Projects:RegistrationLibrary:RegLib C39 - Revision history

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Meier: /* Issues Challenges */

2011-03-24T17:45:00Z

Issues Challenges

Meier at 17:44, 24 March 2011

2011-03-24T17:44:46Z

Meier at 17:44, 24 March 2011

2011-03-24T17:44:19Z

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2011-03-24T17:15:56Z

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= v3.6.1 [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case 39: In Vitro cerebral body CT (thoracic spine) =
=== Input ===
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C39_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_C39_Thumb2.png|150px|lleft|this is the moving image]]
|-
|baseline image
|
|follow-up
|}

=== Modules ===
*'''Slicer 3.6.1 recommended modules: [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit]

===Objective / Background ===
This dataset contains in vitro CT of two human vertibral body segments (T10) before and after regional damage. Goal is to align the two images to study in detail the local changes that occurred.

=== Keywords ===
CT, spine cancer, vertebrae
=== Issues Challenges ===
*two images have very different spatial origins (as defined in original DICOM header): recenter first

*the baseline container contains the vertebra upside down (as apparent from orientation of the pedicle/roots of the vertibral arches coming out of the body, visible in sagittal or coronal view). Hence this image needs to have its z-axis (IS) reversed before registration
*the containers walls and lid contain dominant image content that would prevent a successful automated registration; cropping is required
*the two vertebrae have strong rotational misalignment; manual initial alignment is recommended
===Input Data===
*fixed: CT , 0.342 x 0.342 x 0.20 mm voxel size, axial; 512 x 512 x 193 unsigned short image
*moving: CT , 0.342 x 0.342 x 0.20 mm voxel size, axial; 512 x 512 x 250 unsigned short image
=== Procedure / Pipeline ===
#Open case scene file or import image data: RegLib_C28_SlicerScene1.mrml
#Place L4_intact and L4_defect 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 "L4_intact" node and drag it inside/on top of the "Xf0_AxialFlip" node
###ensure you have L4_intact 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 "L4_intact" 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 "L4_intact_crop"
##delete the ROI nodes (right click: delete node)
##repeat the same for the "L4_defect" image
#Manual Initial Alignment
##in the [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 Data module] again select "Insert new Transform node" as done above
##select the newly created transform node, then in the ''MRML Node Inspector'' below, rename it to "Xf1_ManualInit" or similar
##select the "L4_defect_crop" node and drag it inside/on top of the "Xf1_ManualInit" node
##ensure you have L4_intact_crop selected for background and L4_defect_crop for background
##set the fade slider to halfway between background (B) and foreground (F) so you can see changes happening.
##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module]
##Select "Xf1_ManualInit" from the ''Transform Node'' menu
##adjust the sliders to roughly align the two images
##for more details on manual registration, see the "Manual Registration" tutorial here: [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training]
#Run final 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'': :L4_intact_crop ; ''Moving'': L4_defect_crop
###''Initialize with previously generated transform'': select "Xf1_ManualInit" generated above
###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.

=== Registration Results===
[[Image:RegLib_C28_unreg.gif|400px|original unregistered]] unregistered 
[[Image:RegLib_C28_reg.gif|400px|registered (after flipping axis and cropping volume)]] registered 

===Download ===
*Data
**[[Media:RegLib_C28_Data.zip‎|'''RegLib_C28_Data''': Example Dataset (CT images, Presets, Solution, zip file 194 MB) ]]
*Presets
**[[Media:RegLib_C28_Presets.mrml‎|'''RegLib_C28_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 38: / Line 38: @@
 #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]
+##Go to the [https://www.slicer.org/wiki/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]
+##Go to the [https://www.slicer.org/wiki/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.
@@ Line 50: / Line 50: @@
 ###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]
+##Go to the [https://www.slicer.org/wiki/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"
+##go to back to the [https://www.slicer.org/wiki/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]
+##Go to the [https://www.slicer.org/wiki/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:

@@ Line 29: / Line 29: @@
 *the baseline container contains the vertebra upside down (as apparent from orientation of the pedicle/roots of the vertibral arches coming out of the body, visible in sagittal or coronal view). Hence this image needs to have its z-axis (IS) reversed before registration
 *the containers walls and lid contain dominant image content that would prevent a successful automated registration; cropping is required
-*the two vertebrae have strong rotational misalignment; manual initial alignment is recommended
 ===Input Data===
 *fixed:  CT , 0.6 x 0.6 x 0.40 mm voxel size, axial; 292 x 292 x 91 unsigned short image

@@ Line 4: / Line 4: @@
-= <small>v3.6.1</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]]  Slicer Registration Library Case 39:  In Vitro cerebral body CT  (thoracic spine)  =
+= <small>v3.6.3</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]]  Slicer Registration Library Case 39:  In Vitro cerebral body CT  (thoracic spine)  =
 === Input ===
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
@@ Line 17: / Line 17: @@
 === Modules ===
-*'''Slicer 3.6.1 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit]
+*'''Slicer 3.6.3 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit]
 ===Objective / Background ===

Projects:RegistrationLibrary:RegLib C39 - Revision history

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

Meier: /* Issues Challenges */

Meier at 17:44, 24 March 2011

Meier at 17:44, 24 March 2011

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…'