UpdateBot: Nightly -> 4.6

2016-11-07T08:00:57Z

Nightly -> 4.6

New page

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[Image:OpenCAD.PNG|thumb|center|400px|]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]]<br>
This work is supported by NA-MIC, NCIGT, and the Slicer Community.<br>
Author: Vivek Narayan, Jayender Jagadeesan<br>
Contact: Jayender Jagadeesan <email> jayender@bwh.harvard.edu</email> <br>
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|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

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The {{documentation/modulename}} module is designed to segment tumors from DCE-MRI datasets which include pre-contrast image and post-contrast images at different time points. {{documentation/modulename}} 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.


{{documentation/{{documentation/version}}/module-section|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)
|[[Image:Graph.png|thumb|280px|Classification based on Delayed Curve]]
|}


{{documentation/{{documentation/version}}/module-section|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.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
[[Media:SegmentCADTutorial.pptx|{{documentation/modulename}} Tutorial (pptx)]]‎


{{documentation/{{documentation/version}}/module-section|Data sets}}
[[Media:Breast-data1.zip|Breast DCE-MRI Data Set 1 (zip file containing the nrrd volumes for the {{documentation/modulename}} tutorial)]]‎

[[Media:Breast-data2.zip|Breast DCE-MRI Data Set 2 (zip file containing additional test set of nrrd volumes)]]‎


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|
The GUI of the {{documentation/modulename}} 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.
|[[Image:SegmentCAD-GUI.png|thumb|340px|{{documentation/modulename}} GUI ]]
|}


{{documentation/{{documentation/version}}/module-section|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"


{{documentation/{{documentation/version}}/module-section|Module Output}}
[[Image:SegmentCAD-Output.png|thumb|center|500px|{{documentation/modulename}} Module Output ]]


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


{{documentation/{{documentation/version}}/module-section|References}}
N/A


{{documentation/{{documentation/version}}/module-section|Information for Developers}}

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


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

Documentation/4.6/Modules/SegmentCAD - Revision history

UpdateBot: Nightly -> 4.6