Pre-Processing Module
Warning
This module is currently under development, and details are subject to change without notice.
Currently, the module supports the following tasks:
Segmentation generation or loading
Partial volume cropping and extraction
In the future, we will add support for the following tasks
Virtual Radiograph (VRG) generation
Config file generation
Introduction
The Pre-Processing module in Autoscoper is a crucial step in preparing data for further analysis within the Autoscoper module. In this tutorial, we’ll explore the basic usage of the Pre-Processing module, detailing its functionalities and how to use them effectively.
Before diving into pre-processing, ensure that you have already loaded the data into 3D Slicer. If you haven’t done this yet, you can find detailed instructions in the Slicer Documentation.
Accessing the Pre-Processing Module
To access the Pre-Processing module, open the AutoscoperM module located in the Tracking
category. Next, navigate to the second tab labeled Autoscoper Pre-Processing
.
General Inputs
The Pre-Processing module requires two inputs:
Volume Node: This refers to the volume node containing the CT data.
Output Directory: The primary output directory for the pre-processing results. For more information on the recommended file structure, see the Recommended File Structure section.
Segmentations
You have three options for segmentations:
Auto-generate: Automatically generates segmentations based on the volume node.
Load: Allows you to load existing segmentations from a directory.
Use Slicer to create new segmentation: Utilizes the built-in Slicer tools for segmentation. For more information see the Image Segmentation page of the Slicer documentation.
Auto-Generated Segmentations
To auto-generate a set of segments for your CT data, select the Automatic Segmentation
option and specify a threshold value. The default value is 700 Hounsfield Units (HU), but this value may vary depending on your CT data.
To determine an appropriate threshold value, use the data probe (located in the bottom left corner of the Slicer UI) to explore the volume. The data probe displays the HU value of the voxel under the mouse pointer. Determine the average HU value of the exterior surface of the bone and the average HU value of the flesh and muscle. The threshold value should be high enough to exclude the flesh and muscle, but low enough to include the exterior surface of the bone. Do not worry about the interior of the bone, the auto segmentation will fill in the interior of the bone.
In the example above, we can see that the flesh and muscle have an average HU value of -500 to 300 HU. The exterior surface of the bone has an average HU value of 2000-3000 HU. The default value of 700 HU is a suitable starting point for this data.
Warning
Auto-generating the segmentations will take a long time. It is recommended that you use the Load
option if you have already generated the segmentations.
Once you have selected a threshold value, click the Generate Segmentations
button. This will generate a segmentation for each bone in the volume and they will be named Segment_1
, Segment_1_2
, etc.
After generating the segmentations, you can further edit them using the Segment Editor
module. For more information on segmentation editing, refer to the Segment Editor page in the Slicer documentation.
Switching to the Data
module allows you to view and manage the segmentations. Here you can remove any unnecessary segmentations and rename them for clarity.
Load Segmentations
To load existing segmentations, select the Batch Load from File
option and specify the directory containing the segmentations. The directory should contain segmentation files in one of the following formats:
*.seg.nrrd
*.nrrd
*.wrl
*.iv
*.vtk
*.stl
After selecting the directory, click the Generate Segmentations
button.
The loaded segmentations will appear as individual segments within a single segmentation node.
Warning
Segmentations loaded using this method may require a transformation to align them with the volume node. For more information on applying transformations, refer to the Transforms page in the Slicer documentation.
Partial Volume Cropping and Extraction
Once you have generated or loaded the segmentations, you can use the Partial Volume Generation
section to crop and extract partial volumes. Simply, define the Output Directory
, select a Segmentation Node
under the General Inputs
section, and click the Generate Partial Volumes
button.
This will generate an individual partial volume for each segment in the segmentation node. The partial volumes will be saved as a grayscale TIF files, with filenames corresponding to the names of the segments. The partial volumes will be stored in the Output Directory
as follows:
Output Directory
|-- Volumes
| |-- Segment_1.tif
| |-- Segment_2.tif
| |-- Segment_3.tif
| |-- ...
| |-- Segment_n.tif