HO-example.json

header = {"name": "Harvard-Oxford Cortical and Subcortical Probabilistic Atlas",
          "description": "The HAWG version of the atlas",
          "species": "Homo sapiens",
          "version": "0.0.1",
          "license": "FSL license",
          "provenance": "from FSL 5.0.7",
          "stored_data_type": "volume",
          "coordinate_system": {
                "display_name": "MNI152-clarify",
                "preferred-template": "$FSLDIR/data/standard/MNI152_T1_1mm.nii.gz",
                "alternative-templates": ["$FSLDIR/data/standard/MNI152_T1_2mm.nii.gz"]
                },
        }


structures = {'id1_MTG': {'example_coordinate': [48, 94, 35], 
             'long_name': 'Middle Temporal Gyrus, posterior division',
             "description": "Something jason comes up with",
             "example_color": [23, 86, 96],
             "discrete_index": 12, /*former data_key */
             "tags": ["Middle_Temporal_Gyrus", "Bilateral", "threshold0"]},
             "data_location": {"stored_data_location": "$FSLDIR/data/atlases/HarvardOxford/HarvardOxford-cort-maxprob-thr0-1mm.nii.gz",
                              }
 }

{'id0_MTG': {'example_coordinate': [48, 94, 35], 
      'long_name': 'Middle Temporal Gyrus, posterior division',
      "description": "Something jason comes up with",
      "example_color": [23, 46, 96],
      "tags": ["Middle_Temporal_Gyrus", "Bilateral"],
      "data_location": {"stored_data_location": 
"$FSLDIR/data/atlases/HarvardOxford/HarvardOxford-cort-prob-1mm.nii.gz",
                        "dimension_indexed": 3,
                        "dimension_index": 11,
                        "dimension_base": 0
                       }},
 'id2_MTG': {'example_coordinate': [74, 59, 26], 
      'long_name': 'Middle Temporal Gyrus, anterior division',
      "description": "Something jason comes up with",
      "example_color": [23, 26, 96],
      "tags": ["Middle_Temporal_Gyrus", "Bilateral"],
      "data_location": {"stored_data_location": "$FSLDIR/data/atlases/HarvardOxford/HarvardOxford-cort-prob-1mm.nii.gz",
                        "dimension": 4,
                        "dimension_index": 10,
                        "dimension_base": 0
                       }}
 })

tags = {'Middle_Temporal_Gyrus': {"display_name": "Middle Temporal Gyrus",
                                  "example_colour": [255, 255, 0],
                                  "description": "Some other description from Jason"
                                 }
       }