Update example with new usage of command

Author: omar-rifai

examples/clinica_pipelines/adni-to-bids.jsonld

@@ -12,12 +12,7 @@
 			{
 				"@id": "uuid:38133b39-f2fe-4746-aa3c-e3eca1b8abb4",
 				"label": "adni-to-bids",
-				"command": "clinica convert adni-to-bids src clinical_data bids ",
-				"parameters": {
-					"src": "/path/adni_dir",
-					"clinical_data": "/path/clinical/data/",
-					"bids": "/path/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"
 			}

examples/clinica_pipelines/readme.md

@@ -15,7 +15,7 @@
 from the root of this project
 
 ```bash
-python bids_prov/visualize.py examples/clinica_pipelines/adni-to-bids.json examples/clinica_pipelines/t1linear-mat.json examples/clinica_pipelines/t1linear-nii.json -o clinica_pipelines.png
+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) 

examples/clinica_pipelines/t1linear_mat.jsonld

@@ -10,19 +10,7 @@
 	    {
 		"@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"
-                    ]
-		],
+		"command": "run t1-linear /path/to/bids ws/CAPS_t1linear -np 4 -tsv subjects.tsv -ui",
 		"parameters": {
                     "uncropped_image": true
 		},

examples/clinica_pipelines/t1linear_nii.jsonld

@@ -10,19 +10,7 @@
 	    {
 		"@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"
-                    ]
-		],
+		"command": "clinica run t1-linear /path/to/bids ws/CAPS_t1linear -np 4 -tsv subjects.tsv -ui",
 		"parameters": {
                     "uncropped_image": true
 		},