From 49cdb82fee0ac0f944d8d7f959a26d8c27c8ea75 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Wed, 20 Apr 2022 13:13:58 -0500 Subject: [PATCH 01/23] incomplete first pass at bep012 schema --- .../derivatives/functional_derivatives.yaml | 28 +++++++++++++++++++ .../derivatives/functional_derivatives.yaml | 16 +++++++++++ 2 files changed, 44 insertions(+) create mode 100644 src/schema/rules/datatypes/derivatives/functional_derivatives.yaml create mode 100644 src/schema/rules/sidecars/derivatives/functional_derivatives.yaml diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml new file mode 100644 index 0000000000..b4906d8aca --- /dev/null +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -0,0 +1,28 @@ +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" diff --git a/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml b/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml new file mode 100644 index 0000000000..8e627cd6e9 --- /dev/null +++ b/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml @@ -0,0 +1,16 @@ +BandpassFilter: + selectors: + - dataset.DatasetType == "derivative" + - suffix in ["alff", "falff"] + fields: + BandpassFilter: OPTIONAL +Neighborhood: + selectors: + - dataset.DatasetType == "derivative" + - suffix in ["reho"] + fields: + Neighborhood: OPTIONAL +Threshold: + selectors: + - dataset.DatasetType == "derivative" + - suffix in ["reho"] From a5c130f67c7bd5859d533be3d77c338a77d5d7c4 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Tue, 16 Aug 2022 08:09:36 -0500 Subject: [PATCH 02/23] expand bep12 datatypes --- .../derivatives/functional_derivatives.yaml | 2 +- .../derivatives/functional_derivatives.yaml | 39 +++++++++++++++---- 2 files changed, 32 insertions(+), 9 deletions(-) diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml index b4906d8aca..dd9414a560 100644 --- a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -22,7 +22,7 @@ functional_derivatives_maps: - "dcb" - "dcw" - "ecb" - - "ecw" + - "ecw" - "lfcdb" - "lfcdw" - "vmhc" diff --git a/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml b/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml index 8e627cd6e9..877f03ebfb 100644 --- a/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml @@ -1,16 +1,39 @@ -BandpassFilter: +BandpassFilterOpt: selectors: - dataset.DatasetType == "derivative" - - suffix in ["alff", "falff"] + - '!(["alff", "falff"].includes(suffix))' fields: - BandpassFilter: OPTIONAL -Neighborhood: + BandpassFilter: optional +BandpassFilterReq: selectors: - dataset.DatasetType == "derivative" - - suffix in ["reho"] + - '["alff", "falff"].includes(suffix)' fields: - Neighborhood: OPTIONAL -Threshold: + BandpassFilter: required +NeighborhoodOpt: selectors: - dataset.DatasetType == "derivative" - - suffix in ["reho"] + - '!(["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 + From aa0fb954f0ca7ff495720b63e6a062e73614a1a1 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Tue, 16 Aug 2022 12:39:22 -0500 Subject: [PATCH 03/23] would help if I actually committed the files. --- src/schema/objects/columns.yaml | 87 +++++++++++++++++++ .../derivatives/functional_derivatives.yaml | 65 ++++++++++++++ .../derivatives/functional_derivatives.yaml | 2 +- .../derivatives/functional_derivatives.yaml | 44 ++++++++++ 4 files changed, 197 insertions(+), 1 deletion(-) create mode 100644 src/schema/rules/tabular_data/derivatives/functional_derivatives.yaml diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 60dda15844..d29359e97b 100644 --- a/src/schema/objects/columns.yaml +++ b/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 + description: Discrete cosine basis vectors derived_from: name: derived_from display_name: Derived from @@ -88,6 +99,11 @@ 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 @@ -95,6 +111,12 @@ filename: 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 + description: Legendre polynomial basis vectors +non_steady_state_x: + name: ^non_steady_state_[0-9a-zA-Z]+$ + display_name: Non Steady State + 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 diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml index dd9414a560..3519819b68 100644 --- a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -1,3 +1,4 @@ +--- functional_derivatives_maps: _ref: rules.datatypes.func.func extensions: @@ -26,3 +27,67 @@ functional_derivatives_maps: - "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 diff --git a/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml b/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml index 877f03ebfb..1a87b16d38 100644 --- a/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml @@ -1,3 +1,4 @@ +--- BandpassFilterOpt: selectors: - dataset.DatasetType == "derivative" @@ -36,4 +37,3 @@ ThresholdReq: fields: Threshold: required Method: required - diff --git a/src/schema/rules/tabular_data/derivatives/functional_derivatives.yaml b/src/schema/rules/tabular_data/derivatives/functional_derivatives.yaml new file mode 100644 index 0000000000..f21690952e --- /dev/null +++ b/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 From fee20fba019c18451fb7dc6881933eb5f10c18cf Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Wed, 17 Aug 2022 08:14:17 -0500 Subject: [PATCH 04/23] fix missing quote --- .../rules/sidecars/derivatives/functional_derivatives.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml b/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml index 1a87b16d38..6709af9dc0 100644 --- a/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml @@ -20,7 +20,7 @@ NeighborhoodOpt: NeighborhoodReq: selectors: - dataset.DatasetType == "derivative" - - '["reho"].includes(suffix) + - '["reho"].includes(suffix)' fields: Neighborhood: required ThresholdOpt: From 7452a99244f5433d5b16f4563e47107352d1ec98 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Thu, 18 Aug 2022 14:31:54 -0500 Subject: [PATCH 05/23] Update src/schema/rules/sidecars/derivatives/functional_derivatives.yaml Co-authored-by: Taylor Salo --- .../derivatives/functional_derivatives.yaml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml b/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml index 6709af9dc0..d690245259 100644 --- a/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/sidecars/derivatives/functional_derivatives.yaml @@ -37,3 +37,18 @@ ThresholdReq: fields: Threshold: required Method: required + +TimeseriesMetadata: + selectors: + - dataset.DatasetType == "derivative" + - suffix == "timeseries" + fields: + SamplingFrequency: required + StartTime: optional + +DecompositionMetadata: + selectors: + - dataset.DatasetType == "derivative" + - suffix == "decomposition" + fields: + Method: required From 262b4c6c6d9e6385fd30a66b6c98a8e4789dc2d3 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Fri, 19 Aug 2022 08:21:48 -0500 Subject: [PATCH 06/23] Update src/schema/rules/datatypes/derivatives/functional_derivatives.yaml Co-authored-by: Taylor Salo --- .../rules/datatypes/derivatives/functional_derivatives.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml index 3519819b68..d498799bf0 100644 --- a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -37,7 +37,7 @@ functional_derivatives_timeseries: entities: _ref: rules.datatypes.func.func.entities desc: OPTIONAL - suffixies: + suffixes: - timeseries functional_derivatives_roi_based_timeseries: From 6c67e9a2a641c87d61ddfb5e289319c1b383e3b2 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Fri, 19 Aug 2022 08:22:00 -0500 Subject: [PATCH 07/23] Update src/schema/rules/datatypes/derivatives/functional_derivatives.yaml Co-authored-by: Taylor Salo --- .../rules/datatypes/derivatives/functional_derivatives.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml index d498799bf0..6ea150e7dd 100644 --- a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -78,7 +78,7 @@ functional_derivatives_spatiotemporal_timeseries: - ".nii.gz" entities: _ref: rules.datatypes.func.func.entities - desc: OPTIONAL + description: OPTIONAL suffixies: - mixing - components From fde5ddda5ea7d446782c055f42c3718382c3ca6c Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Fri, 19 Aug 2022 08:22:10 -0500 Subject: [PATCH 08/23] Update src/schema/rules/datatypes/derivatives/functional_derivatives.yaml Co-authored-by: Taylor Salo --- .../rules/datatypes/derivatives/functional_derivatives.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml index 6ea150e7dd..356931ae21 100644 --- a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -88,6 +88,6 @@ functional_derivatives_spatiotemporal_decomp_timeseries: - ".json" entities: _ref: rules.datatypes.func.func.entities - desc: OPTIONAL + description: OPTIONAL suffixies: - decomposition From 06122bbe54d4caf3eaf54a91676b7124acfa507e Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Fri, 19 Aug 2022 08:22:20 -0500 Subject: [PATCH 09/23] Update src/schema/rules/datatypes/derivatives/functional_derivatives.yaml Co-authored-by: Taylor Salo --- .../rules/datatypes/derivatives/functional_derivatives.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml index 356931ae21..d8844173fe 100644 --- a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -49,7 +49,7 @@ functional_derivatives_roi_based_timeseries: _ref: rules.datatypes.func.func.entities desc: OPTIONAL atlas: OPTIONAL - suffixies: + suffixes: - timeseries functional_derivatives_motion_timeseries: From d10b4f67f465beff0efc2242557da662935806cb Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Fri, 19 Aug 2022 08:23:14 -0500 Subject: [PATCH 10/23] Update src/schema/objects/columns.yaml Co-authored-by: Taylor Salo --- src/schema/objects/columns.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index d29359e97b..7b8773e77c 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -53,7 +53,7 @@ color: type: string unit: hexadecimal compcor: - name: ^[a|t|w|c]_compcor_cor_[0-9a-zA-Z]+$ + 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: From 08f1e38d31a70fab83300a3e2c81e6b55a0f6c5d Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Fri, 19 Aug 2022 08:24:12 -0500 Subject: [PATCH 11/23] Update src/schema/rules/datatypes/derivatives/functional_derivatives.yaml Co-authored-by: Taylor Salo --- .../rules/datatypes/derivatives/functional_derivatives.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml index d8844173fe..d9c7476afe 100644 --- a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -59,7 +59,7 @@ functional_derivatives_motion_timeseries: entities: _ref: rules.datatypes.func.func.entities desc: OPTIONAL - suffixies: + suffixes: - motion functional_derivatives_outliers_timeseries: From 65ce47f57c8da2178dc661ed05b9195d8e95ab8d Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Fri, 19 Aug 2022 08:24:25 -0500 Subject: [PATCH 12/23] Update src/schema/rules/datatypes/derivatives/functional_derivatives.yaml Co-authored-by: Taylor Salo --- .../rules/datatypes/derivatives/functional_derivatives.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml index d9c7476afe..2b3c1db669 100644 --- a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -69,7 +69,7 @@ functional_derivatives_outliers_timeseries: entities: _ref: rules.datatypes.func.func.entities desc: OPTIONAL - suffixies: + suffixes: - outliers functional_derivatives_spatiotemporal_timeseries: From 34ad6c34f15dacb6c64f1f0a29f5f5bd9898727a Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Fri, 19 Aug 2022 08:24:54 -0500 Subject: [PATCH 13/23] Update src/schema/rules/datatypes/derivatives/functional_derivatives.yaml Co-authored-by: Taylor Salo --- .../rules/datatypes/derivatives/functional_derivatives.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml index 2b3c1db669..47fae801b4 100644 --- a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -79,7 +79,7 @@ functional_derivatives_spatiotemporal_timeseries: entities: _ref: rules.datatypes.func.func.entities description: OPTIONAL - suffixies: + suffixes: - mixing - components From 203e2b3292ca2ac5f19134bafc60ee8b7d3384d7 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Fri, 19 Aug 2022 08:25:08 -0500 Subject: [PATCH 14/23] Update src/schema/rules/datatypes/derivatives/functional_derivatives.yaml Co-authored-by: Taylor Salo --- .../rules/datatypes/derivatives/functional_derivatives.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml index 47fae801b4..28ee830149 100644 --- a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -11,7 +11,7 @@ functional_derivatives_maps: space: OPTIONAL resolution: OPTIONAL density: OPTIONAL - desc: OPTIONAL + description: OPTIONAL suffixes: - "mean" - "std" From c3a320494015851988dc106e4df24327c74d175d Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Fri, 19 Aug 2022 08:25:20 -0500 Subject: [PATCH 15/23] Update src/schema/rules/datatypes/derivatives/functional_derivatives.yaml Co-authored-by: Taylor Salo --- .../rules/datatypes/derivatives/functional_derivatives.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml index 28ee830149..0739ae8216 100644 --- a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -89,5 +89,5 @@ functional_derivatives_spatiotemporal_decomp_timeseries: entities: _ref: rules.datatypes.func.func.entities description: OPTIONAL - suffixies: + suffixes: - decomposition From 931ae956339546d9852be5df3ff17a7754b86afa Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Fri, 19 Aug 2022 08:25:37 -0500 Subject: [PATCH 16/23] Update src/schema/rules/datatypes/derivatives/functional_derivatives.yaml Co-authored-by: Taylor Salo --- .../rules/datatypes/derivatives/functional_derivatives.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml index 0739ae8216..94b3b11e02 100644 --- a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -36,7 +36,7 @@ functional_derivatives_timeseries: - ".dtseries.nii" entities: _ref: rules.datatypes.func.func.entities - desc: OPTIONAL + description: OPTIONAL suffixes: - timeseries From 11784635ec6d6dca3a3427b7a8fb7a399ff29a25 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Fri, 19 Aug 2022 08:26:23 -0500 Subject: [PATCH 17/23] Update src/schema/rules/datatypes/derivatives/functional_derivatives.yaml Co-authored-by: Taylor Salo --- .../rules/datatypes/derivatives/functional_derivatives.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml index 94b3b11e02..fbe03fc32a 100644 --- a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -47,7 +47,7 @@ functional_derivatives_roi_based_timeseries: - ".json" entities: _ref: rules.datatypes.func.func.entities - desc: OPTIONAL + description: OPTIONAL atlas: OPTIONAL suffixes: - timeseries From 9a592ce3d8c5d5378d4f8bab5b5ae5eab5a19e74 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Fri, 19 Aug 2022 08:26:37 -0500 Subject: [PATCH 18/23] Update src/schema/rules/datatypes/derivatives/functional_derivatives.yaml Co-authored-by: Taylor Salo --- .../rules/datatypes/derivatives/functional_derivatives.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml index fbe03fc32a..5a7290a5ec 100644 --- a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -58,7 +58,7 @@ functional_derivatives_motion_timeseries: - ".json" entities: _ref: rules.datatypes.func.func.entities - desc: OPTIONAL + description: OPTIONAL suffixes: - motion From 09fb79952551048b919a5b5835befa0cf9784ba1 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Fri, 19 Aug 2022 08:26:51 -0500 Subject: [PATCH 19/23] Update src/schema/rules/datatypes/derivatives/functional_derivatives.yaml Co-authored-by: Taylor Salo --- .../rules/datatypes/derivatives/functional_derivatives.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml index 5a7290a5ec..cbd64bf10a 100644 --- a/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml +++ b/src/schema/rules/datatypes/derivatives/functional_derivatives.yaml @@ -68,7 +68,7 @@ functional_derivatives_outliers_timeseries: - ".json" entities: _ref: rules.datatypes.func.func.entities - desc: OPTIONAL + description: OPTIONAL suffixes: - outliers From b2ba2db11a809b9b531e28c9d7390ad7ec276fd7 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Mon, 22 Aug 2022 13:46:08 -0400 Subject: [PATCH 20/23] Add suffix definitions. --- src/schema/objects/suffixes.yaml | 142 +++++++++++++++++++++++++++++++ 1 file changed, 142 insertions(+) diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml index d705c9966e..83833d3409 100644 --- a/src/schema/objects/suffixes.yaml +++ b/src/schema/objects/suffixes.yaml @@ -490,6 +490,13 @@ VFA: Depending on the provided metadata fields and the sequence type, data may be eligible for DESPOT1, DESPOT2 and their variants ([Deoni et al. 2005](https://doi.org/10.1002/mrm.20314)). +alff: + value: alff + display_name: Amplitude low frequency fluctuations + description: | + Amplitude low frequency fluctuations. + + This suffix may only be used in derivative datasets. angio: value: angio display_name: Angiogram @@ -545,12 +552,40 @@ channels: display_name: Channels File description: | Channel information. +components: + value: components + display_name: Timeseries + description: | + Components from a decomposition. + + This suffix may only be used in derivative datasets. coordsystem: value: coordsystem display_name: Coordinate System File description: | A JSON document specifying the coordinate system(s) used for the MEG, EEG, head localization coils, and anatomical landmarks. +dcb: + value: dcb + display_name: Binary degree centrality + description: | + Voxel-wise binary degree centrality. + + This suffix may only be used in derivative datasets. +dcw: + value: dcw + display_name: Weighted degree centrality + description: | + Voxel-wise weighted degree centrality. + + This suffix may only be used in derivative datasets. +decomposition: + value: decomposition + display_name: Decomposition + description: | + Metadata from a decomposition. + + This suffix may only be used in derivative datasets. defacemask: value: defacemask display_name: Defacing Mask @@ -569,6 +604,20 @@ dwi: display_name: Diffusion-weighted image description: | Diffusion-weighted imaging contrast (specialized T2 weighting). +ecb: + value: ecb + display_name: Binary eigenvector centrality + description: | + Voxelwise binary eigenvector centrality. + + This suffix may only be used in derivative datasets. +ecw: + value: ecw + display_name: Weighted eigenvector centrality + description: | + Voxelwise weighted eigenvector centrality. + + This suffix may only be used in derivative datasets. eeg: value: eeg display_name: Electroencephalography @@ -591,6 +640,13 @@ events: display_name: Events description: | Event timing information from a behavioral task. +falff: + value: falff + display_name: Fractional amplitude of low frequency fluctuations + description: | + Fractional amplitude of low frequency fluctuations. + + This suffix may only be used in derivative datasets. fieldmap: value: fieldmap display_name: Fieldmap @@ -622,6 +678,20 @@ inplaneT2: In arbitrary units (arbitrary). T2 weighted structural image matched to a functional (task) image. unit: arbitrary +lfcdb: + value: lfcdb + display_name: Binary local functional connectivity density + description: | + Binary local functional connectivity density. + + This suffix may only be used in derivative datasets. +lfcdw: + value: lfcdw + display_name: Weighted local functional connectivity density + description: | + Weighted local functional connectivity density. + + This suffix may only be used in derivative datasets. m0scan: value: m0scan display_name: M0 image @@ -662,6 +732,13 @@ mask: description: | A binary mask that functions as a discrete "label" for a single structure. + This suffix may only be used in derivative datasets. +mean: + value: mean + display_name: Mean image + description: | + Mean across the temporal/4th dimension of the data. + This suffix may only be used in derivative datasets. meg: value: meg @@ -669,6 +746,27 @@ meg: description: | Unprocessed MEG data stored in the native file format of the MEG instrument with which the data was collected. +mixing: + value: mixing + display_name: Mixing Matrix + description: | + A mixing matrix from a decomposition. + + This suffix may only be used in derivative datasets. +motion: + value: motion + display_name: Motion + description: | + A motion file. + + This suffix may only be used in derivative datasets. +outliers: + value: outliers + display_name: Outliers + description: | + An outliers file. + + This suffix may only be used in derivative datasets. pet: value: pet display_name: Positron Emission Tomography @@ -726,6 +824,14 @@ probseg: description: | A probabilistic segmentation. + This suffix may only be used in derivative datasets. +reho: + value: reho + display_name: Regional homogeneity + description: | + Regional homogeneity image. + Only voxel-wise images are supported with this suffix. + This suffix may only be used in derivative datasets. sbref: value: sbref @@ -761,13 +867,49 @@ sessions: These files MUST include a session_id column and describe each session by one and only one row. Column names in sessions.tsv files MUST be different from group level participant key column names in the participants.tsv file. +sfs: + value: sfs + display_name: Signal fluctuation sensitivity + description: | + Signal fluctuation sensitivity image. + + This suffix may only be used in derivative datasets. +std: + value: std + display_name: Standard deviation + description: | + Standard deviation across the temporal/4th dimension of the data. + + This suffix may only be used in derivative datasets. stim: value: stim display_name: Continuous recording description: | Continuous measures, such as parameters of a film or audio stimulus. +timeseries: + value: timeseries + display_name: Timeseries + description: | + A timeseries file. + + This suffix may only be used in derivative datasets. +tsnr: + value: tsnr + display_name: Temporal signal-to-noise ratio + description: | + Temporal signal-to-noise ratio. + This is defined as the temporal mean divided by the template standard deviation. + + This suffix may only be used in derivative datasets. uCT: value: uCT display_name: Micro-CT description: | Micro-CT imaging data +vmhc: + value: vmhc + display_name: Voxel mirrored homotopic connectivity + description: | + Voxel mirrored homotopic connectivity. + + This suffix may only be used in derivative datasets. From 21c0a20ff1a4d6a077e03ceacaddacdb30e6cf5e Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Mon, 22 Aug 2022 13:46:16 -0400 Subject: [PATCH 21/23] Add extension definitions. --- src/schema/objects/extensions.yaml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/src/schema/objects/extensions.yaml b/src/schema/objects/extensions.yaml index 4e7006ed6b..6cd5ca6a5b 100644 --- a/src/schema/objects/extensions.yaml +++ b/src/schema/objects/extensions.yaml @@ -79,6 +79,13 @@ dlabelnii: description: | A CIFTI-2 dense label file. + This extension may only be used in derivative datasets. +dtseriesnii: + value: .dtseries.nii + display_name: Timeseries CIFTI File + description: | + A CIFTI timeseries file. + This extension may only be used in derivative datasets. edf: value: .edf @@ -251,6 +258,13 @@ tif: display_name: Tag Image File Format description: | A [Tag Image File Format](https://en.wikipedia.org/wiki/TIFF) file. +timegii: + value: .time.gii + display_name: Surface timeseries + description: | + Surface timeseries. + + This extension may only be used in derivative datasets. trg: value: .trg display_name: KRISS TRG From daa34ccd6fb020ca5d13deda18d0bc1e1ab78b6d Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Mon, 22 Aug 2022 13:48:53 -0400 Subject: [PATCH 22/23] Update suffixes.yaml --- src/schema/objects/suffixes.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml index 83833d3409..4e5c6c9282 100644 --- a/src/schema/objects/suffixes.yaml +++ b/src/schema/objects/suffixes.yaml @@ -765,6 +765,8 @@ outliers: display_name: Outliers description: | An outliers file. + Outlier masks are columns of zeros (0), with ones (1) indicating volumes that have been + identified as outliers by some method. This suffix may only be used in derivative datasets. pet: @@ -891,6 +893,7 @@ timeseries: display_name: Timeseries description: | A timeseries file. + Any time series with common timing information may be stored in a timeseries file. This suffix may only be used in derivative datasets. tsnr: From c0c6993d2800f9324c0d86b99b2c9bf9a60a2c76 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Mon, 22 Aug 2022 13:52:36 -0400 Subject: [PATCH 23/23] Add metadata fields. --- src/schema/objects/metadata.yaml | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml index d1effcc1b4..f012de56e2 100644 --- a/src/schema/objects/metadata.yaml +++ b/src/schema/objects/metadata.yaml @@ -258,6 +258,12 @@ BackgroundSuppressionPulseTime: type: number minimum: 0 unit: s +BandpassFilter: + name: BandpassFilter + display_name: Bandpass Filter + description: | + String describing all relevant parameters of the applied bandpass filter. + type: string BasedOn: name: BasedOn display_name: Based On @@ -1878,6 +1884,12 @@ MetaboliteRecoveryCorrectionApplied: If `true`, the `hplc_recovery_fractions` column MUST be present in the corresponding `*_blood.tsv` file. type: boolean +Method: + name: Method + display_name: Method + description: | + String describing method used to calculate measure. + type: string MiscChannelCount: name: MiscChannelCount display_name: Misc Channel Count @@ -1955,6 +1967,12 @@ NegativeContrast: usage of a contrast agent in conjunction with a T2\* weighted acquisition protocol. type: boolean +Neighborhood: + name: Neighborhood + display_name: Neighborhood + description: | + String describing neighborhood for regional measures. + type: string NonlinearGradientCorrection: name: NonlinearGradientCorrection display_name: Nonlinear Gradient Correction @@ -2997,6 +3015,12 @@ TermURL: URL pointing to a formal definition of this type of data in an ontology available on the web. type: string +Threshold: + name: Threshold + display_name: Threshold + description: | + String describing threshold used for determining graph edges. + type: string TimeZero: name: TimeZero display_name: Time Zero