HOS.json

[{
        "@type": "header",
        "@id":"HOS",
        "species": "Homo Sapiens"
        "organ": "brain"
        "name": "Harvard-Oxford Subcortical Probability 2mm",
        "licence": "http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence",
        "citation": "doi:10.1016/j.biopsych.2006.06.027;doi:10.1016/j.neuroimage.2006.01.021",
        "version": "1",
        "contact": ["mailto:steve@fmrib.ox.ac.uk", "http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases"], #Nice to include more than one thing if it exists 
        "comment": "<p>Probabilistic atlases covering 48 cortical and 21 subcortical structural areas, derived from structural data and segmentations kindly provided by the Harvard Center for Morphometric Analysis.</p><p>T1-weighted images of 21 healthy male and 16 healthy female subjects (ages 18-50) were individually segmented by the CMA using semi-automated tools developed in-house. The T1-weighted images were affine-registered to MNI152 space using FLIRT (FSL), and the transforms then applied to the individual labels. Finally, these were combined across subjects to form population probability maps for each label.</p><p>We are very grateful to the following for providing the segmentations used to create these atlases: David Kennedy and Christian Haselgrove, Centre for Morphometric Analysis, Harvard; Bruce Fischl, the Martinos Center for Biomedical Imaging, MGH (NIH grants P41-RR14075, R01 RR16594-01A1, R01 NS052585-01); Janis Breeze and Jean Frazier from the Child and Adolescent Neuropsychiatric Research Program, Cambridge Health Alliance (NIH grants K08 MH01573, K01 MH01798); Larry Seidman and Jill Goldstein from the Department of Psychiatry of Harvard Medical School.</p>",
        "coordinate_system": "ijk", #a standardised naming is needed here(ijk = voxel coordinate)
        "reference_anatomical_file": "$FSLDIR/data/standard/MNI152_T1_2mm" # reference to template
    }, 
    {
        "@id": "dataRef",
        "@type": "datasource",
        "comment": "", #json can’ t handle multi - line 
        "mimeType": "application/x-nifti",
        "source": "NULL",
    }, 
    {
        "@id": "LCWM_structure",
        "@type": "structure",
        "sourceSelector": {
            "datasource": "dataRef",
            "frame_dimension": 4, #should just follow the convention of the data file being pointed at 
            "frame_index": 0, #should just follow the convention of the data file being pointed at
        },
        "annotation": {
            "name": "Left Cerebral White Matter",
            "shortName": "LCWM",
            "laterality": "left"
        },
        "renderOptions": {
            "pointOfInterest": [58, 37, 50]
        },
    }, 
    {
        "@id": "LCTX_structure",
        "@type": "structure",
        "sourceSelector": {
            "datasource": "dataRef",
            "frame_dimension": 4, #should just follow the convention of the data file being pointed at 
            "frame_index": 1, #should just follow the convention of the data file being pointed at
        },
        "annotation": {
            "name": "Left Cerebral Cortex",
            "shortName": "LCTX",
            "laterality": "left"
        },
        "renderOptions": {
            "pointOfInterest": [70, 63, 35]
        },
    }, 
    {
        "@id": "LLV_structure",
        "@type": "structure",
        "sourceSelector": {
            "datasource": "dataRef",
            "frame_dimension": 4,
            "frame_index": 2,
        },
        "annotation": {
            "name": "Left Lateral Ventrical",
            "shortName": "LLV",
            "laterality": "left"
        },
        "renderOptions": {
            "pointOfInterest": [47, 40, 41]
        },
    }, 
    {
        "@id": "LThal_structure",
        "@type": "structure",
        "sourceSelector": {
            "datasource": "dataRef",
            "frame_dimension": 4,
            "frame_index": 3,
        },
        "annotation": {
            "name": "Left Thalamus",
            "shortName": "LThal",
            "laterality": "left",
            "seeAlso": "Thalamus" ## minimal
        },
        "renderOptions": {
            "pointOfInterest": [51, 51, 39]
        },
    },
    {
        "@id": "RThal_structure",
        "@type": "structure",
        "sourceSelector": {
            "datasource": "dataRef",
            "frame_dimension": 4,
            "frame_index": 14,
        },
        "annotation": {
            "name": "Right Thalamus",
            "shortName": "RThal",
            "laterality": "right",
            "seeAlso": "Thalamus" ##not minimal
        },
        "renderOptions": {
            "pointOfInterest": [38, 51, 39]
        },
    }
    #more structures here 
    {
        "@id": "Left_Structures",
        "type": "group",
        "annotation": {
            "name": "Left Structures",
            "description": "Group to identify left hemisphere structures",
            "shortName": "Left",
        },
        "members": ["LThal_structure", "LLV_structure", "LCTX_structure"],
    },
    {
        "@id": "Thalamus",
        "type": "group",
        "annotation": {
            "name": "Thalamus",
            "description": "Group to generate bi-lateral representation of Thalamus",
            "shortName": "Thal",
            "ontologyReferences": ["http://purl.obolibrary.org/obo/FMA_????"]
        },
        "members": ["LThal_structure", "RThal_structure"],
    }
]