https://www.slicer.org/w/index.php?action=history&feed=atom&title=Documentation%2F4.8%2FExtensions%2FVolumeClipDocumentation/4.8/Extensions/VolumeClip - Revision history2026-04-09T07:06:00ZRevision history for this page on the wikiMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=Documentation/4.8/Extensions/VolumeClip&diff=55589&oldid=prevUpdateBot: Nightly -> 4.82017-10-18T07:06:06Z<p>Nightly -> 4.8</p>
<p><b>New page</b></p><div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Authors: Andras Lasso (PerkLab, Queen's University), Matt Lougheed (PerkLab, Queen's University)<br><br />
Contact: Andras Lasso <email>lasso@queensu.ca</email><br><br />
Website: http://www.slicerrt.org/<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
{|<br />
[[Image:VolumeClipLogo.png]]<br />
|<br />
This extension contains modules for clipping image volumes with arbitrary surfaces or region of interest boxes.<br />
|<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
* Volume clip with model<br />
** Removes volume contents inside or outside the selected surface model<br />
** User may define and dynamically edit a 3D clipping surface by markup points (uses Delaunay triangulation, therefore it mostly generates convex surfaces)<br />
** For incremental clipping select the input volume also as output volume<br />
* Volume clip with ROI box<br />
** Removes volume contents inside or outside the selected region of interest box<br />
** For incremental clipping select the input volume also as output volume<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
<br />
=== Remove patient table from CT volumes ===<br />
* Go to Volume clip with model module<br />
* Set:<br />
** Input volume: your input image<br />
** Clipping surface: Create new model<br />
** Clipping surface from markups: Create new MarkupsFiducial<br />
** Fill value: on CT: -1000 (radiological density of air on CT), on MR: 0 (typical background voxel brightness)<br />
** Output volume: Create new volume<br />
* Drop/move a few markup fiducials around your region of interest on a couple of axial slices<br />
* Click apply<br />
<br />
=== Clip irrelevant image areas of the input volume before segmentation ===<br />
* Go to Volume clip with model module<br />
* Set:<br />
** Input volume: your input image<br />
** Clipping surface: Create new model<br />
** Clipping surface from markups: Create new MarkupsFiducial<br />
** Clip outside: uncheck<br />
** Fill value: background voxel value (depending on your imaging modality it may be -1000, 0, or other)<br />
** Output volume: Create new volume<br />
* Drop/move a few markup fiducials around the image areas that you would like to remove<br />
* Click apply<br />
* If there are more areas to remove then set the created Volume node as Output volume and repeat the following steps<br />
** Set: Clipping surface from markups: Create new MarkupsFiducial (or go to the Markups module to remove all fiducials from the current list)<br />
** Drop/move a few markup fiducials around the image areas that you would like to remove<br />
** Click apply<br />
<br />
=== Create quick mask for registration ===<br />
* Go to Volume clip with model module<br />
* Set:<br />
** Input volume: your input image<br />
** Clipping surface: Create new model<br />
** Clipping surface from markups: Create new MarkupsFiducial<br />
** Output volume: Create new volume<br />
* Drop/move a few markup fiducials around your region of interest on 2-3 orthogonal slices (3-4 fiducials on each slice should be enough)<br />
* Click apply<br />
* Set:<br />
** Input volume: Volume (the mask volume that you created)<br />
** Clip outside: uncheck<br />
** Fill value: 100<br />
* Click apply<br />
<gallery widths="200px" perrow="4"><br />
Image:VolumeClipScreenshot1.png|Volume clip with model (before clipping)<br />
Image:VolumeClipScreenshot2.png|Volume clip with model (after clipping)<br />
Image:VolumeClipScreenshot3.png|Volume clip with ROI box<br />
</gallery><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
Short video of volume clipping with model: https://www.youtube.com/watch?v=1mYNwJbE7dQ<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
[[Documentation/{{documentation/version}}/Extensions/ModelClip]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/extension-developerinfo}}<br />
Source code: https://github.com/PerkLab/SlicerVolumeClip<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>UpdateBot