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…ipelines Example clinica pipelines
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{ | ||
"@context": "https://raw.githubusercontent.com/omar-rifai/Provenance/main/context.json", | ||
"records": { | ||
"prov:Agent": [ | ||
{ | ||
"@id": "RRID:Clinica", | ||
"@type": "prov:SoftwareAgent", | ||
"label": "Clinica" | ||
} | ||
], | ||
"prov:Activity": [ | ||
{ | ||
"@id": "uuid:38133b39-f2fe-4746-aa3c-e3eca1b8abb4", | ||
"label": "adni-to-bids", | ||
"command": "clinica convert adni-to-bids path/to/adni/raw path/to/clinical_data path/to/bids", | ||
"wasAssociatedWith": "RRID:Clinica", | ||
"used": "uuid:0c18a16e-11e9-42cf-b004-019bc6aaa76b" | ||
} | ||
], | ||
"prov:Entity": [ | ||
{ | ||
"@id": "uuid:0c18a16e-11e9-42cf-b004-019bc6aaa76b", | ||
"label": "Dicom 022_S_0004", | ||
"prov:atLocation": "/path/to/adni/data/raw/" | ||
}, | ||
{ | ||
"@id": "uuid:6cada670-8bf2-44ef-80ae-71796eb5ecd7", | ||
"label": "sub-ADNI022S0004_ses-M00_T1w.nii.gz", | ||
"atLocation": "/path/to/bids/sub-ADNI022S0004/ses-M00/anat/sub-ADNI022S0004_ses-M00_T1w.nii.gz", | ||
"wasGeneratedBy": "uuid:38133b39-f2fe-4746-aa3c-e3eca1b8abb4" | ||
} | ||
] | ||
} | ||
} |
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## 2-step workflow using Clinica (https://github.com/aramis-lab/clinica) | ||
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--- | ||
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### Workflow | ||
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<center> | ||
<img src="clinica_pipelines.png" width="90%" position="center"> | ||
</center> | ||
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--- | ||
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### Generate a graph | ||
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from the root of this project | ||
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```bash | ||
python bids_prov/visualize.py examples/clinica_pipelines/adni-to-bids.jsonld examples/clinica_pipelines/t1linear_mat.jsonld examples/clinica_pipelines/t1linear_nii.jsonld -o clinica_pipelines.png | ||
``` | ||
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generates the graph illustrating the provenance of files related to two Clinica pipelines (adni-to-bids and t1-linear) |
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{ | ||
"@context": "https://raw.githubusercontent.com/omar-rifai/Provenance/main/context.json", | ||
"records":{ | ||
"prov:Agent" : [{ | ||
"@id": "uuid:5da92f66-bfec-11ec-9d64-0242ac120002", | ||
"RRID": "Clinica", | ||
"@type": "prov:SoftwareAgent", | ||
"Label": "Clinica v0.6.0", | ||
"Version": "v0.6.0" | ||
}], | ||
"prov:Activity": [ | ||
{ | ||
"@id": "uuid:2c2964f2-f865-41cc-a4e9-5d4f4ecaec13", | ||
"label": "t1-linear", | ||
"command": "run t1-linear /path/to/bids ws/CAPS_t1linear -np 4 -tsv subjects.tsv -ui", | ||
"parameters": { | ||
"uncropped_image": true | ||
}, | ||
"wasAssociatedWith": "uuid:5da92f66-bfec-11ec-9d64-0242ac120002", | ||
"used": [ | ||
"uuid:6cada670-8bf2-44ef-80ae-71796eb5ecd7" | ||
] | ||
} | ||
], | ||
"prov:Entity": [ | ||
{ | ||
"@id": "uuid:696a079c-3618-4e0d-87aa-b60965c86127", | ||
"label": "sub-ADN..-MNI152NLin2009cSym_res-1x1x1_affine.mat", | ||
"wasGeneratedBy": "uuid:2c2964f2-f865-41cc-a4e9-5d4f4ecaec13" | ||
} | ||
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] | ||
} | ||
} |
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{ | ||
"@context": "https://raw.githubusercontent.com/omar-rifai/Provenance/main/context.json", | ||
"records":{ | ||
"prov:Agent" : [{ | ||
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"@id": "uuid:5da92f66-bfec-11ec-9d64-0242ac120002", | ||
"RRID": "Clinica", | ||
"@type": "prov:SoftwareAgent", | ||
"Label": "Clinica v0.6.0", | ||
"Version": "v0.6.0" | ||
}], | ||
"prov:Activity": [ | ||
{ | ||
"@id": "uuid:2c2964f2-f865-41cc-a4e9-5d4f4ecaec13", | ||
"label": "t1-linear", | ||
"command": "clinica run t1-linear /path/to/bids ws/CAPS_t1linear -np 4 -tsv subjects.tsv -ui", | ||
"parameters": { | ||
"uncropped_image": true | ||
}, | ||
"wasAssociatedWith": "uuid:5da92f66-bfec-11ec-9d64-0242ac120002", | ||
"used": [ | ||
"uuid:6cada670-8bf2-44ef-80ae-71796eb5ecd7" | ||
] | ||
} | ||
], | ||
"prov:Entity": [ | ||
{ | ||
"@id": "uuid:5ebd15a4-0051-46e1-ada0-d718f39b2e2c", | ||
"label": "sub-ADN..-MNI152NLin2009cSym_res-1x1x1_affine.nii", | ||
"wasGeneratedBy": "uuid:2c2964f2-f865-41cc-a4e9-5d4f4ecaec13" | ||
} | ||
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] | ||
} | ||
} |