Difference between revisions of "Projects:RegistrationLibrary:RegLib C44"

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(Created page with 'Back to ARRA main page <br> Back to Registration main page <br> [[Projects:RegistrationDocumentation:UseCaseInv…')
 
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*moving: CT , 0.6 x 0.6 x 0.40 mm voxel size, axial; 512 x 512 x 107 unsigned short image
 
*moving: CT , 0.6 x 0.6 x 0.40 mm voxel size, axial; 512 x 512 x 107 unsigned short image
 
=== Procedure / Pipeline ===
 
=== Procedure / Pipeline ===
−
#Open case scene file or import image data: RegLib_C28_SlicerScene1.mrml
+
#Open case scene file or import image data: RegLib_C44_SlicerScene.mrml
−
#Place T10intact and T10defect in back- and foreground respectively.
+
#Overall strategy will be
−
#Scroll through sagittal view and note the inverted axis orientation
+
##use ''vhm'' as fixed, ''vhf'' as moving volume
−
#Flip axis
+
##because we're interested in the pelvic bone structure differences, we create a mask that will focus the registration on the skeletal region only.
−
##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 Data module]
+
##perform affine alignment
−
###right-click on the ''Scene'' node and select "Insert Transform Node" from the menu
+
##using above affine alignment as starting point, perform low-level BSpline alignment
−
###select the newly created transform node, then in the ''MRML Node Inspector'' below, rename it to "Xf0_AxialFlip"
+
##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.
−
###select the "T10intact" node and drag it inside/on top of the "Xf0_AxialFlip" node
+
##Visualize the deformation by applying the pure BSpline to a [[Projects:RegistrationDocumentation:UseCaseInventory:Auxiliary grid image]]
−
###ensure you have T10intact selected for background and the fade slider set on background (B) so you can see changes happening.
+
#Change colormap of deformed grid (e.g. hot), window and level to view the gridlines of interest, and overlay on the grayscale images
−
##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module]
+
#Mask generation
−
###Select "Xf0_AxialFlip" from the ''Transform Node'' menu
+
##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor module]
−
###In the 4x4 matrix displayed, click in the field containing the "1.0000" in row 3 and column 3.
+
##"Master Volume": select ''vhm''
−
###hit Return key to activate editing
+
##A new labelmap "vhm-label" will be created
−
###change the number to -1. Hit Enter.
+
##Select "vhm" to be visible in the slice viewer
−
###you should see the image flip in the sagittal and coronal slice views
+
##Select the ''Threshold'' tool from the editor toolbar
−
#Crop Volumes
+
##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.
−
##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:CropVolume-Documentation-3.6 Crop Volume module]
+
##Click Apply
−
##select "T10intact" as ''Input Volume''; select "Create new MRML ROI Node" in the ''ROI'' menu, select "create new volume" in the ''Output Volume" menu
+
##Morphologically clean the segmentation:
−
##you should see a small blue rectangle in all 3 views. Click in the views to expand the region to contain only the L4 vertebra (body and processes)
+
##Run a [http://www.slicer.org/slicerWiki/index.php/Modules:MedianFilter-Documentation-3.6 Median Filter] with a 3x3x3 neighborhood to remove speckle noise
−
##when finished, click on ''Do ROI resample''
+
##Return to the [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor module] and use the ''Change Island'' tool to remove the segmentation of the arms.
−
##go to back to the [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 Data module] and change the name of the new "SubVolume" to "T10intact_crop"
+
##Apply 2-3 rounds of morphological dilation to expand the region to include surrounding area.
−
##delete the ROI nodes (right click: delete node)
+
##Rename the labelmap to "vhm_mask" or similar. You will find a "vhm_mask_dil" in the example dataset for comparison
−
##repeat the same for the "T10defect" image
+
##Repeat the above segmentation procedure for "vhf"
−
#Registration
+
#Registration:
 +
##''''Presets''': for either of the registrations below, you can select the "BRAINSFit_...." presets from the parameter set menu instead of setting the parameters manually.
 +
#Affine Registration
 
##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit module]
 
##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit module]
−
###''''Presets''': select the "BRAINSFit_Affine" from the parameter set menu. See [[Projects:RegistrationDocumentation:ParameterPresetsTutorial|here for a guide]] on how to Load/Save Registration Parameter Presets]]
+
##select the following parameters:  
−
###otherwise select the following parameters:  
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###''Fixed Image Volume'': vhm ''Moving'': vhf
−
###''Fixed Image Volume'': :T10intact_crop ; ''Moving'': T10defect_crop
+
###check boxes for ''Include Rigd registr. phase'' , ''Include ScaleVersor3D'', ''include Affine''
−
###check boxes for "Moments align", ''Include Rigd registr. phase'' , ''Include ScaleVersor3D'', ''include Affine''
 
 
###''Slicer Linear Transform'': select "create new transform", rename to "Xf1_Affine" or similar
 
###''Slicer Linear Transform'': select "create new transform", rename to "Xf1_Affine" or similar
 
###leave rest at defaults. Click ''Apply''
 
###leave rest at defaults. Click ''Apply''
 
###registration should take ~ 10 secs.
 
###registration should take ~ 10 secs.
−
###use fade slider to verify alignment; compare with result snapshots shown below.
+
###use fade slider to verify alignment; compare with result snapshots shown below. Alignment will not be perfect but should be better than before.
 +
#BSpline Registration
 +
##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit module]
 +
##select the following parameters:
 +
###''Fixed Image Volume'': vhm ''Moving'': vhf
 +
###check boxes for ''Include BSpline registr. phase''
 +
###''BSplineTransform'': select "create new transform", rename to "Xf2_BSpline_msk" or similar
 +
###leave rest at defaults. Click ''Apply''
  
 
=== Registration Results===
 
=== Registration Results===

Revision as of 14:04, 12 August 2011

Home < Projects:RegistrationLibrary:RegLib C44

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Back to Registration main page
Back to Registration Use-case Inventory


v3.6.3 Slicer3-6Announcement-v1.png Slicer Registration Library Case 44: Visible Human Pelvis CT

Input

this is the main fixed reference image. All images are ev. aligned into this space lleft this is the moving image
baseline image follow-up

Modules

Objective / Background

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.

Keywords

CT, pelvis, visible human, inter-subject

Issues Challenges

Input Data

  • fixed: CT , 0.6 x 0.6 x 0.40 mm voxel size, axial; 292 x 292 x 91 unsigned short image
  • moving: CT , 0.6 x 0.6 x 0.40 mm voxel size, axial; 512 x 512 x 107 unsigned short image

Procedure / Pipeline

  1. Open case scene file or import image data: RegLib_C44_SlicerScene.mrml
  2. Overall strategy will be
    1. use vhm as fixed, vhf as moving volume
    2. because we're interested in the pelvic bone structure differences, we create a mask that will focus the registration on the skeletal region only.
    3. perform affine alignment
    4. using above affine alignment as starting point, perform low-level BSpline alignment
    5. 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.
    6. Visualize the deformation by applying the pure BSpline to a Projects:RegistrationDocumentation:UseCaseInventory:Auxiliary grid image
  3. Change colormap of deformed grid (e.g. hot), window and level to view the gridlines of interest, and overlay on the grayscale images
  4. Mask generation
    1. Go to the Editor module
    2. "Master Volume": select vhm
    3. A new labelmap "vhm-label" will be created
    4. Select "vhm" to be visible in the slice viewer
    5. Select the Threshold tool from the editor toolbar
    6. 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.
    7. Click Apply
    8. Morphologically clean the segmentation:
    9. Run a Median Filter with a 3x3x3 neighborhood to remove speckle noise
    10. Return to the Editor module and use the Change Island tool to remove the segmentation of the arms.
    11. Apply 2-3 rounds of morphological dilation to expand the region to include surrounding area.
    12. Rename the labelmap to "vhm_mask" or similar. You will find a "vhm_mask_dil" in the example dataset for comparison
    13. Repeat the above segmentation procedure for "vhf"
  5. Registration:
    1. 'Presets: for either of the registrations below, you can select the "BRAINSFit_...." presets from the parameter set menu instead of setting the parameters manually.
  6. Affine Registration
    1. Go to the BRAINSfit module
    2. select the following parameters:
      1. Fixed Image Volume: vhm Moving: vhf
      2. check boxes for Include Rigd registr. phase , Include ScaleVersor3D, include Affine
      3. Slicer Linear Transform: select "create new transform", rename to "Xf1_Affine" or similar
      4. leave rest at defaults. Click Apply
      5. registration should take ~ 10 secs.
      6. use fade slider to verify alignment; compare with result snapshots shown below. Alignment will not be perfect but should be better than before.
  7. BSpline Registration
    1. Go to the BRAINSfit module
    2. select the following parameters:
      1. Fixed Image Volume: vhm Moving: vhf
      2. check boxes for Include BSpline registr. phase
      3. BSplineTransform: select "create new transform", rename to "Xf2_BSpline_msk" or similar
      4. leave rest at defaults. Click Apply

Registration Results

original unregistered unregistered
registered (after flipping axis and cropping volume) registered
registered (after flipping axis and cropping volume) registered
registered (after flipping axis and cropping volume) registered
registered (after flipping axis and cropping volume) registered

Download

Acknowledgments

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