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Use bids::prov/ base IRIs and pyld instead of rdflib
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-109
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‎examples/dcm2niix/code/exp1_merge_prov.py‎

Lines changed: 37 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,39 @@
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import json
2+
13
from rdflib import Graph
4+
from pyld import jsonld
5+
6+
prov_files = [
7+
'prov/common.prov.jsonld',
8+
'prov/software.prov.jsonld',
9+
'prov/environments.prov.jsonld',
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'sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.jsonld',
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'sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld'
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]
13+
14+
with open('prov/bidsprov_context.json', encoding = 'utf-8') as file:
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context = json.load(file)
16+
17+
rdf_graph = ''
18+
for prov_file in prov_files:
19+
with open(prov_file, encoding = 'utf-8') as file:
20+
#expanded = json.dumps(jsonld.flatten(jsonld.expand(json.load(file)), ctx = context, options = {'processingMode': 'json-ld-1.1'}), indent = 2)
21+
#print(expanded)
22+
rdf_graph += jsonld.normalize(
23+
json.load(file), {'algorithm': 'URDNA2015', 'format': 'application/n-quads'})
24+
print(rdf_graph)
25+
#graph.parse(data = expanded, format = 'json-ld')
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228

3-
graph = Graph()
4-
graph.parse("prov/software.prov.jsonld", format = "json-ld")
5-
graph.parse("prov/environments.prov.jsonld", format = "json-ld")
6-
graph.parse("sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.jsonld", format = "json-ld")
7-
graph.parse("sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld", format = "json-ld")
8-
print(len(graph))
9-
graph.serialize(destination = "prov/experiment_1/merged_provenance.ttl")
29+
"""
30+
graph.parse('prov/common.prov.jsonld', format = 'json-ld')
31+
graph.parse('prov/software.prov.jsonld', format = 'json-ld')
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graph.parse('prov/environments.prov.jsonld', format = 'json-ld')
33+
graph.parse('sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.jsonld', format = 'json-ld')
34+
graph.parse('sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld', format = 'json-ld')
35+
"""
36+
#print(len(graph))
37+
#graph.serialize(destination = 'prov/experiment_1/merged_provenance.ttl')
38+
with open('prov/experiment_1/merged_provenance.ttl', 'w' , encoding = 'utf-8') as file:
39+
file.write(rdf_graph)

‎examples/dcm2niix/code/requirements.txt‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1 +1,2 @@
1-
rdflib==7.1.3
1+
rdflib==7.1.3
2+
pyld==2.0.4

‎examples/dcm2niix/prov/common.prov.jsonld‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,4 @@
1+
{
2+
"BIDSProvVersion": "0.0.1",
3+
"@graph":{}
4+
}

‎examples/dcm2niix/prov/environments.prov.jsonld‎

Lines changed: 3 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,12 +1,9 @@
11
{
2-
"@context": [
3-
"bidsprov_context.json"
4-
],
5-
"BIDSProvVersion": "0.0.1",
6-
"@graph": {
2+
"@context": "https://purl.org/nidash/bidsprov/context.json",
3+
"Records": {
74
"Environments": [
85
{
9-
"Id": "fedora",
6+
"Id": "bids::prov/fedora",
107
"Label": "Fedora release 36 (Thirty Six)",
118
"OperatingSystem": " GNU/Linux 6.2.15-100.fc36.x86_64"
129
}

‎examples/dcm2niix/prov/experiment_1/merged_provenance.png‎

174 KB
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‎examples/dcm2niix/prov/experiment_1/merged_provenance.ttl‎

Lines changed: 43 additions & 68 deletions
Original file line numberDiff line numberDiff line change
@@ -1,68 +1,43 @@
1-
@prefix prov: <http://www.w3.org/ns/prov#> .
2-
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
3-
4-
<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json> rdfs:label "sub-02_ses-20130717141500_T1w.json" ;
5-
prov:wasGeneratedBy <urn:conversion-00f3a18f> .
6-
7-
<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii> rdfs:label "sub-02_ses-20130717141500_T1w.nii" ;
8-
prov:wasGeneratedBy <urn:conversion-00f3a18f> .
9-
10-
<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" ;
11-
prov:wasGeneratedBy <urn:conversion-5a66f5be> .
12-
13-
<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" ;
14-
prov:wasGeneratedBy <urn:conversion-5a66f5be> .
15-
16-
<file:///data/dev/BEP028_BIDSprov/examples/dcm2niix/prov/fmriprep-4a586b50> rdfs:label "fmriprep" ;
17-
prov:Revision "v1.0.20220720" .
18-
19-
<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm> rdfs:label "N2D_0001.dcm" .
20-
21-
<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm> rdfs:label "N2D_0002.dcm" .
22-
23-
<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm> rdfs:label "N2D_0003.dcm" .
24-
25-
<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" .
26-
27-
<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" .
28-
29-
<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" .
30-
31-
<file:///data/dev/BEP028_BIDSprov/examples/dcm2niix/prov/dcm2niix-4a586b50> rdfs:label "dcm2niix" ;
32-
prov:Revision "v1.0.20220720" .
33-
34-
<file:///data/dev/BEP028_BIDSprov/examples/dcm2niix/prov/fedora> rdfs:label "Fedora release 36 (Thirty Six)" .
35-
36-
<urn:conversion-00f3a18f> rdfs:label "Conversion" ;
37-
prov:used <bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm>,
38-
<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm>,
39-
<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm>,
40-
<file:///data/dev/BEP028_BIDSprov/examples/dcm2niix/prov/fedora> ;
41-
prov:wasAssociatedWith <file:///data/dev/BEP028_BIDSprov/examples/dcm2niix/prov/dcm2niix-4a586b50> .
42-
43-
<urn:conversion-5a66f5be> rdfs:label "Conversion" ;
44-
prov:used <bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586>,
45-
<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588>,
46-
<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590>,
47-
<file:///data/dev/BEP028_BIDSprov/examples/dcm2niix/prov/fedora> ;
48-
prov:wasAssociatedWith <file:///data/dev/BEP028_BIDSprov/examples/dcm2niix/prov/dcm2niix-4a586b50> .
49-
50-
[] prov:Agent <file:///data/dev/BEP028_BIDSprov/examples/dcm2niix/prov/dcm2niix-4a586b50>,
51-
<file:///data/dev/BEP028_BIDSprov/examples/dcm2niix/prov/fmriprep-4a586b50> .
52-
53-
[] prov:Activity <urn:conversion-5a66f5be> ;
54-
prov:Entity <bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586>,
55-
<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588>,
56-
<bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590>,
57-
<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json>,
58-
<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii> .
59-
60-
[] prov:Entity <file:///data/dev/BEP028_BIDSprov/examples/dcm2niix/prov/fedora> .
61-
62-
[] prov:Activity <urn:conversion-00f3a18f> ;
63-
prov:Entity <bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm>,
64-
<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm>,
65-
<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm>,
66-
<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json>,
67-
<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii> .
68-
1+
<bids::prov/dcm2niix> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Agent> .
2+
<bids::prov/dcm2niix> <http://www.w3.org/2000/01/rdf-schema#label> "dcm2niix" .
3+
<bids::prov/fmriprep> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Agent> .
4+
<bids::prov/fmriprep> <http://www.w3.org/2000/01/rdf-schema#label> "fmriprep" .
5+
<bids::prov/fedora> <http://www.w3.org/2000/01/rdf-schema#label> "Fedora release 36 (Thirty Six)" .
6+
<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> <http://www.w3.org/ns/prov#Entity> .
7+
<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm> <http://www.w3.org/2000/01/rdf-schema#label> "N2D_0001.dcm" .
8+
<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> <http://www.w3.org/ns/prov#Entity> .
9+
<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm> <http://www.w3.org/2000/01/rdf-schema#label> "N2D_0002.dcm" .
10+
<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> <http://www.w3.org/ns/prov#Entity> .
11+
<bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm> <http://www.w3.org/2000/01/rdf-schema#label> "N2D_0003.dcm" .
12+
<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> .
13+
<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json> <http://www.w3.org/2000/01/rdf-schema#label> "sub-02_ses-20130717141500_T1w.json" .
14+
<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json> <http://www.w3.org/ns/prov#wasGeneratedBy> <urn:conversion-00f3a18f> .
15+
<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> .
16+
<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii> <http://www.w3.org/2000/01/rdf-schema#label> "sub-02_ses-20130717141500_T1w.nii" .
17+
<bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii> <http://www.w3.org/ns/prov#wasGeneratedBy> <urn:conversion-00f3a18f> .
18+
<urn:conversion-00f3a18f> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> .
19+
<urn:conversion-00f3a18f> <http://www.w3.org/2000/01/rdf-schema#label> "Conversion" .
20+
<urn:conversion-00f3a18f> <http://www.w3.org/ns/prov#used> <bids::prov/fedora> .
21+
<urn:conversion-00f3a18f> <http://www.w3.org/ns/prov#used> <bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm> .
22+
<urn:conversion-00f3a18f> <http://www.w3.org/ns/prov#used> <bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm> .
23+
<urn:conversion-00f3a18f> <http://www.w3.org/ns/prov#used> <bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm> .
24+
<urn:conversion-00f3a18f> <http://www.w3.org/ns/prov#wasAssociatedWith> <bids::prov/dcm2niix> .
25+
<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> <http://www.w3.org/ns/prov#Entity> .
26+
<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/2000/01/rdf-schema#label> "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586" .
27+
<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> <http://www.w3.org/ns/prov#Entity> .
28+
<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/2000/01/rdf-schema#label> "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588" .
29+
<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> <http://www.w3.org/ns/prov#Entity> .
30+
<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/2000/01/rdf-schema#label> "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590" .
31+
<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> <http://www.w3.org/ns/prov#Entity> .
32+
<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json> <http://www.w3.org/2000/01/rdf-schema#label> "sub-02_ses-20140425155335_task-oneback_run-1_bold.json" .
33+
<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json> <http://www.w3.org/ns/prov#wasGeneratedBy> <urn:conversion-5a66f5be> .
34+
<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> <http://www.w3.org/ns/prov#Entity> .
35+
<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii> <http://www.w3.org/2000/01/rdf-schema#label> "sub-02_ses-20140425155335_task-oneback_run-1_bold.nii" .
36+
<bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii> <http://www.w3.org/ns/prov#wasGeneratedBy> <urn:conversion-5a66f5be> .
37+
<urn:conversion-5a66f5be> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> .
38+
<urn:conversion-5a66f5be> <http://www.w3.org/2000/01/rdf-schema#label> "Conversion" .
39+
<urn:conversion-5a66f5be> <http://www.w3.org/ns/prov#used> <bids::prov/fedora> .
40+
<urn:conversion-5a66f5be> <http://www.w3.org/ns/prov#used> <bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586> .
41+
<urn:conversion-5a66f5be> <http://www.w3.org/ns/prov#used> <bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588> .
42+
<urn:conversion-5a66f5be> <http://www.w3.org/ns/prov#used> <bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590> .
43+
<urn:conversion-5a66f5be> <http://www.w3.org/ns/prov#wasAssociatedWith> <bids::prov/dcm2niix> .

‎examples/dcm2niix/prov/software.prov.jsonld‎

Lines changed: 4 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,17 +1,14 @@
11
{
2-
"@context": [
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"bidsprov_context.json"
4-
],
5-
"BIDSProvVersion": "0.0.1",
6-
"@graph": {
2+
"@context": "https://purl.org/nidash/bidsprov/context.json",
3+
"Records": {
74
"Software": [
85
{
9-
"Id": "dcm2niix-4a586b50",
6+
"Id": "bids::prov/dcm2niix",
107
"Label": "dcm2niix",
118
"Version": "v1.0.20220720"
129
},
1310
{
14-
"Id": "fmriprep-4a586b50",
11+
"Id": "bids::prov/fmriprep",
1512
"Label": "fmriprep",
1613
"Version": "v1.0.20220720"
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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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}
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],
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"BIDSProvVersion": "0.0.1",
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"@graph": {
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"@context": "https://purl.org/nidash/bidsprov/context.json",
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"Records": {
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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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"AssociatedWith": "bids::prov/dcm2niix",
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"Used": [
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"fedora",
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"bids::prov/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"

‎examples/dcm2niix/sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.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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}
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],
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"BIDSProvVersion": "0.0.1",
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"@graph": {
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"@context": "https://purl.org/nidash/bidsprov/context.json",
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"Records": {
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"Activities": [
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{
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"Id": "urn:conversion-5a66f5be",
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"Label": "Conversion",
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"Command": "dcm2niix -o . -f sub-%i/ses-%t/func/sub-%i_ses-%t_task-oneback_run-1_bold sourcedata/acq1/dicoms/example-dicom-structural-master/dicoms/",
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"AssociatedWith": "dcm2niix-4a586b50",
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"AssociatedWith": "bids::prov/dcm2niix",
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"Used": [
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"fedora",
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"bids::prov/fedora",
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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",
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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",
2014
"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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