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Introduction and Acknowledgements
This work is supported by NA-MIC, NCIGT, and the Slicer Community.
Author: Vivek Narayan, Jayender Jagadeesan
Contact: Jayender Jagadeesan <email> firstname.lastname@example.org</email>
This project is supported by...
The OpenCAD is designed to segment tumors from DCE-MRI datasets which include 1 pre-contrast image and 2-4 post-contrast images at different time points. OpenCAD uses blackbox methods to calculate the wash-in and wash-out slopes of the contrast dye based on voxel intensity values. The segmentation output is a Label Map with red, yellow, and blue colors respectively identifying washout, plateau, and persistent voxels.
- Blue for Persistent curve
- Slope of delayed curve > 0.2 | 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 | Type III
Classification based on Delayed Curve
- Interactive Charting -
- Volume Rendering -
- Label Statistics -
OpenCAD Tutorial (pptx)
Breast DCE-MRI Data Set 1 (zip file containing the nrrd volumes for the OpenCAD tutorial)
Breast DCE-MRI Data Set 2 (zip file containing additional test set of nrrd volumes)
Liver DCE-MRI Data Set 1 (zip file containing additional test set of nrrd volumes)
Panels and their use
The GUI of the OpenCAD 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: (optional) Select the Post-contrast Image at the Second time point. This will only be used for the Interactive Charting feature.
- Third Post-contrast Volume: (optional) 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 OpenCAD Label Map
- Output OpenCAD 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 OpenCAD 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.
- 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.
- 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.
- OpenCAD 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). Logic is derived from the Label Statistics Module.
- 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 Final Post-contrast. Y-axis represents percentage change from baseline intensity.
Information for Developers
Source code: https://github.com/vnarayan13/Slicer-OpenCAD