[SCHEMA] bep012 functional derivatives

src/schema/objects/columns.yaml

@@ -52,6 +52,17 @@ color:
     Hexadecimal. Label color for visualization.
   type: string
   unit: hexadecimal
+compcor:
+  name: ^[a|t|w|c]_compcor_cor_[0-9a-zA-Z]+$
+  display_name: CompCor
+  description: |
+    CompCor (Behzadi, et al., 2007) calculated with voxels chosen based on:
+    a: anatomically derived ROIs (white matter and CSF),
+    t: temporal variance, w: white matter voxels only, c: CSF voxels only
+cosine_x:
+  name: ^cosine_[0-9a-zA-Z]+$
+  display_name: Cosine <X>
+  description: Discrete cosine basis vectors
 derived_from:
   name: derived_from
   display_name: Derived from
@@ -88,13 +99,24 @@ duration:
   - type: string
     enum:
     - n/a
+dvars:
+  name: dvars
+  display_name: DVARS
+  description: Change in variance (Brett, 2006, Power, et al., 2012)
+  type: number
 filename:
   name: filename
   display_name: Filename
   description: |
     Relative paths to files.
   type: string
   format: participant_relative
+framwise_displacement:
+  name: framewise_displacement
+  display_name: Framwise Displacement
+  description: Framewise displacement (Power, et al., 2012)
+  type: number
+  unit: mm
 group__channel:
   name: group
   display_name: Channel group
@@ -179,6 +201,14 @@ index:
   description: |
     The label integer index.
   type: integer
+legendre_x:
+  name: ^legendre_[0-9a-zA-Z]+$
+  display_name: Legendre <X>
+  description: Legendre polynomial basis vectors
+non_steady_state_x:
+  name: ^non_steady_state_[0-9a-zA-Z]+$
+  display_name: Non Steady State <X>
+  description: Initial non-steady-state volumes. One column per volume.
 low_cutoff:
   name: low_cutoff
   display_name: Low cutoff
@@ -204,6 +234,10 @@ mapping:
   description: |
     Corresponding integer label in the standard BIDS label lookup.
   type: integer
+melodic:
+  name: ^melodic_[0-9a-zA-Z]+$
+  display_name: FSL MELODIC
+  description: Columns from the mixing matrix in FSL MELODIC
 material:
   name: material
   display_name: Electrode material
@@ -341,6 +375,36 @@ response_time:
   - type: string
     enum:
     - n/a
+rmsd:
+  name: rmsd
+  display_name: Root Mean Square Derivation
+  description: Root mean square deviation (Jenkinson, 1999)
+  type: number
+  unit: mm
+rms:
+  name: rms
+  display_name: Root Mean Square
+  description: Root mean square of translation parameters (Van Dijk, et al., 2012)
+  type: number
+  unit: mm
+rot_x:
+  name: rot_x
+  display_name: X Axis Rotation
+  description: Rotation parameters
+  type: number
+  unit: rad
+rot_y:
+  name: rot_y
+  display_name: Y Axis Rotation
+  description: Rotation parameters
+  type: number
+  unit: rad
+rot_z:
+  name: rot_z
+  display_name: Z Axis Rotation
+  description: Rotation parameters
+  type: number
+  unit: rad
 sample:
   name: sample
   display_name: Sample index
@@ -470,6 +534,11 @@ status_description:
     Freeform text description of noise or artifact affecting data quality on the channel.
     It is meant to explain why the channel was declared bad in the `status` column.
   type: string
+std_dvars:
+  name: std_dvars
+  display_name: Standardized DVARS
+  description: Standardized DVARS (Nichols, 2013)
+  type: number
 stim_file:
   name: stim_file
   display_name: Stimulus file
@@ -508,6 +577,24 @@ time:
     For example, 5.
   type: number
   unit: s
+trans_x:
+  name: trans_x
+  display_name: X Axis Translation
+  description: Translation parameters
+  type: number
+  unit: mm
+trans_y:
+  name: trans_y
+  display_name: Y Axis Translation
+  description: Translation parameters
+  type: number
+  unit: mm
+trans_z:
+  name: trans_z
+  display_name: Z Axis Translation
+  description: Translation parameters
+  type: number
+  unit: mm
 trial_type:
   name: trial_type
   display_name: Trial type

src/schema/rules/datatypes/derivatives/functional_derivatives.yaml

@@ -0,0 +1,93 @@
+---
+functional_derivatives_maps:
+  _ref: rules.datatypes.func.func
+  extensions:
+  - ".nii"
+  - ".nii.gz"
+  - ".gii"
+  - ".dscalar.nii"
+  entities:
+    _ref: rules.datatypes.func.func.entities
+    space: OPTIONAL
+    resolution: OPTIONAL
+    density: OPTIONAL
+    desc: OPTIONAL
+  suffixes:
+  - "mean"
+  - "std"
+  - "tsnr"
+  - "sfs"
+  - "alff"
+  - "falff"
+  - "reho"
+  - "dcb"
+  - "dcw"
+  - "ecb"
+  - "ecw"
+  - "lfcdb"
+  - "lfcdw"
+  - "vmhc"
+
+functional_derivatives_timeseries:
+  extensions:
+  - ".tsv"
+  - ".json"
+  - ".time.gii"
+  - ".dtseries.nii"
+  entities:
+    _ref: rules.datatypes.func.func.entities
+    desc: OPTIONAL
+  suffixies:
+  - timeseries
+
+functional_derivatives_roi_based_timeseries:
+  extensions:
+  - ".nii"
+  - ".tsv"
+  - ".json"
+  entities:
+    _ref: rules.datatypes.func.func.entities
+    desc: OPTIONAL
+    atlas: OPTIONAL
+  suffixies:
+  - timeseries
+
+functional_derivatives_motion_timeseries:
+  extensions:
+  - ".tsv"
+  - ".json"
+  entities:
+    _ref: rules.datatypes.func.func.entities
+    desc: OPTIONAL
+  suffixies:
+  - motion
+
+functional_derivatives_outliers_timeseries:
+  extensions:
+  - ".tsv"
+  - ".json"
+  entities:
+    _ref: rules.datatypes.func.func.entities
+    desc: OPTIONAL
+  suffixies:
+  - outliers
+
+functional_derivatives_spatiotemporal_timeseries:
+  extensions:
+  - ".tsv"
+  - ".nii.gz"
+  entities:
+    _ref: rules.datatypes.func.func.entities
+    desc: OPTIONAL
+  suffixies:
+  - mixing
+  - components
+
+functional_derivatives_spatiotemporal_decomp_timeseries:
+  extensions:
+  - ".json"
+  entities:
+    _ref: rules.datatypes.func.func.entities
+    desc: OPTIONAL
+  suffixies:
+  - decomposition

src/schema/rules/sidecars/derivatives/functional_derivatives.yaml

@@ -0,0 +1,39 @@
+---
+BandpassFilterOpt:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - '!(["alff", "falff"].includes(suffix))'
+  fields:
+    BandpassFilter: optional
+BandpassFilterReq:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - '["alff", "falff"].includes(suffix)'
+  fields:
+    BandpassFilter: required
+NeighborhoodOpt:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - '!(["reho"].includes(suffix))'
+  fields:
+    Neighborhood: optional
+NeighborhoodReq:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - '["reho"].includes(suffix)
+  fields:
+    Neighborhood: required
+ThresholdOpt:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - '!(["dcb", "dcw", "ecb", "ecw"].includes(suffix))'
+  fields:
+    Threshold: optional
+    Method: optional
+ThresholdReq:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - '["dcb", "dcw", "ecb", "ecw"].includes(suffix)'
+  fields:
+    Threshold: required
+    Method: required

src/schema/rules/tabular_data/derivatives/functional_derivatives.yaml

@@ -0,0 +1,44 @@
+---
+MotionRelatedTimeSeries:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - suffix == 'motion'
+  columns:
+  - trans_x: optional
+  - trans_y: optional
+  - trans_z: optional
+  - rot_x: optional
+  - rot_y: optional
+  - rot_z: optional
+  - framewise_displacement: optional
+  - rmsd: optional
+  - rms: optional
+  additional_columns: allowed_if_defined
+
+TemporalOutlierMasks:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - suffix == 'outlier'
+  columns:
+  - non_steady_state_x: optional
+  additional_columns: allowed_if_defined
+
+OtherTimeSeries:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - suffix == 'outlier'
+  columns:
+  - dvars: optional
+  - std_dvars: optional
+  - cosine_x: optional
+  - legendre: optional
+  additional_columns: allowed_if_defined
+
+SpatiotemporalDecompositions:
+  selectors:
+  - dataset.DatasetType == "derivative"
+  - '["components", "mixing"].includes(suffix)'
+  columns:
+  - compcor: optional
+  - melodic_x: optional
+  additional_columns: allowed_if_defined