Documentation:Nightly:Registration:RegistrationLibrary:RegLib C44
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Contents
Slicer Registration Library Case 44: Visible Human Pelvis CT
Input
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baseline image | follow-up |
Modules used
Description
This dataset contains CT of the visible human male and female pelvis. This serves as a test example for exploring non-rigid registration for inter-subject comparison from CT.
- Open case scene file or import image data: RegLib_C44_SlicerScene.mrml
- Overall strategy will be
- use vhm as fixed, vhf as moving volume
- because we're interested in the pelvic bone structure differences, we create a mask that will focus the registration on the skeletal region only.
- perform affine alignment
- using above affine alignment as starting point, perform low-level BSpline alignment
- To study the deformation only, extract the BSpline deformation from the transform, i.e. remove the affine portion. This can be done in a text editor, or by first resampling the vhf volume with the Affine before computing the BSpline.
- Visualize the deformation by applying the pure BSpline to a auxiliary grid image
- Change colormap of deformed grid (e.g. hot), window and level to view the gridlines of interest, and overlay on the grayscale images
Download
RegLib_C44.mrb
(input data only, Slicer mrb file. 74 MB)
RegLib_C44_full.mrb
(input data + results, Slicer mrb file. 82 MB).
Video Screencasts
- Movie/screencast showing generating a registration mask
- Movie/screencast showing affine and nonrigid BSpline registration
- Movie/screencast showing visualization of the deformation via the Transform Visualizer module
Keywords
CT, pelvis, visible human, inter-subject
Procedure / Pipeline
- Mask generation
- Go to the Editor module
- "Master Volume": select vhm
- A new labelmap "vhm-label" will be created
- Select "vhm" to be visible in the slice viewer
- Select the Threshold tool from the editor toolbar
- Adjust the lower threshold (slider bar) until most of the bone is highlighted, e.g. somewhere around an intensity value of 80. Leave the upper threshold unchanged at the max.
- Click Apply
- Morphologically clean the segmentation:
- Run a Median Filter with a 3x3x3 neighborhood to remove speckle noise
- Return to the Editor module and use the Change Island tool to remove the segmentation of the arms.
- Apply 2-3 rounds of morphological dilation to expand the region to include surrounding area.
- Rename the labelmap to "vhm_mask" or similar. You will find a "vhm_mask_dil" in the example dataset for comparison
- Repeat the above segmentation procedure for "vhf"
- Registration:
- Go to the General Registration (BRAINS)
- Fixed Image Volume: vhm
- Moving Volume: vhf
- check boxes for Include Rigd registr. phase , Include ScaleVersor3D, include Affine
- Slicer Linear Transform: select "create new transform", rename to "Xf1_Affine" or similar
- leave rest at defaults. Click Apply
- registration should take ~ 10 secs.
- use fade slider to verify alignment; compare with result snapshots shown below. Alignment will not be perfect but should be better than before.
- note: you can also change the colormaps for the fixed and moving volumes to better judge the alignment: go to the Volumes module and in the Display tab, select "green" and "magenta" as the respective colormaps for the two volumes (vhf, vhm)
- Go to the General Registration (BRAINS)
- BSpline Registration
- Go to the General Registration (BRAINS)
- Fixed Image Volume: vhm Moving: vhf
- Registration phases: from Initialize with previously generated transform', select "Xf1_Affine" node created before.
- Registration phases: uncheck boxes for rigid, scale and affine and check box for BSpline
- Output: Slicer Linear transform: set to None
- Output: Slicer BSpline transform: create new, rename to "Xf2_BSpline_msk" or similar
- Output Image Volume: create new, rename to "vhf_Xf2"; Pixel Type: "short"
- Registration Parameters: increase Number Of Samples to 200,000; Number of Grid Subdivisions: 7,7,7
- Control Of Mask Processing Tab: check ROI box, for Input Fixed Mask and Input Moving Mask select the two dilated labelmaps from above
- Leave all other settings at default
- click apply
- Go to the General Registration (BRAINS)
Registration Results
unregistered
registered (affine)]
registered (nonrigid w/o masking)
registered (nonrigid+masking)
registered deformation only of vhf
deformation visualized by grid image overlay
Acknowledgments
Original CT from the Visible Human Project shared by the University of Iowa.