<commit_before>{
    "name": "fsl-bet",
    "label": "FSL: Brain Extraction Tool (BET2)",
    "description": "Brain Extraction Tool (bet2). FMRIB Software Library (FSL) v5.0",
    "maintainer": "<NAME> <<EMAIL>>",
    "author": "Analysis Group, FMRIB, Oxford, UK.",
    "url": "http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET",
    "source": "https://github.com/scitran/apps/analysis/fsl-bet",
    "license": "Apache-2.0",
    "flywheel": "0",
    "version": "0.0.6",
    "config": {},
    "inputs": {
        "nifti": {
            "base": "file",
            "type": {
                "enum": [
                    "nifti"
                ]
            }
        }
    },
    "custom": {
        "docker-image": "scitran/fsl-bet"
    }
}<commit_msg>fsl-bet-v0.1.0<commit_after>{
    "name": "fsl-bet",
    "label": "FSL: Brain Extraction Tool (BET2)",
    "description": "Brain Extraction Tool (BET2) from FMRIB Software Library (FSL) v5.0. BET (Brain Extraction Tool) deletes non-brain tissue from an image of the whole head. It can also estimate the inner and outer skull surfaces, and outer scalp surface, if you have good quality T1 and T2 input images.",
    "maintainer": "<NAME> <<EMAIL>>",
    "author": "Analysis Group, FMRIB, Oxford, UK.",
    "url": "http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET",
    "source": "https://github.com/scitran-apps/fsl-bet",
    "license": "Apache-2.0",
    "flywheel": "0",
    "version": "0.1.0",
    "custom": {
        "docker-image": "scitran/fsl-bet:v0.1.0"
    },
    "config": {
      "fractional_intensity_threshold": {
        "description": "Fractional intensity threshold (0->1); default=0.5; smaller values give larger brain outline estimates. Changing Fractional intensity threshold from its default value of 0.5 will cause the overall segmented brain to become larger (<0.5) or smaller (>0.5). This threshold must lie between 0 and 1.",
        "default": 0.5,
        "minimum": 0,
        "maximum": 1,
        "type": "number",
        "id": "-f"
      },
      "brain_surf_outline": {
        "description": "Generate brain surface outline overlaid onto original image.",
        "default": false,
        "type": "boolean",
        "id": "-o"
      },
      "binary_brain_mask": {
        "description": "Generate binary brain mask.",
        "default": false,
        "type": "boolean",
        "id": "-m"
      },
      "skull_image": {
        "description": "Generate rough skull image.",
        "default": false,
        "type": "boolean",
        "id": "-s"
      },
      "vertical_gradient_intensity_threshold": {
        "description": "Vertical gradient in fractional intensity threshold (-1->1); default=0; positive values give larger brain outline at bottom, smaller at top.",
        "default": 0,
        "minimum": -1,
        "maximum": 1,
        "type": "number",
        "id": "-g"
      },
      "apply_mask_thresholding": {
        "description": "Apply thresholding to segmented brain image and mask.",
        "default": false,
        "type": "boolean",
        "id": "-t"
      },
      "vtk_surface_mesh": {
        "description": "Generates brain surface as mesh in .vtk format.",
        "default": false,
        "type": "boolean",
        "id": "-e"
      }
    },
    "inputs": {
        "nifti": {
            "description": "Input NIfTI file for BET aglorithm.",
            "base": "file",
            "type": {
                "enum": [
                "nifti"
                ]
            }
        }
    }
}
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