Documentation/4.3/Modules/SegmentCAD

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Introduction and Acknowledgements

Extension: OpenCAD Module: SegmentCAD This work is supported by NA-MIC, NCIGT, and the Slicer Community. Author: Vivek Narayan, Jayender Jagadeesan Contact: <email> jayender@bwh.harvard.edu</email>

NA-MIC   NCIGT   SPL   This project is supported by P41 RR019703/RR/NCRR NIH HHS/United States, P01 CA067165/CA/NCI NIH HHS/United States and P41 EB015898/EB/NIBIB NIH HHS/United States

Module Description

The SegmentCAD module is designed to segment tumors from DCE-MRI datasets which include pre-contrast image and post-contrast images at different time points. SegmentCAD uses blackbox methods to calculate the wash-in and wash-out slopes from the time-intensity curves. The segmentation output is a Label Map with red, yellow, and blue colors respectively identifying washout (Type III), plateau (Type II), and persistent (Type I) voxels.

Methods

Only Voxels with a percent increase from pre-contrast to the first post-contrast time point greater than the Minimum Threshold of Increase (default = 75.00%) are considered for segmentation and classification. Slope of delayed curve for each voxel is calculated as (Intensity at 4th time point - Intensity at 1st time point) / (Intensity at 1st time point). Segmented voxels are individually classified by color according to slope of delayed curve: Blue for Persistent curve Slope of delayed curve > 0.2 (default) (Type I) Yellow for Plateau curve -0.2 < Slope of delayed curve < 0.2 (Type II) Red for Washout curve Slope of delayed curve < -0.2 (default) (Type III)

Classification based on Delayed Curve

Features

• Segmentation - Generate Label Map delineating the regions of enhanced perfusion corresponding to the tumor with color representing the Type of Curve.
• Interactive Charting - Calculates and displays the percent increase from baseline(pre-contrast intensity) of the voxel under the current mouse pointer location, at each time point. On the X-axis, 0.0 is Pre-contrast, 1.0 is First Post-contrast, ..., 4.0 is the Final Post-contrast time point. The Y-axis represents percentage change from baseline/pre-contrast intensity.
• Volume Rendering - A 3D Volume Rendering of the output Label Map is displayed in the 3D viewer after segmentation.
• Label Statistics - Tabular display of statistics of all First Post-contrast time point voxels highlighted in the output Label Map and grouped according to curve type (Type I, II, and III). These statistics include: Voxel Count, Volume mm^3, Volume cc, Minimum Intensity, Maximum Intensity, Mean Intensity, Standard Deviation.

Tutorials

SegmentCAD Tutorial (pptx)‎

Data sets

Breast DCE-MRI Data Set 1 (zip file containing the nrrd volumes for the SegmentCAD tutorial)‎

Breast DCE-MRI Data Set 2 (zip file containing additional test set of nrrd volumes)‎

Panels and their use

The GUI of the SegmentCAD module contains 5 sections: Select DCE-MRI Volumes for Segmentation Pre-contrast Volume: Select the Pre-contrast Image First Post-contrast Volume: Select the Post-contrast Image at the First time point Second Post-contrast Volume: Select the Post-contrast Image at the Second time point. This will only be used for the Interactive Charting feature. Third Post-contrast Volume: Select the Post-contrast Image at the Third time point. This will only be used for the Interactive Charting feature. Fourth Post-contrast Volume: Select the Post-contrast Image at the Fourth or Final time point. Use Label Map as ROI: Enable this to select a custom label map input to restrict the segmentation analysis to a specific ROI. Select or Create Output SegmentCAD Label Map Output SegmentCAD Label Map: Create or select a label map volume node to represent the output of the segmentation. Legend | |: A reference for what type of curves are represented by the colors of the label map. Display Volume Rendering: Enable this to display a 3D Volume Rendering of the Label Map output in the 3D viewer after segmentation. Calculate SegmentCAD Label statistics: Enable this to calculate and display statistics of all the First Post-contrast time point voxels highlighted in the output Label Map. Set Advanced Segmentation Parameters Minimum Threshold of Increase: The minimum percentage increase from pre-contrast to the first post-contrast time point for a voxel to be included in the segmentation output and classified (default set at 75%). Type I (Persistent) Curve Minimum Slope: The minimum slope of the delayed curve for a voxel to be classified as having a Type I Persistent Curve (default set at 0.2). Type 3 (Washout) Curve Maximum Slope: The maximum slope of the delayed curve for a voxel to be classified as having a Type III Washout Curve (default set at -0.2). Apply SegmentCAD: Perform Segmentation. SegmentCAD Label Statistics Statistics Table: Table displaying statistics of all First Post-contrast time point voxels highlighted by the Label Map and grouped according to curve type (Type I, II, and III). Chart Statistics: Generates bar graph comparing all labels in the label map based on the statistical criterion specified in the menu. Menu Items: Volume, Curve Type, Voxel Count, Volume mm^3, Volume cc, Minimum Intensity, Maximum Intensity, Mean Intensity, Standard Deviation Ignore Zero label: Ignore the unsegmented region of the First Post-contrast image when displaying bar graph. Interactive Charting Settings Enable/Disable Interactive Charting: Toggle the calculation and display of the percent increase from baseline(pre-contrast intensity) of the voxel under the current mouse pointer location, at each time point. On the X-axis, 0.0 is Pre-contrast, 1.0 is First Post-contrast, ..., 4.0 is the Final Post-contrast. Y-axis represents percentage change from baseline intensity.

SegmentCAD GUI

Quick Instructions for Use

• Select the pre-contrast volume
• Select the first post-contrast volume
• Select the second post-contrast volume
• Select the third post-contrast volume
• Select the fourth post-contrast volume
• Uncheck 'Use Label Map as ROI'
• Create or select a label map volume node to represent the output of the segmentation
• Click "Apply SegmentCAD"

Module Output

SegmentCAD Module Output

Similar Modules

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References

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Information for Developers

Source code: https://github.com/vnarayan13/Slicer-OpenCAD