SlicerLiver is an extension for the medical research software 3D Slicer providing tools for analysis, quantification and therapy planning for hepatic interventions.
The extension provides a fast and accurate solution for:
E
.Install Extensions
tab.Install
and give okay to install other extensions if asked.Switch to module
.To test the extension, the LiverVolume and LiverSementation data can be loaded from the Sample Data module, after installing Slicer-Liver. To properly load the data in the plugin, it is advised to first open the extension and afterwards to navigate to the Sample module and to load the data.
The extension is separated in the following three sections:
Each section is oriented towards one part of the liver resection planning workflow but, if desired, can work independently of the other ones. At the end of the workflow, the distance map, resection plan and liver segments can be saved to a given output directory.
The computation of the Distance Map can be done using the following steps:
Reference Volume
CT data.Segmentation
, i.e the binary labelmap representation which stores the segmentation of the liver, tumour and vascular territories.Tumor
segmentation.Liver
segmentation.Output Distance Map
.Compute Distance Map
.The liver resection can be planned through the following process:
Resection
.Liver Segmentation
.Liver
segmentation.Distance Map
.Resection grid
, Resection margin
and Uncertainty margin
as desired.Preview resection
checkbox if you want to visualize the final resection plan.There are multiple options to create visualizations for the resection (color, opacity, configurable grid, etc).
Our approach to liver vascular territory segments definition consist of the defintion of a vascular territory by the centerline connecting user-defined sets of points. These centerlines will be the base for computation of liver segments in image space. The computation is based on shortest-distance mapping. The Liver segments can be defined using the following steps:
Vascular Territory Segmentation
Segmentation
.Hide
.Segment
. The 3D view will then automatically switch to landmark "Place Mode"
and a Vessel points
list will be automatically generated.Add Vessel Centerline
.Vascular Territory
and "Create new territory ID".Calculate Vascular Territory Segmentation
. The generated vascular territories will then be visible in the 3D- and 2D Views.Vascular Territory Segmentation
.
Then repeat steps 2-9.Slicer-Liver depends on the VMTK which can be installed in Slicer3D using the extension manager or built following the steps for developers here: https://github.com/vmtk/SlicerExtension-VMTK#for-developers.
SLICER_BUILD_DIR=/path/to/Slicer-SuperBuild
git clone https://github.com/ALive-research/Slicer-Liver.git
cmake -DSlicer_DIR:PATH=SLICER_BUILD_DIR/Slicer-build -S ../Slicer-Liver
make -j5
make package
To enable the developer mode go to :
Then check the Enable developer mode
check box. The application may need to be restarted for this modification to be taken into account.
To run the unit tests, open the Slicer-Liver extension, expand the Reload & Test
menu and click on the Reload and Test
button.
To visualize the test results, open the Python console by going to: View > Python Interactor.
The number and the result of the tests will be displayed in the console. Should any of the test fail, please don't hesitate to open an issue or contact us through the Slicer forum.
Contact: rafael.palomar@ous-research.no
This software is open source distributed under the 3-Clause BSD License
This software has partially been funded by The Research Council of Norway through the ALive project (grant nr. 311393).