How can I create a 3D ROI of irregular shape (not rectangular prism)? Is the Closed Curve option in the Create and Place menu the only way to do this? I also want to be able to use this sort of irregular 3D ROI to create a mask within a scripted module that has the same shape as the input image, an…

There are lots of options for defining 3D ROIs. What shape are you creating? What is your overall goal?

I would like some tool that gives the user a lot of flexibility about how to define the shape – irregular contour. For my application, the 3D ROI, which is defined using a vtkMRMLAnnotationROINode, may contain some unwanted parts of the body in addition to the tumor we are interested in. The irregu…

Do you want to segment tumors? Then the most suitable tool is probably Segment Editor. If there is visible brightness difference between the tumor and surrounding region then probably the fastest is to use “Grow from seeds” (see “Tumor segmentation” section of Neurosurgical planning tutorial for st…

Thanks for the comment, but segmentation is not the issue I’m concerned with. In fact, the whole purpose of my module is to perform a specific method of tumor segmentation within the region that the user specifies as containing tumor. The problem I’m concerned with is related to ROI selection. Spec…

For quick approximate segmentation (to create include/exclude regions) you can use Surface Cut effect: [New "Surface cut" and "Mask volume" tools for 3D Slicer segment editor] You can also add/remove entire regions using Scissors effect in slice views. You may also be able to create m…

Is there a way that we can create a cylinder and a cube by defining points in slicer view like in the case, Manipulating objects in the slice viewer in the 3D slicer scrip repository which creates a sphere. How to define/edit a circular region of interest in a slice

Yes, instead of a vtkSphereSource, you can use a vtkCylinderSource or vtkCubeSource.

found this searching for the same exact point . i want to create ROI around a mandible " very irregular shape" so i can do different rendering for the mandible only , then segment a lesion within the mandible . with the regular cube , i have to include maxilla and part of temporal bone . if poss…

You should be able to use the Mask Volume effect for that: [image] New segment editor effects: Mask volume and Surface cut Support See short demo video of the new “Mask volume” and “Surface cut” Segment editor effects here: These effects were developed by Kyle Macneil (…

How to replace it, I know a little about python

Irregular shaped ROI and conversion to mask

Development

pieper (Steve Pieper (Isomics, Inc.)) March 2, 2021, 12:40pm 11

You should be able to use the Mask Volume effect for that:

Topic		Replies	Views
Creating custom ROI Support	6	1106	July 16, 2019
Crop volume using ellipse, rectangle, or freeform shape Support	1	1113	November 3, 2017
Drawing an irregular ROI in the image Support	5	240	January 22, 2024
Local Threshold --> restrict threshold operation to user-defined 3D region --> how to? Support segmentation , threshold	1	430	January 23, 2023
Creating masked nifti from ROI Support	2	1251	March 12, 2020

Irregular shaped ROI and conversion to mask

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