Merge pull request #67 from omar-rifai/example_clinica_pipelines

Example clinica pipelines
bids-standard · May 22, 2024 · 874bc70 · 874bc70
2 parents 2ec70ea + 048d7a5
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diff --git a/examples/clinica_pipelines/adni-to-bids.jsonld 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"
+			}
+		]
+	}
+}
diff --git a/examples/clinica_pipelines/clinica_pipelines.png b/examples/clinica_pipelines/clinica_pipelines.png
diff --git a/examples/clinica_pipelines/readme.md b/examples/clinica_pipelines/readme.md
@@ -0,0 +1,21 @@
+## 2-step workflow using Clinica (https://github.com/aramis-lab/clinica)
+
+---
+
+### Workflow
+
+<center>
+<img src="clinica_pipelines.png" width="90%" position="center">
+</center>
+
+---
+
+### 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
@@ -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
@@ -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"
+	    }
+
+	]
+    }
+}
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