diff --git a/examples/clinica_pipelines/adni-to-bids.jsonld b/examples/clinica_pipelines/adni-to-bids.jsonld new file mode 100644 index 000000000..a2ce64503 --- /dev/null +++ b/examples/clinica_pipelines/adni-to-bids.jsonld @@ -0,0 +1,34 @@ +{ + "@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" + } + ] + } +} \ No newline at end of file diff --git a/examples/clinica_pipelines/clinica_pipelines.png b/examples/clinica_pipelines/clinica_pipelines.png new file mode 100644 index 000000000..a78a66989 Binary files /dev/null and b/examples/clinica_pipelines/clinica_pipelines.png differ diff --git a/examples/clinica_pipelines/readme.md b/examples/clinica_pipelines/readme.md new file mode 100644 index 000000000..f89639866 --- /dev/null +++ b/examples/clinica_pipelines/readme.md @@ -0,0 +1,21 @@ +## 2-step workflow using Clinica (https://github.com/aramis-lab/clinica) + +--- + +### Workflow + +
+ +
+ +--- + +### Generate a graph + +from the root of this project + +```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 +``` + +generates the graph illustrating the provenance of files related to two Clinica pipelines (adni-to-bids and t1-linear) diff --git a/examples/clinica_pipelines/t1linear_mat.jsonld b/examples/clinica_pipelines/t1linear_mat.jsonld new file mode 100644 index 000000000..a6f8b5806 --- /dev/null +++ b/examples/clinica_pipelines/t1linear_mat.jsonld @@ -0,0 +1,34 @@ +{ + "@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" + } + + ] + } +} diff --git a/examples/clinica_pipelines/t1linear_nii.jsonld b/examples/clinica_pipelines/t1linear_nii.jsonld new file mode 100644 index 000000000..4a4795eff --- /dev/null +++ b/examples/clinica_pipelines/t1linear_nii.jsonld @@ -0,0 +1,35 @@ +{ + "@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": "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" + } + + ] + } +} diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc.png b/examples/from_parsers/afni/afni_alt_onesided_proc.png new file mode 100644 index 000000000..0f82f2954 Binary files /dev/null and b/examples/from_parsers/afni/afni_alt_onesided_proc.png differ diff --git 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