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Gold standard - Learning tool

An application for the Image Quizzer is to use it as a educational tool. You can have a user contour a lesion on one page and on the following page, display the user's contour along with a pre-defined gold standard.

Prep

A sample dataset is not currently available on Slicer that has a predefined tumor segmentation so creating a gold standard has to be done manually in order for the example script to work.

Download and save Slicer's MRBrainTumor1 dataset as described in the sample data section.

Suggested folder structure to match script:


.
└─ ImageQuizzerData/
      └─ ImageVolumes/
          └─ MRBrainTumor1/
               ├─ MRBrainTumor1.nrrd
               └─ MRBrainTumor1-GoldStandard.seg.nrrd   (created manually - not in download)

A pseudo gold standard file can be captured by running the following script in the Image Quizzer up to the first page. Create a contour and then use Slicer's functionality in File>Save to capture the contour as a segmentation file (.seg.nrrd format), rename it and store it in the folder as described above.

Script example

<Session>
    <Page ID="Patient 1" Descriptor="Contouring Challenge" EnableSegmentEditor="Y" SegmentRequiredOnAnyImage="Y">
        <Image Type="Volume" ID="MR" RotateToAcquisition="Y" LabelMapID="MR_Contour" InitialSliceOffset="25">
            <DefaultDestination>Red</DefaultDestination>
            <Layer>Background</Layer>
            <DefaultOrientation>Axial</DefaultOrientation>
            <Path>ImageVolumes\MRBrainTumor1\MRBrainTumor1.nrrd</Path>
        </Image>
        <Image Type="Volume" ID="MR" RotateToAcquisition="Y" InitialSliceOffset="0.468">
            <DefaultDestination>Green</DefaultDestination>
            <Layer>Background</Layer>
            <DefaultOrientation>Sagittal</DefaultOrientation>
            <Path>ImageVolumes\MRBrainTumor1\MRBrainTumor1.nrrd</Path>
        </Image>
        <Image Type="Volume" ID="MR" RotateToAcquisition="Y" InitialSliceOffset="35.15">
            <DefaultDestination>Yellow</DefaultDestination>
            <Layer>Background</Layer>
            <DefaultOrientation>Coronal</DefaultOrientation>
            <Path>ImageVolumes\MRBrainTumor1\MRBrainTumor1.nrrd</Path>
        </Image>
        <QuestionSet ID="Contouring Challenge" Descriptor="">
            <Question Type="InfoBox" Descriptor="Segmentation Instructions">
                <Option>Contour the tumor using the segment editor.</Option>
            </Question>
        </QuestionSet>
    </Page>
    <Page ID="Patient 1" Descriptor="Contouring Challenge"  EnableSegmentEditor="Y" SegmentRequiredOnAnyImage="Y">
        <Image Type="Volume" ID="MR" RotateToAcquisition="Y" DisplayLabelMapID="MR_Contour">
            <DefaultDestination>Red</DefaultDestination>
            <Layer>Background</Layer>
            <DefaultOrientation>Axial</DefaultOrientation>
            <Path>ImageVolumes\MRBrainTumor1\MRBrainTumor1.nrrd</Path>
        </Image>
        <Image Type="Volume" ID="MR" RotateToAcquisition="Y" DisplayLabelMapID="MR_Contour">
            <DefaultDestination>Green</DefaultDestination>
            <Layer>Background</Layer>
            <DefaultOrientation>Sagittal</DefaultOrientation>
            <Path>ImageVolumes\MRBrainTumor1\MRBrainTumor1.nrrd</Path>
        </Image>
        <Image Type="Volume" ID="MR" RotateToAcquisition="Y" DisplayLabelMapID="MR_Contour">
            <DefaultDestination>Yellow</DefaultDestination>
            <Layer>Background</Layer>
            <DefaultOrientation>Coronal</DefaultOrientation>
            <Path>ImageVolumes\MRBrainTumor1\MRBrainTumor1.nrrd</Path>
        </Image>
        <Image Type="Segmentation" ID="Gold" RotateToAcquisition="Y">
            <DefaultDestination>Red</DefaultDestination>
            <Layer>Segmentation</Layer>
            <Path>ImageVolumes\MRBrainTumor1\MRBrainTumor1-GoldStandard.seg.nrrd</Path>
            <ROIs ROIVisibilityCode='All'></ROIs>
        </Image>
        <Image Type="Segmentation" ID="Gold" RotateToAcquisition="Y">
            <DefaultDestination>Green</DefaultDestination>
            <Layer>Segmentation</Layer>
            <Path>ImageVolumes\MRBrainTumor1\MRBrainTumor1-GoldStandard.seg.nrrd</Path>
            <ROIs ROIVisibilityCode='All'></ROIs>
        </Image>
        <Image Type="Segmentation" ID="Gold" RotateToAcquisition="Y">
            <DefaultDestination>Yellow</DefaultDestination>
            <Layer>Segmentation</Layer>
            <Path>ImageVolumes\MRBrainTumor1\MRBrainTumor1-GoldStandard.seg.nrrd</Path>
            <ROIs ROIVisibilityCode='All'></ROIs>
        </Image>
        <QuestionSet ID="Gold Standard Display" Descriptor="">
            <Question Type="InfoBox" Descriptor="Compare to gold standard">
                <Option>The gold standard is presented over the user's contour.</Option>
            </Question>
        </QuestionSet>
    </Page>
</Session>