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Plotting graphs for dcm2niix examples
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‎examples/dcm2niix/README.md‎

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See the `dcm2niix.prov.jsonld` file that contains all provenance traces relative to the conversion steps.
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Two file level provenance files (`.prov.jsonld` sidecars) are also available, representing the provenance of the associated files:
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* sub-02_ses-20130717141500_T1w.prov.jsonld
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* sub-02_ses-20140425155335_task-oneback_run-1_bold.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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We are able to visualize these provenance files using the following commands (current directory is `examples/dcm2niix/`):
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```shell
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python ../../bids_prov/visualize.py --input_file prov/dcm2niix.prov.jsonld --output_file prov/dcm2niix.prov.png
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```
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![](examples/dcm2niix/prov/dcm2niix.prov.png)
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```shell
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python ../../bids_prov/visualize.py --input_file sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.jsonld --output_file sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.png
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```
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![](examples/dcm2niix/sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.png)
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```shell
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python ../../bids_prov/visualize.py --input_file sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld --output_file sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.png
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```
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![](examples/dcm2niix/sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.png)
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## Limitations
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‎examples/dcm2niix/dcm2niix.prov.jsonld‎ renamed to ‎examples/dcm2niix/prov/dcm2niix.prov.jsonld‎

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"@context": "https://purl.org/nidash/bidsprov/context.json",
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"BIDSProvVersion": "0.0.1",
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"Records": {
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"Environments": [
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"prov:Entity": [
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{
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"Id": "urn:fedora",
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"Label": "Fedora release 36 (Thirty Six)",
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],
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"Software": [
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{
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"Id": "urn:dcm2niix-4a586b50",
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"Id": "urn:dcm2niix",
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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": "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": "urn:dcm2niix-4a586b50",
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"Command": "dcm2niix -o . -f sub-%i/ses-%t/anat/sub-%i_ses-%t_T1w sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/",
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"AssociatedWith": "urn:dcm2niix",
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"Used": [
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"urn: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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"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": "urn:dcm2niix-4a586b50",
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"Command": "dcm2niix -o . -f sub-%i/ses-%t/func/sub-%i_ses-%t_task-oneback_run-1_bold sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/",
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"AssociatedWith": "urn:dcm2niix",
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"Used": [
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"urn: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",
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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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"Id": "bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json",
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"Label": "sub-02_ses-20140425155335_task-oneback_run-1_bold.json",
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"GeneratedBy": "urn:conversion-5a66f5be"
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},
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}
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]
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}
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}

‎examples/dcm2niix/prov/dcm2niix.prov.png‎

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

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"@context": "https://purl.org/nidash/bidsprov/context.json",
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"BIDSProvVersion": "0.0.1",
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"Records": {
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"Environments": [
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"prov:Entity": [
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{
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"Id": "urn:fedora",
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"Label": "Fedora release 36 (Thirty Six)",
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],
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"Software": [
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{
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"Id": "urn:dcm2niix-4a586b50",
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"Id": "urn:dcm2niix",
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"Label": "dcm2niix",
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"Version": "v1.0.20220720"
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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": "urn:dcm2niix-4a586b50",
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"AssociatedWith": "urn:dcm2niix",
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"Used": [
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"urn: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_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.png‎

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‎examples/dcm2niix/sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii‎

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‎examples/dcm2niix/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld‎ renamed to ‎examples/dcm2niix/sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld‎

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"@context": "https://purl.org/nidash/bidsprov/context.json",
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"BIDSProvVersion": "0.0.1",
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"Records": {
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"Environments": [
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"prov:Entity": [
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{
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"Id": "urn:fedora",
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"Label": "Fedora release 36 (Thirty Six)",
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],
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"Software": [
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{
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"Id": "urn:dcm2niix-4a586b50",
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"Id": "urn:dcm2niix",
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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": "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": "urn:dcm2niix-4a586b50",
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"Command": "dcm2niix -o . -f sub-%i/ses-%t/func/sub-%i_ses-%t_task-oneback_run-1_bold sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/",
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"AssociatedWith": "urn:dcm2niix",
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"Used": [
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"urn: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",
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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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"Id": "bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json",
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"Label": "sub-02_ses-20140425155335_task-oneback_run-1_bold.json",
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"GeneratedBy": "urn:conversion-5a66f5be"
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},
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}
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]
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}
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}

‎examples/dcm2niix/sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.png‎

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