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ISMR2023_Environment_Test

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Junichi Tokuda edited this page Apr 15, 2023 · 2 revisions

Starting 3D Slicer (Docker)

The 3D Slicer binary is installed under /root/slicer/Slicer-5.2 (Lightweight Docker image) or /root/slicer/Slicer-SuperBuild-Release/Slicer-build (full Docker image). Before launching 3D Slicer, make sure to source ROS's setup script:

# source /root/ros2_ws/install/setup.bash
# <path to 3D Slicer>/Slicer

Alternatively, run the launch script that comes with the Docker image:

# ./start-slicer-ros2.bash

If successful, 3D Slicer's main window should appear on the desktop.

Installing the SegmentationUNet module (Intel-based machine only)

If your host computer is equipped with x86 CPU(s), you can run deep-learning-based ultrasound segmentation. To install the segmentation module, run the installation script that comes with the Docker image:

# ./install-segmentation-unet.bash

Do not use this script if your host computer is not an x86 system (e.g., Mac with Apple Silicon CPU). The segmentation module installs the TensorFlow library that uses Intel's AVX instructions, which are unavailable in the emulated environment. Once the module has been installed, the Slicer will not start properly.

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