Difference between revisions of "Documentation:Nightly:Registration:RegistrationLibrary:RegLib C44"

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{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
 
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
 
|[[Image:RegLib_C44_Thumb1.png|150px|lleft|this is the main fixed reference image. All images are ev. aligned into this space]]  
 
|[[Image:RegLib_C44_Thumb1.png|150px|lleft|this is the main fixed reference image. All images are ev. aligned into this space]]  
|[[Image:RegArrow_Affine.png|70px|lleft]]  
+
|[[Image:RegArrow_NonRigid.png|70px|lleft]]  
 
|[[Image:RegLib_C44_Thumb2.png|150px|lleft|this is the moving image]]  
 
|[[Image:RegLib_C44_Thumb2.png|150px|lleft|this is the moving image]]  
 
|-
 
|-
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== Modules used ==
 
== Modules used ==
 
*[[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]
 
*[[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]
 +
*[[Documentation/Nightly/Modules/DeformationFieldVisualizer| ''Deformation Field Visualizer'']]
  
=== Description ===
+
== 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.
+
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. The overall strategy will be to register "vhf" to "vhm" via first affine and then BSpline registration. We will generate a mask to focus the registration on the bone structure only and ignore the soft tissue when computing the deformation. Because our original images are quite large (512x512x150), we will subsample the vhf pair for use with the [[Documentation/Nightly/Modules/DeformationFieldVisualizer| ''Deformation Field Visualizer'']] module, which might otherwise become too memory intensive.
#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 [[Projects:RegistrationDocumentation:UseCaseInventory:Auxiliary|'''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 ==
 
==Download ==
*Data
+
<small>''Why 2 sets of files?  The "input data" mrb includes only the unregistered data to try the method yourself from start to finish. The full dataset includes intermediate files and results (transforms, resampled images etc.). If you use the full dataset we recommend to choose different names for the images/results you create yourself to distinguish the old data from the new one you generated yourself. ''</small>
**[[Media:RegLib_C44_Data.zip‎|'''RegLib_C44_Data''': Example Dataset <small> (CT images, Presets, Solution, zip file 171 MB) </small>]]
+
*[http://slicer.kitware.com/midas3/download/?items=119555 '''RegLib_C44.mrb'''] <small>(input data only, Slicer mrb file. 74 MB) </small><br>
*Presets
+
*[http://slicer.kitware.com/midas3/download/?items=119554 '''RegLib_C44_full.mrb''']<small>(input data + results, Slicer mrb file. 82 MB). </small>
**[[Media:RegLib_C44_Presets.mrml‎|'''RegLib_C44_Presets.mrml''': registration parameter presets<small> (.mrml text file 16 kB) </small>]]
 
  
 
== Video Screencasts ==
 
== Video Screencasts ==
#[[Media:RegLib_C44_Masking.mov|Movie/screencast showing generating a registration mask to exclude the tumor]]
+
#[[Media:RegLib_C44_1_Masking.mov|Movie/screencast showing generating a registration mask]]
#[[Media:RegLib_C44_Registration.mov|Movie/screencast showing rigid and affine registration]]
+
#[[Media:RegLib_C44_2_Registration.mov|Movie/screencast showing affine and nonrigid BSpline registration]]
#[[Media:RegLib_C44_Deformation.mov|Movie/screencast showing visualization of the deformation via the Transform Visualizer module]]
+
#[[Media:RegLib_C44_3_Deformation.mov|Movie/screencast showing visualization of the deformation via the Transform Visualizer module]]
  
 
== Keywords ==
 
== Keywords ==
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== Procedure / Pipeline ==
 
== Procedure / Pipeline ==
#Mask generation
+
#'''Mask generation''': open the [[Documentation/Nightly/Modules/Editor|''Editor'']] module. [[Media:RegLib_C44_1_Masking.mov|Movie/screencast showing this step]]
##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor module]
 
 
##"Master Volume": select ''vhm''
 
##"Master Volume": select ''vhm''
 
##A new labelmap "vhm-label" will be created
 
##A new labelmap "vhm-label" will be created
 
##Select "vhm" to be visible in the slice viewer
 
##Select "vhm" to be visible in the slice viewer
 
##Select the ''Threshold'' tool from the editor toolbar
 
##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.
+
##Adjust the lower threshold (slider bar) until most of the bone is highlighted,just before speckle noise starts to become included e.g. somewhere around an intensity value of 80. Leave the upper threshold unchanged at the max.
 
##Click Apply
 
##Click Apply
##Morphologically clean the segmentation:
+
##clean the segmentation:
##Run a [http://www.slicer.org/slicerWiki/index.php/Modules:MedianFilter-Documentation-3.6 Median Filter] with a 3x3x3 neighborhood to remove speckle noise
+
##Select the "Identify Islands" editor effect. [[Image:IdentifyIslandsEffectIcon.png|30px]] This will identify all continuous areas that are disconnected from each other. Click "Apply"
##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.  
+
##you should see the bones of the arms being assigned a different label value & color. We can now delete them with one click:
##Apply 2-3 rounds of morphological dilation to expand the region to include surrounding area.
+
##select the "Change Island" effect [[Image:ChangeIslandsEffectIcon.png|30px]] . Change the label value to 0 (zero).  
##Rename the labelmap to "vhm_mask" or similar. You will find a "vhm_mask_dil" in the example dataset for comparison
+
##in the axial (red) view, click the left mouse within the segmented areas of the arms.  
##Repeat the above segmentation procedure for "vhf"
+
##select the "Dilate" effect  [[Image:DilateEffectIcon.png|30px]]. Click the "Apply" button 3-4 times until the boundary of the segmentation extends well beyond the bone, including a several pixel wide layer of adjacent tissue.
#Registration:
+
##repeat the above for "vhf".
##Go to the [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]
+
##save the two segmentations.
###''Fixed Image Volume'': vhm  
+
#'''Affine Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']] module. [[Media:RegLib_C44_2_Registration.mov|Movie/screencast showing this step]]  
###''Moving Volume'': vhf
+
##''Fixed Image Volume'': vhm  
###check boxes for ''Include Rigd registr. phase'' , ''Include ScaleVersor3D'', ''include Affine''
+
##''Moving Volume'': vhf
###''Slicer Linear Transform'': select "create new transform", rename to "Xf1_Affine" or similar
+
##check boxes for ''Include Rigd registr. phase'' , ''Include ScaleVersor3D'', ''include Affine''
###leave rest at defaults. Click ''Apply''
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##''Slicer Linear Transform'': select "create new transform", rename to "Xf1_Affine" or similar
###registration should take ~ 10 secs.
+
##leave rest at defaults. Click ''Apply''
###use fade slider to verify alignment; compare with result snapshots shown below. Alignment will not be perfect but should be better than before.
+
##registration should take ~ 10 secs.
###note: you can also change the colormaps for the fixed and moving volumes to better judge the alignment: go to the  [[Documentation/Nightly/Modules/Volumes| ''Volumes'']] module and in the ''Display'' tab, select "green" and "magenta" as the respective colormaps for the two volumes (vhf, vhm)
+
##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
+
##note: you can also change the colormaps for the fixed and moving volumes to better judge the alignment: go to the  [[Documentation/Nightly/Modules/Volumes| ''Volumes'']] module and in the ''Display'' tab, select "green" and "magenta" as the respective colormaps for the two volumes (vhf, vhm)
##Go to the [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]
+
#'''Nonrigid Registration (masked)''': open the [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]. [[Media:RegLib_C44_2_Registration.mov|Movie/screencast showing this step]]
###''Fixed Image Volume'': vhm ''Moving'': vhf
+
##''Fixed Image Volume'': vhm ''Moving'': vhf
 
##Registration phases: from ''Initialize with previously generated transform', select "Xf1_Affine" node created before.
 
##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''
 
##Registration phases: uncheck boxes for rigid, scale and affine and check box for  ''BSpline''
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##Leave all other settings at default
 
##Leave all other settings at default
 
##click apply
 
##click apply
 +
#'''Deformation Visualization''':  [[Media:RegLib_C44_3_Deformation.mov|Movie/screencast showing this step]]
 +
##if you have not yet installed the [[Documentation/Nightly/Modules/DeformationFieldVisualizer| ''Deformation Field Visualizer'']] extension, [[Documentation/Nightly/RegistrationVideoTutorials#Registration_Validation__How_do_I_check_.2F_visualize_a_registration_result_.3F|see here]] for a movie clip on how to install it.
 +
##we first generate a smaller version of our image to save memory:
 +
###open the '''Resize Image (BRAINS)''' module (under Registration)
 +
###''Image To Warp'': select "vhf"
 +
###''Output Image'': create new, rename to "vhf_small" or similar
 +
###''Pixel Type'': select "short"
 +
###''Scale Factor'': leave at 2.0
 +
###click ''Apply''
 +
##open the [[Documentation/Nightly/Modules/DeformationFieldVisualizer| ''Transform Visualizer'']]  module (under: All Modules)
 +
###Deformation: select "Xf2_BSpline"
 +
###Reference Image: select "vhf_small" generated above
 +
###Visualization mode: click on "Grid Slice"
 +
###Grid Slice Options: Slice: red; Spacing: 20mm
 +
###Click Apply. you should see the deformation field overlay. Adjust slice, spacing etc. to taste.
  
 
== Registration Results==
 
== Registration Results==
 
[[Image:RegLib_C44_unregistered.gif|400px|original unregistered]] unregistered <br>
 
[[Image:RegLib_C44_unregistered.gif|400px|original unregistered]] unregistered <br>
[[Image:RegLib_C44_registered_affine.gif|400px|registered (affine)]] registered  (affine)]<br>
+
[[Image:RegLib_C44_registered_affine.gif|400px|registered (affine)]] registered  (affine)<br>
 
[[Image:RegLib_C44_registered_noMask.gif|400px|registered (nonrigid w/o masking)]] registered  (nonrigid w/o masking)<br>
 
[[Image:RegLib_C44_registered_noMask.gif|400px|registered (nonrigid w/o masking)]] registered  (nonrigid w/o masking)<br>
 
[[Image:RegLib_C44_registered_withMask.gif|400px|registered (nonrigid+masking)]] registered (nonrigid+masking)<br>
 
[[Image:RegLib_C44_registered_withMask.gif|400px|registered (nonrigid+masking)]] registered (nonrigid+masking)<br>

Latest revision as of 18:14, 1 October 2013

Home < Documentation:Nightly:Registration:RegistrationLibrary:RegLib C44

Back to Registration Library

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 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. The overall strategy will be to register "vhf" to "vhm" via first affine and then BSpline registration. We will generate a mask to focus the registration on the bone structure only and ignore the soft tissue when computing the deformation. Because our original images are quite large (512x512x150), we will subsample the vhf pair for use with the Deformation Field Visualizer module, which might otherwise become too memory intensive.

Download

Why 2 sets of files? The "input data" mrb includes only the unregistered data to try the method yourself from start to finish. The full dataset includes intermediate files and results (transforms, resampled images etc.). If you use the full dataset we recommend to choose different names for the images/results you create yourself to distinguish the old data from the new one you generated yourself.

Video Screencasts

  1. Movie/screencast showing generating a registration mask
  2. Movie/screencast showing affine and nonrigid BSpline registration
  3. Movie/screencast showing visualization of the deformation via the Transform Visualizer module

Keywords

CT, pelvis, visible human, inter-subject

Procedure / Pipeline

  1. Mask generation: open the Editor module. Movie/screencast showing this step
    1. "Master Volume": select vhm
    2. A new labelmap "vhm-label" will be created
    3. Select "vhm" to be visible in the slice viewer
    4. Select the Threshold tool from the editor toolbar
    5. Adjust the lower threshold (slider bar) until most of the bone is highlighted,just before speckle noise starts to become included e.g. somewhere around an intensity value of 80. Leave the upper threshold unchanged at the max.
    6. Click Apply
    7. clean the segmentation:
    8. Select the "Identify Islands" editor effect. IdentifyIslandsEffectIcon.png This will identify all continuous areas that are disconnected from each other. Click "Apply"
    9. you should see the bones of the arms being assigned a different label value & color. We can now delete them with one click:
    10. select the "Change Island" effect ChangeIslandsEffectIcon.png . Change the label value to 0 (zero).
    11. in the axial (red) view, click the left mouse within the segmented areas of the arms.
    12. select the "Dilate" effect DilateEffectIcon.png. Click the "Apply" button 3-4 times until the boundary of the segmentation extends well beyond the bone, including a several pixel wide layer of adjacent tissue.
    13. repeat the above for "vhf".
    14. save the two segmentations.
  2. Affine Registration: open the General Registration (BRAINS) module. Movie/screencast showing this step
    1. Fixed Image Volume: vhm
    2. Moving Volume: vhf
    3. check boxes for Include Rigd registr. phase , Include ScaleVersor3D, include Affine
    4. Slicer Linear Transform: select "create new transform", rename to "Xf1_Affine" or similar
    5. leave rest at defaults. Click Apply
    6. registration should take ~ 10 secs.
    7. use fade slider to verify alignment; compare with result snapshots shown below. Alignment will not be perfect but should be better than before.
    8. 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)
  3. Nonrigid Registration (masked): open the General Registration (BRAINS). Movie/screencast showing this step
    1. Fixed Image Volume: vhm Moving: vhf
    2. Registration phases: from Initialize with previously generated transform', select "Xf1_Affine" node created before.
    3. Registration phases: uncheck boxes for rigid, scale and affine and check box for BSpline
    4. Output: Slicer Linear transform: set to None
    5. Output: Slicer BSpline transform: create new, rename to "Xf2_BSpline_msk" or similar
    6. Output Image Volume: create new, rename to "vhf_Xf2"; Pixel Type: "short"
    7. Registration Parameters: increase Number Of Samples to 200,000; Number of Grid Subdivisions: 7,7,7
    8. Control Of Mask Processing Tab: check ROI box, for Input Fixed Mask and Input Moving Mask select the two dilated labelmaps from above
    9. Leave all other settings at default
    10. click apply
  4. Deformation Visualization: Movie/screencast showing this step
    1. if you have not yet installed the Deformation Field Visualizer extension, see here for a movie clip on how to install it.
    2. we first generate a smaller version of our image to save memory:
      1. open the Resize Image (BRAINS) module (under Registration)
      2. Image To Warp: select "vhf"
      3. Output Image: create new, rename to "vhf_small" or similar
      4. Pixel Type: select "short"
      5. Scale Factor: leave at 2.0
      6. click Apply
    3. open the Transform Visualizer module (under: All Modules)
      1. Deformation: select "Xf2_BSpline"
      2. Reference Image: select "vhf_small" generated above
      3. Visualization mode: click on "Grid Slice"
      4. Grid Slice Options: Slice: red; Spacing: 20mm
      5. Click Apply. you should see the deformation field overlay. Adjust slice, spacing etc. to taste.

Registration Results

original unregistered unregistered
registered (affine) registered (affine)
registered (nonrigid w/o masking) registered (nonrigid w/o masking)
registered (nonrigid+masking) registered (nonrigid+masking)
deformation only of vhf registered deformation only of vhf
deformation grid deformation visualized by grid image overlay

Acknowledgments

Original CT from the Visible Human Project shared by the University of Iowa.