File Converter Module

The File Converter Module is used to convert files in .AIM or .ISQ format. SCANCO imaging devices (XTremeCT I & II) produce output files in .AIM or .ISQ format, which cannot be opened by Slicer.

Setup

Using this module requires the ITK and ITK-IOScanco packages to be installed. Slicer uses a separate Python library from the system, so an installation must be performed even if the packages are already installed on the system version of Python.

Option 1: Command Line/Terminal

Windows: In Command Prompt, navigate to the directory containing Slicer installation files and run the following commands:

"bin\PythonSlicer.exe" -m pip install itk
"bin\PythonSlicer.exe" -m pip install itk-ioscanco

The Slicer directory is typically located in \Users[username]\AppData\Local\NA-MIC\Slicer

Linux/MacOS: In Terminal, navigate to the directory containing Slicer installation files and run the following commands:

bin/PythonSlicer -m pip install itk
bin/PythonSlicer -m pip install itk-ioscanco

The Slicer directory is typically located in /Applications/Slicer.App/Contents

Option 2: Slicer Python Interactor

In Slicer, open the Python Interactor and enter the following commands:

slicer.util.pip_install('itk')
slicer.util.pip_install('itk-ioscanco')

Converting to Volume

This widget converts a file to a 3D Slicer volume. This volume can be directly used in other modules.

Select the type of file (.AIM or .ISQ) you want to convert. Click Browse to open a file explorer window. Find the file to be converted and select it. Select a volume to store the converted image into, then click Convert. The resulting volume can be used to complete an erosion analysis.

Files can only be converted one at a time using this module.

Coverting to Files

This widget converts one or more files to .mha format.

Click Browse to open a file explorer window. Select all .AIM and .ISQ files to be converted and confirm. If you want to choose an output folder, click Browse and select the destination folder. By default, the converted files will be stored in the same location as the original. Click Convert afterwards.

Only files can be selected in this module. To convert a folder, use the command line version of this module.