.

---
 src/schema/rules/sidecars/eeg.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/sidecars/eeg.yaml b/src/schema/rules/sidecars/eeg.yaml
index 224558cc06..4b1902bd23 100644
--- a/src/schema/rules/sidecars/eeg.yaml
+++ b/src/schema/rules/sidecars/eeg.yaml
@@ -89,7 +89,7 @@ EEGCoordsystemGeneral:
         IntendedFor:
             level: OPTIONAL
             addendum: |
-                This identifies the MRI or CT scan associations with the electrodes,
+                This identifies the MRI or CT scan associated with the electrodes,
                 landmarks, and fiducials.
 
 # Fields relating to the EEG electrode positions