I tried to ask ChatGPT about 3D Slicer. Here is it’s frighteningly good responses. In some (most?) cases, the responses are convincing but wrong. In general, ChatGPT is very good at writing code, though. I include several questions and answers here:
Q: How do I write an extension module for 3D Slicer?
A: To write an extension module for 3D Slicer, follow these steps:
- Install 3D Slicer on your computer.
- Create a new folder in the “Modules” directory in the 3D Slicer installation folder. This will be the directory for your extension module.
- In your extension module directory, create a file called “CMakeLists.txt” and include the following code:
slicerMacroBuildScriptedModule(
NAME MyModule
SCRIPT_FILENAME MyModule.py
RESOURCES MyModule.png
)
- Create a Python script called “MyModule.py” in your extension module directory. This script will contain the code for your extension module.
- In the “MyModule.py” script, define a class that subclasses “vtk.vtkMRMLAbstractLogic”. This class will contain the logic and functionality of your extension module.
- In the class definition, define a method called “processMRMLNodesEvents(self, caller, event, callData)” which will be called whenever a MRML node is modified in 3D Slicer.
- Define any additional methods or functions that you want your extension module to have.
- In the “MyModule.py” script, create an instance of your class and call the “register()” method on it to register the extension module with 3D Slicer.
- In the “Modules” directory, run the “build_all.py” script to build your extension module.
- In 3D Slicer, go to the “Modules” menu and select “MyModule” to use your extension module.
Q: How do I create a 3D Slicer module using Qt and Python?
A: To create a 3D Slicer module using Qt and Python, follow these steps:
- Install 3D Slicer on your computer and make sure that Qt is included in the installation.
- Create a new folder in the “Modules” directory in the 3D Slicer installation folder. This will be the directory for your module.
- In your module directory, create a file called “CMakeLists.txt” and include the following code:
slicerMacroBuildScriptedModule(
NAME MyModule
SCRIPT_FILENAME MyModule.py
RESOURCES MyModule.png
WITH_PYTHONQT
)
- Create a Python script called “MyModule.py” in your module directory. This script will contain the code for your module.
- In the “MyModule.py” script, import the necessary modules from Qt and Slicer:
from PythonQt import QtCore, QtGui
import slicer
- Define a class that subclasses “slicer.qSlicerAbstractModuleWidget” and “QtGui.QWidget”. This class will contain the GUI and functionality of your module.
- In the class definition, override the “setup()” method to set up the GUI for your module. Use Qt designer to design the GUI and then use the “loadUi()” method to load the GUI into your module.
- Define any additional methods or functions that you want your module to have.
- In the “MyModule.py” script, create an instance of your class and call the “register()” method on it to register the module with 3D Slicer.
- In the “Modules” directory, run the “build_all.py” script to build your module.
- In 3D Slicer, go to the “Modules” menu and select “MyModule” to use your module.
Q: How about a C++ Slicer extension using Qt?
A: To create a 3D Slicer extension using C++ and Qt, follow these steps:
- Install 3D Slicer on your computer and make sure that Qt is included in the installation.
- Create a new folder in the “Modules” directory in the 3D Slicer installation folder. This will be the directory for your extension.
- In your extension directory, create a file called “CMakeLists.txt” and include the following code:
slicerMacroBuildModule(
NAME MyModule
SRCS MyModule.cxx
MOC_SRCS MyModule.h
RESOURCES MyModule.qrc
)
- Create a C++ file called “MyModule.cxx” in your extension directory. This file will contain the code for your extension.
- In the “MyModule.cxx” file, include the necessary Qt and Slicer headers:
#include <QtGui>
#include <vtkSlicerConfigure.h>
#include "MyModule.h"
- Define a class that subclasses “vtkSlicerModuleLogic” and “QObject”. This class will contain the logic and functionality of your extension.
- In the class definition, override the “SetMRMLSceneInternal(vtkMRMLScene* newScene)” method to set up the extension when it is added to the MRML scene.
- Define any additional methods or functions that you want your extension to have.
- In the “MyModule.cxx” file, create an instance of your class and call the “Register()” method on it to register the extension with 3D Slicer.
- In the “Modules” directory, run the “build_all.py” script to build your extension.
- In 3D Slicer, go to the “Modules” menu and select “MyModule” to use your extension.
Q: how do I volume render a nifti file containing CT data in 3D Slicer?
A: To volume render a NIFTI file containing CT data in 3D Slicer, follow these steps:
- Load the NIFTI file into 3D Slicer by going to the “File” menu and selecting “Add Data”.
- In the “Modules” menu, select “Volume Rendering” to open the volume rendering module.
- In the “Volume Rendering” module, select the NIFTI file in the “Input Volume” dropdown menu.
- Click the “Apply” button to display the volume in the 3D view.
- In the “Volume Rendering” module, adjust the rendering settings as desired, such as the color map, threshold, and opacity.
- Click the “Apply” button to update the volume rendering with the new settings.
- To save the volume rendering, go to the “File” menu and select “Save Screenshot”. Choose a file name and location, and select “Volume” in the “What to Save” dropdown menu. Click “Save” to save the volume rendering.
Q: What is OpenAnatomy?
[oops! ChatGPT is confidently wrong!]
OpenAnatomy is a software platform that enables users to view, explore, and analyze 3D anatomy data. It is designed to facilitate the development and dissemination of open anatomy resources, including segmented models of organs, bones, and other structures. OpenAnatomy can be used in a variety of settings, including education, research, and clinical practice. It is developed and maintained by the BioMedical Informatics Research Network (BIRN) and is open source, meaning that users can access and modify the source code.
Q: Can you describe the DICOM coordinate system?
[I believe this isn’t correct.]
The DICOM (Digital Imaging and Communications in Medicine) coordinate system is a standardized system used to represent the location of points and objects in 3D space. It is used in medical imaging to describe the position and orientation of images, as well as the position of structures within the images.
In the DICOM coordinate system, the origin is located at the center of the imaging volume. The x-axis points to the right [is this subject right or observer right?], the y-axis points anteriorly (towards the front of the body) [I believe that’s wrong], and the z-axis points superiorly (towards the head). The orientation of the axes is determined by the orientation of the patient’s body during the imaging process.
The DICOM coordinate system is a right-handed coordinate system, meaning that if the x-axis, y-axis, and z-axis are visualized as three perpendicular lines, then the direction in which the lines form a positive rotation (like the hands on a clock) is considered “right-handed”.
In the DICOM coordinate system, the unit of measure is the millimeter (mm). The dimensions of the imaging volume are also specified in millimeters.
