Modules:ExtractSubvolumeROI-Documentation-3.5

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Subvolume extraction with ROI widget

ExtractSubvolumeROI

Input and initialization of SubvolumeExtractROI

Visualization of the extracted subvolume

General Information

Module Type & Category

Type: Interactive

Category: Converters

Authors, Collaborators & Contact

• Andriy Fedorov, BWH
• Ron Kikinis, BWH
• Contact: Andriy Fedorov, fedorov at bwh

Module Description

This module allows to extract rectangular subvolume from an image, with the subvolume defined by Slicer ROI widget.

Usage

Examples, Use Cases & Tutorials

• ExtractSubvolumeROI allows to extract a parallelepiped-shaped subvolume, located arbitrarily within a larger 3D volume. The module allows to control the spacing of the resulting volume, and gives control over the interpolation mode.
• The module is particularly useful in cases when the amount of computation or its complexity can be reduced by limiting the processing to the region of interest.
• The subvolume produced by the module is located precisely in the space of the original image.

Quick Tour of Features and Use

List all the panels in your interface, their features, what they mean, and how to use them. For instance: Input/initialization parameters panel: Input volume defines the input image from which you need to extract an ROI ROI is a Region of Interest (see the documentation here), which can be defined outside ExtractSubvolumeROI, or by creating new MRMLROINode from the selector menu. The ROI can be adjusted using the widget handles in 3D view panel. ROI visibility allows to turn the visibility of the 3D widget on or off in the 3D view panel. Output volume is the volume node where the result of ROI extraction will be stored. Note, that the output volume cannot be identical to the input volume. The module will give you an error if this is the case. Input spacing scaling constant is the coefficient used to determine the spacing of the output volume. The output spacing is defined by multiplying the input spacing in each dimension by the user-specified coefficient. For example, if the input spacing is 1x1x1.4, and the scaling coefficient is 0.5, the output volume will have spacing 0.5x0.5x0.7, effectively doubling the resolution of the output image. Interpolation type allows to select between Nearest Neighbor, Linear or Cubic interpolators. For subvolumes being extracted from a label volume, you should use Nearest Neighbor interpolator. Otherwise Cubic is the preferred choice. Linear interpolator requires less computation, which may be important for very large ROIs. Do ROI resample initiates the subvolume extraction based on the inputs and parameters. Parameters panel: Output panel: Viewing panel:

ExtractSubvolumeROI control panel Input image Extracted subvolume with scaling constant 0.5 -- note the difference in the image spacing

Development

Major limitations:

• Input volume must be axis-aligned for consistent result.
• Neither input volume, nor ROI widget can be under a transform in MRML hierarchy

Dependencies

Volumes module.

Known bugs

Follow this link to the Slicer3 bug tracker.

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

Source code can accessed here

Links to documentation generated by doxygen.

More Information

Acknowledgment

Supported by Brain Science Foundation.