Projects:RegistrationLibrary:RegLib C44 - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T17:58:51Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Meier: /* Overall Strategy */

2011-08-12T14:24:15Z

Overall Strategy

Meier: /* v3.6.3 150px Slicer Registration Library Case 44: Visible Human Pelvis CT */

2011-08-12T14:23:41Z

v3.6.3 150px Slicer Registration Library Case 44: Visible Human Pelvis CT

Meier at 14:22, 12 August 2011

2011-08-12T14:22:23Z

Meier: /* Registration Results */

2011-08-12T14:19:25Z

Registration Results

Meier: /* Registration Results */

2011-08-12T14:16:48Z

Registration Results

Meier: /* Procedure / Pipeline */

2011-08-12T14:13:03Z

Procedure / Pipeline

Meier: /* Procedure / Pipeline */

2011-08-12T14:04:59Z

Procedure / Pipeline

Meier: Created page with 'Back to ARRA main page
Back to Registration main page
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2011-08-05T21:03:49Z

Created page with 'Back to ARRA main page Back to Registration main page [[Projects:RegistrationDocumentation:UseCaseInv…'

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= v3.6.3 [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case 44: Visible Human Pelvis CT =
=== Input ===
{| 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:RegArrow_Affine.png|70px|lleft]]
|[[Image:RegLib_C44_Thumb2.png|150px|lleft|this is the moving image]]
|-
|baseline image
|
|follow-up
|}

=== Modules ===
*'''Slicer 3.6.3 recommended modules: [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit]

===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 ===
#Open case scene file or import image data: RegLib_C28_SlicerScene1.mrml
#Place T10intact and T10defect in back- and foreground respectively.
#Scroll through sagittal view and note the inverted axis orientation
#Flip axis
##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 Data module]
###right-click on the ''Scene'' node and select "Insert Transform Node" from the menu
###select the newly created transform node, then in the ''MRML Node Inspector'' below, rename it to "Xf0_AxialFlip"
###select the "T10intact" node and drag it inside/on top of the "Xf0_AxialFlip" node
###ensure you have T10intact selected for background and the fade slider set on background (B) so you can see changes happening.
##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module]
###Select "Xf0_AxialFlip" from the ''Transform Node'' menu
###In the 4x4 matrix displayed, click in the field containing the "1.0000" in row 3 and column 3.
###hit Return key to activate editing
###change the number to -1. Hit Enter.
###you should see the image flip in the sagittal and coronal slice views
#Crop Volumes
##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:CropVolume-Documentation-3.6 Crop Volume module]
##select "T10intact" as ''Input Volume''; select "Create new MRML ROI Node" in the ''ROI'' menu, select "create new volume" in the ''Output Volume" menu
##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)
##when finished, click on ''Do ROI resample''
##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"
##delete the ROI nodes (right click: delete node)
##repeat the same for the "T10defect" image
#Registration
##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]]
###otherwise select the following parameters:
###''Fixed Image Volume'': :T10intact_crop ; ''Moving'': T10defect_crop
###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
###leave rest at defaults. Click ''Apply''
###registration should take ~ 10 secs.
###use fade slider to verify alignment; compare with result snapshots shown below.

=== Registration Results===
[[Image:RegLib_C44_unregistered.gif|400px|original unregistered]] unregistered 
[[Image:RegLib_C44_affine.gif|400px|registered (after flipping axis and cropping volume)]] registered 
[[Image:RegLib_C44_registered_Xf2.gif|400px|registered (after flipping axis and cropping volume)]] registered 
[[Image:RegLib_C44_registered_Xf3.gif|400px|registered (after flipping axis and cropping volume)]] registered 
[[Image:RegLib_C44_defromOnly_Xf3.gif|400px|registered (after flipping axis and cropping volume)]] registered 

===Download ===
*Data
**[[Media:RegLib_C44_Data.zip‎|'''RegLib_C44_Data''': Example Dataset (CT images, Presets, Solution, zip file 30 MB) ]]
*Presets
**[[Media:RegLib_C44_Presets.mrml‎|'''RegLib_C44_Presets.mrml''': registration parameter presets (.mrml text file 12 kB) ]]

=== Acknowledgments ===

@@ Line 17: / Line 17: @@
 === Modules ===
-*'''Slicer 3.6.3 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit]
+*'''Slicer 3.6.3 recommended modules:  [https://www.slicer.org/wiki/Modules:BRAINSFit BRAINSFit]
 ===Objective / Background ===
@@ Line 48: / Line 48: @@
 === Procedure / Pipeline ===
 #Mask generation
-##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor module]
+##Go to the [https://www.slicer.org/wiki/Modules:Editor-Documentation-3.6 Editor module]
 ##"Master Volume": select ''vhm''
 ##A new labelmap "vhm-label" will be created
@@ Line 56: / Line 56: @@
 ##Click Apply
 ##Morphologically 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
+##Run a [https://www.slicer.org/wiki/Modules:MedianFilter-Documentation-3.6 Median Filter] with a 3x3x3 neighborhood to remove speckle noise
-##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.
+##Return to the  [https://www.slicer.org/wiki/Modules:Editor-Documentation-3.6 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
@@ Line 64: / Line 64: @@
 ##''''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 [https://www.slicer.org/wiki/Modules:BRAINSFit BRAINSfit module]
 ##select the following parameters:
 ###''Fixed Image Volume'': vhm ''Moving'': vhf
@@ Line 73: / Line 73: @@
 ###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]
+##Go to the [https://www.slicer.org/wiki/Modules:BRAINSFit BRAINSfit module]
 ##select the following parameters:
 ###''Fixed Image Volume'': vhm ''Moving'': vhf

@@ Line 43: / Line 43: @@
 ##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|grid image]]
+##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
 === Procedure / Pipeline ===
 #Mask generation

@@ Line 35: / Line 35: @@
 *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 ===
+=== Overall Strategy  ===
 #Open case scene file or import image data: RegLib_C44_SlicerScene.mrml
 #Overall strategy will be
@@ Line 43: / Line 43: @@
 ##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 grid image]]
+##Visualize the deformation by applying the pure BSpline to a [[Projects:RegistrationDocumentation:UseCaseInventory: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
 #Mask generation
 ##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor module]

@@ Line 79: / Line 79: @@
 === Registration Results===
 [[Image:RegLib_C44_unregistered.gif|400px|original unregistered]] unregistered <br>
-[[Image:RegLib_C44_affine.gif|400px|registered (after flipping axis and cropping volume)]] registered <br>
+[[Image:RegLib_C44_affine.gif|400px|registered (affine)]] registered  (affine)]<br>
-[[Image:RegLib_C44_registered_Xf2.gif|400px|registered (after flipping axis and cropping volume)]] registered <br>
+[[Image:RegLib_C44_registered_Xf2.gif|400px|registered (nonrigid w/o masking)]] registered  (nonrigid w/o masking)<br>
-[[Image:RegLib_C44_registered_Xf3.gif|400px|registered (after flipping axis and cropping volume)]] registered <br>
+[[Image:RegLib_C44_registered_Xf3.gif|400px|registered (nonrigid+masking)]] registered (nonrigid+masking)<br>
-[[Image:RegLib_C44_deformOnly_Xf3.gif|400px|registered (after flipping axis and cropping volume)]] registered <br>
+[[Image:RegLib_C44_deformOnly_Xf3.gif|400px|deformation only of vhf]] registered deformation only of vhf<br>
 ===Download ===

@@ Line 82: / Line 82: @@
 [[Image:RegLib_C44_registered_Xf2.gif|400px|registered (after flipping axis and cropping volume)]] registered <br>
 [[Image:RegLib_C44_registered_Xf3.gif|400px|registered (after flipping axis and cropping volume)]] registered <br>
-[[Image:RegLib_C44_defromOnly_Xf3.gif|400px|registered (after flipping axis and cropping volume)]] registered <br>
+[[Image:RegLib_C44_deformOnly_Xf3.gif|400px|registered (after flipping axis and cropping volume)]] registered <br>
 ===Download ===

@@ Line 21: / Line 21: @@
 ===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 ===
@@ Line 84: / Line 90: @@
 [[Image:RegLib_C44_deformOnly_Xf3.gif|400px|deformation only of vhf]] registered deformation only of vhf<br>
 [[Image:RegLib_C44_gridXf3.png|400px|deformation grid]] deformation visualized by grid image overlay <br>
 === Acknowledgments ===

@@ Line 68: / Line 68: @@
 ##select the following parameters:
 ###''Fixed Image Volume'': vhm ''Moving'': vhf
-###check boxes for ''Include BSpline registr. phase''
+##Registration phases: from ''Initialize with previously generated transform', select "Xf2_..." node created before.
-###''BSplineTransform'': select "create new transform", rename to "Xf2_BSpline_msk" or similar
+##Registration phases: check boxes for  ''Include BSpline registration phase''
-###leave rest at defaults. Click ''Apply''
+##Output: Slicer BSpline transform: create new, rename to "Xf2_BSpline_msk" or similar
 === Registration Results===

@@ Line 30: / Line 30: @@
 *moving: CT , 0.6 x 0.6 x 0.40 mm voxel size, axial; 512 x 512 x 107 unsigned short image
 === 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:
 ##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:
+###''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''
 ###''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.
+###use fade slider to verify alignment; compare with result snapshots shown below. Alignment will not be perfect but should be better than before.
 === Registration Results===

Projects:RegistrationLibrary:RegLib C44 - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Meier: /* Overall Strategy */

Meier: /* v3.6.3 150px Slicer Registration Library Case 44: Visible Human Pelvis CT */

Meier at 14:22, 12 August 2011

Meier: /* Registration Results */

Meier: /* Registration Results */

Meier: /* Procedure / Pipeline */

Meier: /* Procedure / Pipeline */

Meier: Created page with 'Back to ARRA main page Back to Registration main page [[Projects:RegistrationDocumentation:UseCaseInv…'

Meier: Created page with 'Back to ARRA main page
Back to Registration main page
[[Projects:RegistrationDocumentation:UseCaseInv…'