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cmaumet
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Update example and spec
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‎doc/content/specs/nidm-results_dev.html‎

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@@ -884,6 +884,12 @@ <h1 label="nidm:MaskMap">nidm:MaskMap</h1>
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<ul>
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<li><span class="attribute" id="nidm:MaskMap.label">rdfs:label</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> human readable description of the nidm:MaskMap.</li>
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<li><span class="attribute" id="nidm:MaskMap.nidm:hasMapHeader">
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<a>nidm:hasMapHeader</a>
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</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> . (range <a>nidm:MapHeader</a>)</li>
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<li><span class="attribute" id="nidm:MaskMap.nidm:inCoordinateSpace">
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<a>nidm:inCoordinateSpace</a>
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</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property of a DataArray to associate a CoordinateSpace with a physical file. (range <a>nidm:CoordinateSpace</a>)</li>
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<li><span class="attribute" id="nidm:MaskMap.nidm:isUserDefined">
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<dfn>nidm:isUserDefined</dfn>
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</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> a binary flag defining whether the mask was specified by the user (true) or automatically generated during the analysis (false). (range <a title="xsd:boolean" href="http://www.w3.org/2001/XMLSchema#boolean">xsd:boolean</a>)</li>
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<ul>
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<li><span class="attribute" id="nidm:DisplayMaskMap.label">rdfs:label</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> human readable description of the nidm:DisplayMaskMap.</li>
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<li><span class="attribute" id="nidm:DisplayMaskMap.nidm:hasMapHeader">
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<a>nidm:hasMapHeader</a>
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</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> . (range <a>nidm:MapHeader</a>)</li>
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<li><span class="attribute" id="nidm:DisplayMaskMap.nidm:inCoordinateSpace">
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<a>nidm:inCoordinateSpace</a>
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</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property of a DataArray to associate a CoordinateSpace with a physical file. (range <a>nidm:CoordinateSpace</a>)</li>
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<li><span class="attribute" id="nidm:DisplayMaskMap.nidm:isUserDefined">
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<a>nidm:isUserDefined</a>
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</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> a binary flag defining whether the mask was specified by the user (true) or automatically generated during the analysis (false). (range <a title="xsd:boolean" href="http://www.w3.org/2001/XMLSchema#boolean">xsd:boolean</a>)</li>
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<ul>
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<li><span class="attribute" id="nidm:SearchSpaceMaskMap.label">rdfs:label</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> human readable description of the nidm:SearchSpaceMaskMap.</li>
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<li><span class="attribute" id="nidm:SearchSpaceMaskMap.nidm:hasMapHeader">
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<a>nidm:hasMapHeader</a>
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</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> . (range <a>nidm:MapHeader</a>)</li>
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<li><span class="attribute" id="nidm:SearchSpaceMaskMap.nidm:inCoordinateSpace">
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<a>nidm:inCoordinateSpace</a>
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</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property of a DataArray to associate a CoordinateSpace with a physical file. (range <a>nidm:CoordinateSpace</a>)</li>
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<li><span class="attribute" id="nidm:SearchSpaceMaskMap.nidm:isUserDefined">
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<a>nidm:isUserDefined</a>
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</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> a binary flag defining whether the mask was specified by the user (true) or automatically generated during the analysis (false). (range <a title="xsd:boolean" href="http://www.w3.org/2001/XMLSchema#boolean">xsd:boolean</a>)</li>
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<li><span class="attribute" id="nidm:SearchSpaceMaskMap.nidm:randomFieldStationarity">
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<dfn>nidm:randomFieldStationarity</dfn>
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</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> is the random field assumed to be stationary across the entire search volume?. (range <a title="xsd:boolean" href="http://www.w3.org/2001/XMLSchema#boolean">xsd:boolean</a>)</li>

‎nidm/nidm-results/extensions/non_parametric/spm/example001/README.md‎

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Prov store: https://provenance.ecs.soton.ac.uk/store/documents/76838/
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Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/76838.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/76838.ttl),
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Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/76838.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/76838.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/76838.png)
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![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/76838.png)
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‎nidm/nidm-results/extensions/non_parametric/spm/example001/spm_nonparametric.provn‎

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document
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prefix crypto <http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#>
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prefix neurolex <http://neurolex.org/wiki/>
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prefix obo <http://purl.obolibrary.org/obo/>
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prefix dct <http://purl.org/dc/terms/>
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prefix spm <http://www.incf.org/ns/nidash/spm#>
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prefix pre_0 <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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prefix fsl <http://www.incf.org/ns/nidash/fsl#>
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prefix rdfs <http://www.w3.org/2000/01/rdf-schema#>
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prefix nfo <http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#>
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prefix nidm <http://www.incf.org/ns/nidash/nidm#>
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prefix niiri <http://iri.nidash.org/>
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prefix xsd <http://www.w3.org/2001/XMLSchema>
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prefix bnode <http://openprovenance.org/provtoolbox/bnode/>
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prefix dctype <http://purl.org/dc/dcmitype/>
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prefix dc <http://purl.org/dc/elements/1.1/>
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activity(niiri:inference_id_1,-,-,[prov:type = 'nidm:Inference', prov:label = "Inference", nidm:isParametricTest = "false" %% xsd:boolean, nidm:hasAlternativeHypothesis = 'nidm:OneTailedTest'])
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entity(niiri:non_parametric_null_dististribution_id,[prov:type = 'nidm:NonParametricNullDistribution', prov:label = "Non-Parametric Null Distribution", nidm:numberOfPermutations = "5000" %% xsd:int, nidm:exchangeabilityBlockSize = "4" %% xsd:int])
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entity(niiri:statistic_map_id,[prov:type = 'nidm:StatisticMap', prov:label = "Smoothed Variance T-Statistic Map: passive listening > rest", prov:location = "file://./SmoothedVarianceTStatistic.nii.gz" %% xsd:anyURI, nidm:statisticType = 'nidm:SmoothedVarianceTStatistic', nfo:fileName = "SmoothedVarianceTStatistic.nii.gz" %% xsd:string, dct:format = "image/nifti" %% xsd:string, nidm:contrastName = "passive listening > rest" %% xsd:string, nidm:effectDegreesOfFreedom = "1" %% xsd:float, nidm:inCoordinateSpace = 'niiri:coordinate_space_id_1', crypto:sha512 = "799e9bbf8c15b35c0098bca4" %% xsd:string, nidm:varianceSmoothingFWHM = "[6 6 6]" %% xsd:string])
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entity(niiri:coordinate_space_id_1,[prov:type = 'nidm:CoordinateSpace', prov:label = "Coordinate space 1", nidm:voxelToWorldMapping = "[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, -70],[0, 0, 0, 1]]" %% xsd:string, nidm:voxelUnits = "['mm', 'mm', 'mm']" %% xsd:string, nidm:voxelSize = "[3, 3, 3]" %% xsd:string, nidm:inWorldCoordinateSystem = 'nidm:MNICoordinateSystem', nidm:numberOfDimensions = "3" %% xsd:int, nidm:dimensionsInVoxels = "[53,63,52]" %% xsd:string])
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used(niiri:inference_id_1,niiri:non_parametric_null_dististribution_id,-)
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used(niiri:inference_id_1,niiri:statistic_map_id,-)
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wasGeneratedBy(niiri:statistic_map_id,niiri:contrast_estimation_id,-)
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endDocument

‎nidm/nidm-results/extensions/non_parametric/spm/example001/spm_nonparametric.ttl‎

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@prefix prov: <http://www.w3.org/ns/prov#> .
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@prefix crypto: <http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#> .
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@prefix neurolex: <http://neurolex.org/wiki/> .
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@prefix dc: <http://purl.org/dc/elements/1.1/> .
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@prefix dct: <http://purl.org/dc/terms/> .
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@prefix dctype: <http://purl.org/dc/dcmitype/> .
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@prefix spm: <http://www.incf.org/ns/nidash/spm#> .
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@prefix fsl: <http://www.incf.org/ns/nidash/fsl#> .
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@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
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@prefix nidm: <http://www.incf.org/ns/nidash/nidm#> .
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@prefix niiri: <http://iri.nidash.org/> .
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@prefix nfo: <http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#> .
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@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
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@prefix obo: <http://purl.obolibrary.org/obo/> .
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niiri:coordinate_space_id_1 a prov:Entity , nidm:CoordinateSpace ;
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rdfs:label "Coordinate space 1" ;
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nidm:voxelToWorldMapping "[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, -70],[0, 0, 0, 1]]"^^xsd:string ;
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nidm:voxelUnits "['mm', 'mm', 'mm']"^^xsd:string ;
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nidm:voxelSize "[3, 3, 3]"^^xsd:string ;
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nidm:inWorldCoordinateSystem nidm:MNICoordinateSystem ;
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nidm:numberOfDimensions "3"^^xsd:int ;
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nidm:dimensionsInVoxels "[53,63,52]"^^xsd:string .
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niiri:inference_id_1 a prov:Activity , nidm:Inference ;
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rdfs:label "Inference" ;
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nidm:isParametricTest "false"^^xsd:boolean ;
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nidm:hasAlternativeHypothesis nidm:OneTailedTest ;
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prov:used niiri:non_parametric_null_dististribution_id, niiri:statistic_map_id .
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niiri:non_parametric_null_dististribution_id a prov:Entity , nidm:NonParametricNullDistribution;
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rdfs:label "Non-Parametric Null Distribution" ;
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nidm:numberOfPermutations "5000"^^xsd:int ;
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nidm:exchangeabilityBlockSize "4"^^xsd:int .
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niiri:statistic_map_id a prov:Entity , nidm:StatisticMap ;
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rdfs:label "Smoothed Variance T-Statistic Map: passive listening > rest" ;
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prov:atLocation "file://./SmoothedVarianceTStatistic.nii.gz"^^xsd:anyURI ;
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nidm:statisticType nidm:SmoothedVarianceTStatistic ; #
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nfo:fileName "SmoothedVarianceTStatistic.nii.gz"^^xsd:string ;
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dct:format "image/nifti"^^xsd:string ;
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nidm:contrastName "passive listening > rest"^^xsd:string ;
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nidm:effectDegreesOfFreedom "1"^^xsd:float ;
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nidm:inCoordinateSpace niiri:coordinate_space_id_1 ;
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crypto:sha512 "799e9bbf8c15b35c0098bca4"^^xsd:string ;
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prov:wasGeneratedBy niiri:contrast_estimation_id;
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nidm:varianceSmoothingFWHM "[6 6 6]"^^xsd:string .
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