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Mass univariate analysis and spatially varying design matrix #207

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69fdb38
Specify if estimation is mass/local uni/multivariate...
Oct 27, 2014
7d501d2
Add dependenceSpatialModel attribute to design matrix
Oct 27, 2014
f0ce79b
Map-wise estimation methods as individuals
Oct 27, 2014
c12514c
voxelWiseEstimation -> hasVoxelWiseEstimation
Oct 28, 2014
4f8e6ac
dependenceSpatialModel has domain DesignMatrix
Oct 28, 2014
bcfb963
Update Prov Store links
Oct 31, 2014
1741021
fix: remaining conflict in owl
Oct 31, 2014
f56b547
voxelWiseEstimation -> hasVoxelWiseEstimation
Oct 31, 2014
f344677
Update turtle serialisations
Nov 4, 2014
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8 changes: 4 additions & 4 deletions nidm/nidm-results/fsl/README.md
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Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31459/
Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31480/

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![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31459.png)
![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31480.png)


8 changes: 4 additions & 4 deletions nidm/nidm-results/fsl/example001/README.md
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Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31458/
Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31483/

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Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/31483.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/31483.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/31483.png)

![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31458.png)
![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31483.png)


2 changes: 2 additions & 0 deletions nidm/nidm-results/fsl/example001/fsl_nidm.provn
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Expand Up @@ -295,6 +295,7 @@ document
entity(niiri:design_matrix_id,
[prov:type = 'nidm:DesignMatrix',
prov:location = "file://./DesignMatrix.csv" %% xsd:anyURI,
nidm:dependenceSpatialModel = 'nidm:SpatiallyGlobalModel',
prov:label = "Design Matrix" %% xsd:string])

entity(niiri:contrast_id_1,
Expand All @@ -316,6 +317,7 @@ document
activity(niiri:model_parameters_estimation_id,
[prov:type = 'nidm:ModelParametersEstimation',
nidm:withEstimationMethod = 'nidm:GeneralizedLeastSquares',
nidm:hasVoxelWiseEstimation = 'nidm:MassUnivariate',
prov:label = "Model Parameters Estimation"])

activity(niiri:contrast_estimation_id_1,
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6 changes: 4 additions & 2 deletions nidm/nidm-results/fsl/example001/fsl_nidm.ttl
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Expand Up @@ -268,7 +268,8 @@ niiri:model_parameters_estimation_id prov:used niiri:data_id .

niiri:design_matrix_id a prov:Entity , nidm:DesignMatrix ;
rdfs:label "Design Matrix" ;
prov:atLocation "file://./DesignMatrix.csv"^^xsd:anyURI .
prov:atLocation "file://./DesignMatrix.csv"^^xsd:anyURI ;
nidm:dependenceSpatialModel nidm:SpatiallyGlobalModel .

niiri:contrast_id_1 a prov:Entity , nidm:ContrastWeights ;
rdfs:label "Contrast Weights: Generation" ;
Expand All @@ -286,7 +287,8 @@ niiri:error_model_id a prov:Entity , nidm:ErrorModel ;
niiri:model_parameters_estimation_id prov:used niiri:error_model_id ;
a prov:Activity , nidm:ModelParametersEstimation ;
rdfs:label "Model Parameters Estimation" ;
nidm:withEstimationMethod nidm:GeneralizedLeastSquares .
nidm:withEstimationMethod nidm:GeneralizedLeastSquares ;
nidm:hasVoxelWiseEstimation nidm:MassUnivariate .

niiri:contrast_estimation_id_1 a prov:Activity , nidm:ContrastEstimation ;
rdfs:label "Contrast estimation: Generation" .
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2 changes: 2 additions & 0 deletions nidm/nidm-results/fsl/fsl_results.provn
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Expand Up @@ -156,6 +156,7 @@ document
entity(niiri:design_matrix_id,
[prov:type = 'nidm:DesignMatrix',
prov:location = "file:///path/to/DesignMatrix.csv" %% xsd:anyURI,
nidm:dependenceSpatialModel = 'nidm:SpatiallyGlobalModel',
prov:label = "Design Matrix" %% xsd:string])
entity(niiri:contrast_id,
[prov:type = 'nidm:ContrastWeights',
Expand All @@ -176,6 +177,7 @@ document
activity(niiri:model_pe_id,
[prov:type = 'nidm:ModelParametersEstimation',
nidm:withEstimationMethod = 'nidm:OrdinaryLeastSquares',
nidm:hasVoxelWiseEstimation = 'nidm:MassUnivariate',
prov:label = "Model parameters estimation"])

activity(niiri:contrast_estimation_id,
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6 changes: 4 additions & 2 deletions nidm/nidm-results/fsl/fsl_results.ttl
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Expand Up @@ -147,7 +147,8 @@ niiri:resels_per_voxel_map_id prov:wasGeneratedBy niiri:model_pe_id .

niiri:design_matrix_id a prov:Entity , nidm:DesignMatrix ;
rdfs:label "Design Matrix" ;
prov:atLocation "file:///path/to/DesignMatrix.csv"^^xsd:anyURI .
prov:atLocation "file:///path/to/DesignMatrix.csv"^^xsd:anyURI ;
nidm:dependenceSpatialModel nidm:SpatiallyGlobalModel .

niiri:contrast_id a prov:Entity , nidm:ContrastWeights ;
rdfs:label "Contrast weights: listening > rest" ;
Expand All @@ -165,7 +166,8 @@ niiri:error_model_id a prov:Entity , nidm:ErrorModel ;
niiri:model_pe_id prov:used niiri:error_model_id ;
a prov:Activity , nidm:ModelParametersEstimation ;
rdfs:label "Model parameters estimation" ;
nidm:withEstimationMethod nidm:OrdinaryLeastSquares .
nidm:withEstimationMethod nidm:OrdinaryLeastSquares ;
nidm:hasVoxelWiseEstimation nidm:MassUnivariate .

niiri:contrast_estimation_id a prov:Activity , nidm:ContrastEstimation ;
rdfs:label "Contrast estimation" .
Expand Down
8 changes: 4 additions & 4 deletions nidm/nidm-results/spm/README.md
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Prov store: https://provenance.ecs.soton.ac.uk/store/documents/30689/
Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31476/

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![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/30689.png)
![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31476.png)


8 changes: 4 additions & 4 deletions nidm/nidm-results/spm/example001/README.md
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Prov store: https://provenance.ecs.soton.ac.uk/store/documents/30693/
Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31481/

Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/30693.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/30693.ttl),
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Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/31481.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/31481.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/31481.png)

![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/30693.png)
![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31481.png)


2 changes: 2 additions & 0 deletions nidm/nidm-results/spm/example001/example001_spm_results.provn
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Expand Up @@ -155,6 +155,7 @@ document
[prov:type = 'nidm:DesignMatrix',
prov:location = "file://./DesignMatrix.csv" %% xsd:anyURI,
nidm:filename = "DesignMatrix.csv" %% xsd:string,
nidm:dependenceSpatialModel = 'nidm:SpatiallyGlobalModel',
dct:format = "text/csv" %% xsd:string,
nidm:visualisation = 'niiri:design_matrix_png_id',
prov:label = "Design Matrix" %% xsd:string])
Expand Down Expand Up @@ -183,6 +184,7 @@ document
activity(niiri:model_pe_id,
[prov:type = 'nidm:ModelParametersEstimation',
nidm:withEstimationMethod = 'nidm:GeneralizedLeastSquares',
nidm:hasVoxelWiseEstimation = 'nidm:MassUnivariate',
prov:label = "Model parameters estimation"])
wasAssociatedWith(niiri:model_pe_id, niiri:software_id,-)
used(niiri:model_pe_id, niiri:design_matrix_id,-)
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2 changes: 2 additions & 0 deletions nidm/nidm-results/spm/example001/example001_spm_results.ttl
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Expand Up @@ -163,6 +163,7 @@ niiri:design_matrix_id a prov:Entity , nidm:DesignMatrix ;
rdfs:label "Design Matrix" ;
prov:atLocation "file://./DesignMatrix.csv"^^xsd:anyURI ;
nidm:filename "DesignMatrix.csv"^^xsd:string ;
nidm:dependenceSpatialModel nidm:SpatiallyGlobalModel ;
dct:format "text/csv"^^xsd:string ;
nidm:visualisation niiri:design_matrix_png_id .

Expand All @@ -188,6 +189,7 @@ niiri:model_pe_id prov:used niiri:error_model_id ;
a prov:Activity , nidm:ModelParametersEstimation ;
rdfs:label "Model parameters estimation" ;
nidm:withEstimationMethod nidm:GeneralizedLeastSquares ;
nidm:hasVoxelWiseEstimation nidm:MassUnivariate ;
prov:wasAssociatedWith niiri:software_id ;
prov:used niiri:design_matrix_id .

Expand Down
8 changes: 4 additions & 4 deletions nidm/nidm-results/spm/example002/README.md
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Prov store: https://provenance.ecs.soton.ac.uk/store/documents/30691/
Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31479/

Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/30691.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/30691.ttl),
Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/30691.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/30691.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/30691.png)
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Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/31479.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/31479.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/31479.png)

![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/30691.png)
![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31479.png)


2 changes: 2 additions & 0 deletions nidm/nidm-results/spm/example002/spm_results_2contrasts.provn
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Expand Up @@ -168,6 +168,7 @@ document
activity(niiri:model_fitting_id,
[prov:type = 'nidm:ModelParametersEstimation',
nidm:withEstimationMethod = 'nidm:OrdinaryLeastSquares',
nidm:hasVoxelWiseEstimation = 'nidm:MassUnivariate',
prov:label = "Model Parameters Estimation"])
wasAssociatedWith(niiri:model_fitting_id, niiri:software_id,-)
used(niiri:model_fitting_id, niiri:design_matrix_id,-)
Expand Down Expand Up @@ -230,6 +231,7 @@ document
entity(niiri:design_matrix_id,
[prov:type = 'nidm:DesignMatrix',
prov:location = "file:///path/to/DesignMatrix.csv" %% xsd:anyURI,
nidm:dependenceSpatialModel = 'nidm:SpatiallyGlobalModel',
prov:label = "Design Matrix" %% xsd:string])
entity(niiri:contrast_id,
[prov:type = 'nidm:ContrastWeights',
Expand Down
4 changes: 3 additions & 1 deletion nidm/nidm-results/spm/example002/spm_results_2contrasts.ttl
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Expand Up @@ -162,6 +162,7 @@ niiri:model_fitting_id prov:used niiri:error_model_id ;
a prov:Activity , nidm:ModelParametersEstimation ;
rdfs:label "Model Parameters Estimation" ;
nidm:withEstimationMethod nidm:OrdinaryLeastSquares ;
nidm:hasVoxelWiseEstimation nidm:MassUnivariate ;
prov:wasAssociatedWith niiri:software_id ;
prov:used niiri:design_matrix_id .

Expand Down Expand Up @@ -225,7 +226,8 @@ niiri:residual_mean_squares_map_id a prov:Entity , nidm:ResidualMeanSquaresMap ;

niiri:design_matrix_id a prov:Entity , nidm:DesignMatrix ;
rdfs:label "Design Matrix" ;
prov:atLocation "file:///path/to/DesignMatrix.csv"^^xsd:anyURI .
prov:atLocation "file:///path/to/DesignMatrix.csv"^^xsd:anyURI ;
nidm:dependenceSpatialModel nidm:SpatiallyGlobalModel .

niiri:contrast_id a prov:Entity , nidm:ContrastWeights ;
rdfs:label "T Contrast weights: 1 -1 0 0" ;
Expand Down
8 changes: 4 additions & 4 deletions nidm/nidm-results/spm/example003/README.md
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@@ -1,9 +1,9 @@

Prov store: https://provenance.ecs.soton.ac.uk/store/documents/30690/
Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31477/

Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/30690.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/30690.ttl),
Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/30690.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/30690.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/30690.png)
Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/31477.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/31477.ttl),
Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/31477.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/31477.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/31477.png)

![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/30690.png)
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2 changes: 2 additions & 0 deletions nidm/nidm-results/spm/example003/spm_results_conjunction.provn
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Expand Up @@ -172,6 +172,7 @@ document
activity(niiri:model_fitting_id,
[prov:type = 'nidm:ModelParametersEstimation',
nidm:withEstimationMethod = 'nidm:OrdinaryLeastSquares',
nidm:hasVoxelWiseEstimation = 'nidm:MassUnivariate',
prov:label = "Model Parameters Estimation"])
wasAssociatedWith(niiri:model_fitting_id, niiri:software_id,-)
used(niiri:model_fitting_id, niiri:design_matrix_id,-)
Expand Down Expand Up @@ -234,6 +235,7 @@ document
entity(niiri:design_matrix_id,
[prov:type = 'nidm:DesignMatrix',
prov:location = "file:///path/to/DesignMatrix.csv" %% xsd:anyURI,
nidm:dependenceSpatialModel = 'nidm:SpatiallyGlobalModel',
prov:label = "Design Matrix" %% xsd:string])
entity(niiri:contrast_id,
[prov:type = 'nidm:ContrastWeights',
Expand Down
4 changes: 3 additions & 1 deletion nidm/nidm-results/spm/example003/spm_results_conjunction.ttl
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Expand Up @@ -159,6 +159,7 @@ niiri:model_fitting_id prov:used niiri:error_model_id ;
a prov:Activity , nidm:ModelParametersEstimation ;
rdfs:label "Model Parameters Estimation" ;
nidm:withEstimationMethod nidm:OrdinaryLeastSquares ;
nidm:hasVoxelWiseEstimation nidm:MassUnivariate ;
prov:wasAssociatedWith niiri:software_id ;
prov:used niiri:design_matrix_id .

Expand Down Expand Up @@ -222,7 +223,8 @@ niiri:residual_mean_squares_map_id a prov:Entity , nidm:ResidualMeanSquaresMap ;

niiri:design_matrix_id a prov:Entity , nidm:DesignMatrix ;
rdfs:label "Design Matrix" ;
prov:atLocation "file:///path/to/DesignMatrix.csv"^^xsd:anyURI .
prov:atLocation "file:///path/to/DesignMatrix.csv"^^xsd:anyURI ;
nidm:dependenceSpatialModel nidm:SpatiallyGlobalModel .

niiri:contrast_id a prov:Entity , nidm:ContrastWeights ;
rdfs:label "T Contrast weights: 1 -1 0 0" ;
Expand Down
4 changes: 3 additions & 1 deletion nidm/nidm-results/spm/spm_results.provn
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Expand Up @@ -201,6 +201,7 @@ document
prov:location = "file:///path/to/DesignMatrix.csv" %% xsd:anyURI,
dct:format = "text/csv",
nidm:filename = "DesignMatrix.csv",
nidm:dependenceSpatialModel = 'nidm:SpatiallyGlobalModel',
nidm:visualisation = 'niiri:design_matrix_png_id',
prov:label = "Design Matrix" %% xsd:string])
entity(niiri:design_matrix_png_id,
Expand Down Expand Up @@ -242,7 +243,8 @@ document
activity(niiri:model_pe_id,
[prov:type = 'nidm:ModelParametersEstimation',
prov:label = "Model parameters estimation",
nidm:withEstimationMethod = 'nidm:OrdinaryLeastSquares'
nidm:withEstimationMethod = 'nidm:OrdinaryLeastSquares',
nidm:hasVoxelWiseEstimation = 'nidm:MassUnivariate'
])
wasAssociatedWith(niiri:model_pe_id, niiri:software_id,-)
used(niiri:model_pe_id, niiri:design_matrix_id,-)
Expand Down
2 changes: 2 additions & 0 deletions nidm/nidm-results/spm/spm_results.ttl
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Expand Up @@ -208,6 +208,7 @@ niiri:design_matrix_id a prov:Entity , nidm:DesignMatrix ;
prov:atLocation "file:///path/to/DesignMatrix.csv"^^xsd:anyURI ;
dct:format "text/csv"^^xsd:string ;
nidm:filename "DesignMatrix.csv"^^xsd:string ;
nidm:dependenceSpatialModel nidm:SpatiallyGlobalModel ;
nidm:visualisation niiri:design_matrix_png_id .

niiri:design_matrix_png_id a prov:Entity , nidm:Image ;
Expand Down Expand Up @@ -249,6 +250,7 @@ niiri:model_pe_id prov:used niiri:error_model_id ;
a prov:Activity , nidm:ModelParametersEstimation ;
rdfs:label "Model parameters estimation" ;
nidm:withEstimationMethod nidm:OrdinaryLeastSquares ;
nidm:hasVoxelWiseEstimation nidm:MassUnivariate ;
prov:wasAssociatedWith niiri:software_id ;
prov:used niiri:design_matrix_id .

Expand Down
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