Modifying the BrainSuite Dashboard

To modify group-level analysis parameters, modify the brainsuite_dashboard_config.json file in the QC folder. This folder should already exist in the QC folder if you have run participant level mode using --stages QC.

{
    "GroupNames": ["Cortical Surface Extraction","Thickness","Registration","Diffusion Pipeline","Functional Pipeline"],
    "StageNames": ["bse", "bfc", "pvc", "cerebro", "cortex", "scrub mask", "tca", "dewisp", "inner cortical surface", "pial surface", "hemisplit", "thickness", "svreg", "bdp", "bfp"],
    "Contents" : [
        { "img": "bse.png", "stage": 1, "desc": "T1w + BSE Mask", "group": 0, "surface": false, "show": true, "width": 0, "height": 0 },
        { "img": "bfc.png", "stage": 2, "desc": "BFC", "group": 0, "surface": false, "show": true, "width": 0, "height": 0 },
        { "img": "pvc.png", "stage": 3, "desc": "PVC", "group": 0, "surface": false, "show": true, "width": 0, "height": 0 },
        { "img": "hemilabel.png", "stage": 4, "desc": "T1w + Hemi Label ", "group": 0, "surface": false, "show": true, "width": 0, "height": 0 },
        { "img": "cerebro.png", "stage": 4, "desc": "T1w + Cerebrum Mask", "group": 0, "surface": false, "show": true, "width": 0, "height": 0 },
        { "img": "dewisp.png", "stage": 8, "desc": "BFC + Dewisp (axial)", "group": 0, "surface": false, "show": true, "width": 0, "height": 0 },
        { "img": "dewispCor.png", "stage": 8, "desc": "BFC + Dewisp (coronal)", "group": 0, "surface": false, "show": true, "width": 0, "height": 0 },
        { "img": "dfsLeft.png", "stage": 9, "desc": "Inner Cortex (left)", "group": 0, "surface": true, "show": true, "width": 256, "height": 256 },
        { "img": "dfsRight.png", "stage": 9, "desc": "Inner Cortex (right)", "group": 0, "surface": true, "show": true, "width": 256, "height": 256 },
        { "img": "dfsSup.png", "stage": 9, "desc": "Inner Cortex (superior)", "group": 0, "surface": true, "show": true, "width": 256, "height": 256 },
        { "img": "dfsInf.png", "stage": 9, "desc": "Inner Cortex (inferior)", "group": 0, "surface": true, "show": true, "width": 256, "height": 256 },
        { "img": "hemisplit.png", "stage": 11, "desc": "Pial Cortex (HemiSplit)", "group": 0, "surface": true, "show": true, "width": 256, "height": 256 },
        { "img": "ThickdfsLeft.png", "stage": 12, "desc": "cortical thickness(left)", "group": 1, "surface": true, "show": true, "width": 256, "height": 256 },
        { "img": "ThickdfsRight.png", "stage": 12, "desc": "cortical thickness(right)", "group": 1, "surface": true, "show": true, "width": 256, "height": 256 },
        { "img": "ThickdfsSup.png", "stage": 12, "desc": "cortical thickness(sup)", "group": 1, "surface": true, "show": true, "width": 256, "height": 256 },
        { "img": "ThickdfsInf.png", "stage": 12, "desc": "cortical thickness(inf)", "group": 1, "surface": true, "show": true, "width": 256, "height": 256 },

    ]
}
  • GroupNames : Defines the pipeline names that are to be associated with the snapshot PNG files that are rendered. For instance, the “Contents” field, refers to this field, and enumerates the group names in ascending order. Must be in list form.

  • StageNames : Defines the stage names that are to be associated with the snapshot PNG files that are rendered. Must be in list form.

  • Contents :
    • img : Snapshot PNG file name that is rendered.

    • stage : The associated stage name (refers to the “StageNames” field and enumerates the stages in ascending order).

    • desc : Description string to be displayed on the Dashboard under each snapshot image.

    • surface : Indicates whether the snapshot image is an image of a surface file (true) or a volumetric file (false). This is for formatting purposes.

    • show : Indicates whether you would like to show this image on the Dashboard; show (true), not show (false).

    • width : Specifies the width of the image in pixels.

    • height : Specifies the height of the image in pixels.