Automatic Contour Module
The Automatic Contour module identifies the periosteal bone surface and creates a binary mask. The resulting mask can be manually corrected. If the mask has already been created elsewhere, load the mask and the greyscale scan into Slicer, and switch to the ErosionVolume Module.
Load the greyscale scan, and the contour/mask if available, into Slicer. Either drag-and-drop the files to the application window or hit the Add Data button
and select the files. The contours/masks need to be loaded as LabelMapVolumes. Check the Show Options check box at the top right corner of the Add Data prompt window, and check the LabelMap option.
This step is only necessary if the bones in the scan appear to be close or even connected to each other. The purpose is to create a rough mask to be used in Step 2. The goal of this step is to cover each bone with a different label.
First way - Fill between slices (recommended):
- Select the greyscale scan at Volume to be separated.
- Hit the Initialize button #1, and the editor tools will be activated. To switch to a different greyscale image, hit the Cancel button and select a different image at Volume to be separated.
- Hit the Add or the Remove button to add or remove segments. The selected segment is highlighted in blue.
- Using the Draw tool, completely cover each bone on the first slice, the last slice, and a few middle slices with a different label. Skip any number of slices in between.
- Switch to the Fill between slices tool. Hit the Initialize button #2 below Fill between slices. A previewed result will be initialized. Slicer will only fill slices between the first and last slices that have been labeled, and ignore all other slices. The fill between slices tool does not consider greyscale intensities.
- Hit the Apply button #3 below the Initialize button to save the result in the segments.
- Once completed editing, hit the Apply button #4.
Second way - Grow from seeds:
- Select the loaded scan at Volume to be separated.
- Hit the Initialize button #1, and the editor tools will be activated.
- Hit the Add or the Remove buttons to add or remove segments.
- Roughly label each bone on the first slice, the last slice, and a few middle slices with Paint or Draw tools. Skip any number of slices in between.
- Switch to the Grow from seeds tool. Hit the Initialize button #2 below Grow from seeds. A previewed result will be initialized.
- Hit the Apply button #3 below the Initialize button to save the result in the segments.
- Lastly, hit the Apply button #4
The result will be a LabelMap named with a post-fix "_separated".
The goal of this step is to identify the periosteal bone surface. The cortical breaks will be filled.
Parameters:
- Input Volume: the greyscale scan.
- Output Contour: the mask for each bone will be labeled differently.
- Lower Threshold/Upper Threshold: global thresholds, in Scanco intensity units.
- Number of Bones: will be used if no bone separation map / rough mask is provided.
- Dilate/Erode Radius: the dilate/erode distance in voxels in the morphological operations.
- Rough mask: rough mask created in Step 1. If None, the bones will be separated automatically with a connectivity filter.
Once all the parameters are set, hit the Get Contour button.
The output from Step 2 can be manually corrected.
Select the output from Step 2 at Contour to be Corrected, and the greyscale scan at Master Volume.
Hit the Initialize button #1, and the editor tools will be activated.
Select the contour segment and edit.
Once editing is completed, hit the Apply button #2.
