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First example of splitted provenance
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‎examples/dcm2niix/README.md‎

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# BIDS Prov example for `dcm2niix`
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This example aims at showing the capture of provenance for a [`dcm2niix`](https://github.com/rordenlab/dcm2niix) usecase: converting DICOM data to Nifti files within a BIDS dataset.
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Source data for this example can be found here: https://github.com/psychoinformatics-de/hirni-demo. This is a datalad dataset containing anatomical and functional MRI acquisitions. The contents of this dataset can be downloaded using:
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```shell
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mkdir sourcedata
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cd sourcedata
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datalad install --recursive https://github.com/psychoinformatics-de/hirni-demo.git
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```
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> [!NOTE] Note that the dataset must be added inside the `sourcedata/` directory.
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## Experiment #1
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We describe the provenance records inside the following files:
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```
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.
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├── prov
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│ ├── bidsprov_context.json
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│ ├── environments.prov.jsonld
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│ └── software.prov.jsonld
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└── sub_02
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├── ses_20130717141500
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│ └── anat
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│ └── sub-02_ses-20130717141500_T1w.prov.jsonld
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└── ses_20140425155335
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└── func
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└── sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld
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```
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* `sub-02_ses-20130717141500_T1w.prov.jsonld` and `sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld` are sidecars defining provenance for the corresponding `.nii` files.
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* `bidsprov_context.json` is the BIDS Prov context from https://purl.org/nidash/bidsprov/context.json, with minor changes.
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* `environments.prov.jsonld` mutualises the declaration of software environments objects for lower level prov files
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* `software.prov.jsonld` mutualises the declaration of software pieces objects for lower level prov files
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The python script `code/exp1_merge_prov.py` aims at merging all these provenance records into one RFD graph.
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```shell
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pip install -r code/requirements.txt
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mkdir prov/experiment_1/
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python code/exp1_merge_prov.py
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```
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From that, we generate the RDF graph `prov/experiment_1/merged_provenance.ttl`.
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Notice that starting from line 50 of the file, the generated triplets are not correct.
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```turtle
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[] prov:Activity <urn:conversion-5a66f5be> ;
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```
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This is probably due to the fact that rdflib 7.1.3 does not conform with JSON-LD 1.1 and is therefore not able to parse graphs using [type indexing](https://www.w3.org/TR/json-ld11/#example-106-indexing-data-in-json-ld-by-type) as we used it e.g. in the `Records_hirni-demo_software` term of the `prov/software.prov.jsonld` file.
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Furthermore, all the triplets describing the type of node objects are missing because of rdflib not understanding type indexing.
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As a workaround, replaced the incorrect lines (50 to the end) by triplets describing the type of the objects in the merged document, as presented in `prov/experiment_1/merged_provenance_2.ttl`.
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From that we were able to plot the following graph `prov/experiment_1/merged_provenance_2.ttl`.
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![](/examples/dcm2niix/prov/experiment_1/merged_provenance_2.ttl)

‎examples/dcm2niix/code/exp1_merge_prov.py‎

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from rdflib import Graph
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graph = Graph()
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graph.parse("prov/software.prov.jsonld", format = "json-ld")
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graph.parse("prov/environments.prov.jsonld", format = "json-ld")
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graph.parse("sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.jsonld", format = "json-ld")
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graph.parse("sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld", format = "json-ld")
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print(len(graph))
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graph.serialize(destination = "prov/experiment_1/merged_provenance.ttl")

‎examples/dcm2niix/code/requirements.txt‎

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rdflib==7.1.3

‎examples/dcm2niix/prov/environments.prov.jsonld‎

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{
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"@context": [
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"bidsprov_context.json",
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{
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"Records_hirni-demo_environments": "Records"
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}
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],
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"BIDSProvVersion": "0.0.1",
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"Records_hirni-demo_environments": {
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"Environments": [
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{
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"Id": "fedora",
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"Label": "Fedora release 36 (Thirty Six)",
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"OperatingSystem": " GNU/Linux 6.2.15-100.fc36.x86_64"
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}
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]
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}
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}

‎examples/dcm2niix/prov/experiment_1/merged_provenance.ttl‎

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@prefix prov: <http://www.w3.org/ns/prov#> .
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@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
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<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json> rdfs:label "sub-02_ses-20130717141500_T1w.json" ;
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prov:wasGeneratedBy <urn:conversion-00f3a18f> .
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<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii> rdfs:label "sub-02_ses-20130717141500_T1w.nii" ;
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prov:wasGeneratedBy <urn:conversion-00f3a18f> .
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<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json> rdfs:label "sub-02_ses-20140425155335_task-oneback_run-1_bold.json" ;
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prov:wasGeneratedBy <urn:conversion-5a66f5be> .
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<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii> rdfs:label "sub-02_ses-20140425155335_task-oneback_run-1_bold.nii" ;
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prov:wasGeneratedBy <urn:conversion-5a66f5be> .
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<file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/fmriprep-4a586b50> rdfs:label "fmriprep" ;
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prov:Revision "v1.0.20220720" .
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm> rdfs:label "N2D_0001.dcm" .
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm> rdfs:label "N2D_0002.dcm" .
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm> rdfs:label "N2D_0003.dcm" .
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<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586> rdfs:label "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586" .
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<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588> rdfs:label "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588" .
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<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590> rdfs:label "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590" .
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<file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/dcm2niix-4a586b50> rdfs:label "dcm2niix" ;
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prov:Revision "v1.0.20220720" .
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<file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/fedora> rdfs:label "Fedora release 36 (Thirty Six)" .
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<urn:conversion-00f3a18f> rdfs:label "Conversion" ;
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prov:used <bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm>,
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm>,
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm>,
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<file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/fedora> ;
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prov:wasAssociatedWith <file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/dcm2niix-4a586b50> .
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<urn:conversion-5a66f5be> rdfs:label "Conversion" ;
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prov:used <bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586>,
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<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588>,
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<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590>,
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<file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/fedora> ;
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prov:wasAssociatedWith <file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/dcm2niix-4a586b50> .
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[] prov:Activity <urn:conversion-5a66f5be> ;
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prov:Entity <bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586>,
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<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588>,
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<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590>,
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<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json>,
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<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii> .
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[] prov:Activity <urn:conversion-00f3a18f> ;
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prov:Entity <bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm>,
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm>,
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm>,
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<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json>,
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<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii> .
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[] prov:Entity <file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/fedora> .
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[] prov:Agent <file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/dcm2niix-4a586b50>,
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<file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/fmriprep-4a586b50> .
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‎examples/dcm2niix/prov/experiment_1/merged_provenance_2.png‎

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‎examples/dcm2niix/prov/experiment_1/merged_provenance_2.ttl‎

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@prefix prov: <http://www.w3.org/ns/prov#> .
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@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
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<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json> rdfs:label "sub-02_ses-20130717141500_T1w.json" ;
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prov:wasGeneratedBy <urn:conversion-00f3a18f> .
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<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii> rdfs:label "sub-02_ses-20130717141500_T1w.nii" ;
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prov:wasGeneratedBy <urn:conversion-00f3a18f> .
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<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json> rdfs:label "sub-02_ses-20140425155335_task-oneback_run-1_bold.json" ;
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prov:wasGeneratedBy <urn:conversion-5a66f5be> .
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<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii> rdfs:label "sub-02_ses-20140425155335_task-oneback_run-1_bold.nii" ;
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prov:wasGeneratedBy <urn:conversion-5a66f5be> .
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<file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/fmriprep-4a586b50> rdfs:label "fmriprep" ;
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prov:Revision "v1.0.20220720" .
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm> rdfs:label "N2D_0001.dcm" .
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm> rdfs:label "N2D_0002.dcm" .
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm> rdfs:label "N2D_0003.dcm" .
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<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586> rdfs:label "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586" .
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<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588> rdfs:label "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588" .
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<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590> rdfs:label "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590" .
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<file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/dcm2niix-4a586b50> rdfs:label "dcm2niix" ;
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prov:Revision "v1.0.20220720" .
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<file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/fedora> rdfs:label "Fedora release 36 (Thirty Six)" .
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<urn:conversion-00f3a18f> rdfs:label "Conversion" ;
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prov:used <bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm>,
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm>,
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm>,
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<file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/fedora> ;
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prov:wasAssociatedWith <file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/dcm2niix-4a586b50> .
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<urn:conversion-5a66f5be> rdfs:label "Conversion" ;
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prov:used <bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586>,
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<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588>,
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<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590>,
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<file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/fedora> ;
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prov:wasAssociatedWith <file:///dev/BEP028_BIDSprov/examples/dcm2niix/prov/dcm2niix-4a586b50> .
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<urn:conversion-00f3a18f> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> prov:Activity .
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> prov:Entity .
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> prov:Entity .
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<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> prov:Entity .
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<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> prov:Entity .
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<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> prov:Entity .
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<file:///dev/tests/bids_prov/split_data/prov/dcm2niix-4a586b50> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> prov:Agent .
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<file:///dev/tests/bids_prov/split_data/prov/fmriprep-4a586b50> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> prov:Agent .
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<file:///dev/tests/bids_prov/split_data/prov/fedora> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> prov:Entity .
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<urn:conversion-5a66f5be> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> prov:Activity .
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<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> prov:Entity .
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<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> prov:Entity .
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<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> prov:Entity .
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<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> prov:Entity .
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<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> prov:Entity .
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‎examples/dcm2niix/prov/software.prov.jsonld‎

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{
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"@context": [
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"bidsprov_context.json",
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{
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"Records_hirni-demo_software": "Records"
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}
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],
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"BIDSProvVersion": "0.0.1",
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"Records_hirni-demo_software": {
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"Software": [
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{
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"Id": "dcm2niix-4a586b50",
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"Label": "dcm2niix",
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"Version": "v1.0.20220720"
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},
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{
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"Id": "fmriprep-4a586b50",
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"Label": "fmriprep",
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"Version": "v1.0.20220720"
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}
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]
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}
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}

‎examples/dcm2niix/sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.nii‎

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‎examples/dcm2niix/sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.jsonld‎

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{
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"@context": [
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"../../../prov/bidsprov_context.json",
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{
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"@base": "../../../prov/",
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"Records_sub-02_ses-20130717141500_T1w": "Records"
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}
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],
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"BIDSProvVersion": "0.0.1",
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"Records_sub-02_ses-20130717141500_T1w": {
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"Activities": [
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{
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"Id": "urn:conversion-00f3a18f",
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"Label": "Conversion",
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"Command": "dcm2niix -o . -f sub-%i/ses-%t/anat/sub-%i_ses-%t_T1w sourcedata/acq1/dicoms/example-dicom-structural-master/dicoms/",
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"AssociatedWith": "dcm2niix-4a586b50",
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"Used": [
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"fedora",
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"bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm",
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"bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm",
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"bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm"
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]
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}
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],
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"Entities": [
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{
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"Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm",
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"Label": "N2D_0001.dcm"
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},
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{
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"Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm",
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"Label": "N2D_0002.dcm"
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},
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{
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"Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm",
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"Label": "N2D_0003.dcm"
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},
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{
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"Id": "bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii",
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"Label": "sub-02_ses-20130717141500_T1w.nii",
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"GeneratedBy": "urn:conversion-00f3a18f"
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},
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{
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"Id": "bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json",
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"Label": "sub-02_ses-20130717141500_T1w.json",
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"GeneratedBy": "urn:conversion-00f3a18f"
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}
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]
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}
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}

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