NA-MIC National Alliance for Medical Image Computing Connected Threshold Image Filter Salma Bengali, Alan Morris, Josh Cates, Rob.

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NA-MIC National Alliance for Medical Image Computing Connected Threshold Image Filter Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod SCI Institute/CARMA Center University of Utah © 2012, All Rights Reserved

National Alliance for Medical Image Computing Learning Objective Connected Threshold Image Filter in Slicer © 2012, All Rights Reserved

National Alliance for Medical Image Computing Current Workflow Cardiac LGE-MRI Image Segmented Image © 2012, All Rights Reserved

National Alliance for Medical Image Computing Slicer: Release Data: CARMA Slicer Extension Tutorial Data Required Materials © 2012, All Rights Reserved

National Alliance for Medical Image Computing Additional Sample Data 60 patients © 2012, All Rights Reserved

National Alliance for Medical Image Computing Pre-Requisite Tutorial © 2012, All Rights Reserved

National Alliance for Medical Image Computing Platforms © 2012, All Rights Reserved DevelopedTested

National Alliance for Medical Image Computing Overview © 2012, All Rights Reserved Load the module Load the dataset Connected Threshold Filter

National Alliance for Medical Image Computing Loading the Module Select View>Extension Manager in the menu bar (or push ⌘ 4) If the Extension Manager isn’t revealed, see the next 2 slides; otherwise, skip them © 2012, All Rights Reserved

National Alliance for Medical Image Computing Loading the Module To load the Extension Manager, Select Edit>Application Settings in the menu bar (or push ⌘ 2) © 2012, All Rights Reserved

National Alliance for Medical Image Computing Loading the Module Under the Extension menu, make sure ‘Enable extension manager’ is checked © 2012, All Rights Reserved

National Alliance for Medical Image Computing Loading the Module Select CARMA in the sidebar and click the extensions © 2012, All Rights Reserved

National Alliance for Medical Image Computing Loading the Module Restart to install the extension © 2012, All Rights Reserved

National Alliance for Medical Image Computing Loading the Data Select ‘Choose Directory to Add’ in the pop-up menu © 2012, All Rights Reserved

National Alliance for Medical Image Computing Loading the Data Select the directory containing your dataset © 2012, All Rights Reserved

National Alliance for Medical Image Computing Loading the Data

National Alliance for Medical Image Computing Image Segmentation Fiducials Output volume Input volume © 2012, All Rights Reserved

National Alliance for Medical Image Computing Image Segmentation 2. Select the Annotations menu option © 2012, All Rights Reserved 1. Set the lower and upper thresholds depending on the intensity of the region being segmented

National Alliance for Medical Image Computing Image Segmentation Create a set of fiducials inside the region to be segmented. © 2012, All Rights Reserved

National Alliance for Medical Image Computing Image Segmentation Apply the segmentation © 2012, All Rights Reserved

National Alliance for Medical Image Computing Image Segmentation Viewer automatically updates to show the resulting output © 2012, All Rights Reserved

National Alliance for Medical Image Computing Conclusion This module can be used to segment the endocardium region from an LGE-MRI or MRA scan. © 2012, All Rights Reserved