Projects:RegistrationLibrary:RegLib C28 - Revision history

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

2017-07-10T18:07:14Z

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

Meier: /* Acknowledgments */

2011-05-13T20:45:40Z

Acknowledgments

Meier: /* Acknowledgments */

2011-05-13T20:43:26Z

Acknowledgments

Meier: /* Acknowledgments */

2011-05-13T20:43:03Z

Acknowledgments

Meier at 16:56, 24 March 2011

2011-03-24T16:56:46Z

Meier: /* Download */

2011-03-24T16:56:10Z

Download

Meier: /* Registration Results */

2011-03-24T16:54:19Z

Registration Results

Meier at 16:36, 24 March 2011

2011-03-24T16:36:21Z

Meier: /* Procedure / Pipeline */

2011-03-24T16:28:37Z

Procedure / Pipeline

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

2011-03-24T16:11:30Z

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

New page

[[Projects:ARRASuplements|Back to ARRA main page]] 
[[Projects:RegistrationDocumentation|Back to Registration main page]] 
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= v3.6.1 [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case 28: In Vitro cerebral body CT (intra subject) =
=== Input ===
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C28_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_C28_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 (L4) 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 ===
*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
##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

##Input Surface: S02_femur
##Target Surface: S01_femur
##Output Transform: create new transform, rename to "Xf1_surf_S2-S1"
##Select/check ''Mean distance mode: RMS''
##Leave defaults: iterations: 50, landmarks: 200
##Select/check ''Start by matching centroids''
##Select/check ''Check mean distance''
##Click: ''Apply''; process duration: ~ seconds
#Go to the ''Data'' module
##find the newly created transform node "Xf1_surf_S2-S1" and drag the "S02_femur" model node (and all other S02 entities) inside the transform.
##for the 3D viewer turn on the visibility of the surface models (should be on already)
##the surfaces for the two femur models should now align in basic position and orientation
#for additional details see tutorial downloads below

=== Registration Results===
[[Image:RegLib C05 AGif reg.gif|200px|femur surface models before/after registration]]

===Download ===
*Data
**[[Media:RegLib_C05_Data.zip‎|'''RegLib_C05_Data''': Example Dataset (MRI images, surface models,Presets, Solution, zip file 9.5 MB) ]]
*Presets
**[[Media:RegLib_C05_Presets.mrml‎|'''RegLib_C05_Presets.mrml''': registration parameter presets (.mrml text file 12 kB) ]]
*[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
*Documentation
**[[Media:RegLib_C05_Tutorial.ppt|'''RegLib_C05_Tutorial''': Powerpoint file (.ppt file 1 MB) ]]
**[[Media:RegLib_C05_Tutorial.ppt|'''RegLib_C05_Tutorial''': PDF file (.pdf file 0.5 MB) ]]

=== Acknowledgments ===

@@ Line 17: / Line 17: @@
 === Modules ===
-*'''Slicer 3.6.1 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit]
+*'''Slicer 3.6.1 recommended modules:  [https://www.slicer.org/wiki/Modules:BRAINSFit BRAINSFit]
 ===Objective / Background ===
@@ Line 36: / Line 36: @@
 #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 "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]
+##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 48: / Line 48: @@
 ###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 "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"
+##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 "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
+##in the [https://www.slicer.org/wiki/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]
+##Go to the [https://www.slicer.org/wiki/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]
+##for more details on manual registration, see the "Manual Registration" tutorial here: [https://www.slicer.org/wiki/Slicer_3.6:Training]
 #Run final 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:

← Older revision		Revision as of 20:45, 13 May 2011
Line 88:		Line 88:

	=== Acknowledgments ===		=== Acknowledgments ===
−	Thanks to Dr.Ron ~~Akalay~~ and the Center for Advanced Orthopaedic Studies at Beth Israel Deaconess Medical Center (BIDMC) for providing the example data.	+	Thanks to Dr.Ron Alkalay and the Center for Advanced Orthopaedic Studies at Beth Israel Deaconess Medical Center (BIDMC) for providing the example data. Details about their research [http://obl.bidmc.harvard.edu/research.html can be found here].

← Older revision		Revision as of 20:43, 13 May 2011
Line 88:		Line 88:

	=== Acknowledgments ===		=== Acknowledgments ===
−	Thanks to ~~Prof~~. Ron Akalay and the Center for Advanced Orthopaedic Studies at Beth Israel Deaconess Medical Center (BIDMC) for providing the example data.	+	Thanks to Dr.Ron Akalay and the Center for Advanced Orthopaedic Studies at Beth Israel Deaconess Medical Center (BIDMC) for providing the example data.

← Older revision		Revision as of 20:43, 13 May 2011
Line 88:		Line 88:

	=== Acknowledgments ===		=== Acknowledgments ===
		+	Thanks to Prof. Ron Akalay and the Center for Advanced Orthopaedic Studies at Beth Israel Deaconess Medical Center (BIDMC) for providing the example data.

@@ Line 4: / Line 4: @@
-= <small>v3.6.1</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]]  Slicer Registration Library Case 28: <br>  In Vitro cerebral body CT (intra subject)  =
+= <small>v3.6.1</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]]  Slicer Registration Library Case 28:  In Vitro cerebral body CT (intra subject)  =
 === Input ===
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"

@@ Line 83: / Line 83: @@
 ===Download ===
 *Data
-**[[Media:RegLib_C28_Data.zip‎|'''RegLib_C28_Data''': Example Dataset <small> (CT images, Presets, Solution, zip file 9.5 MB) </small>]]
+**[[Media:RegLib_C28_Data.zip‎|'''RegLib_C28_Data''': Example Dataset <small> (CT images, Presets, Solution, zip file 194 MB) </small>]]
 *Presets
 **[[Media:RegLib_C28_Presets.mrml‎|'''RegLib_C28_Presets.mrml''': registration parameter presets<small> (.mrml text file 12 kB) </small>]]
 === Acknowledgments ===

@@ Line 78: / Line 78: @@
 === Registration Results===
-[[Image:RegLib_C28_unreg.gif|200px|original unregistered]]
+[[Image:RegLib_C28_unreg.gif|400px|original unregistered]] unregistered <br>
-[[Image:RegLib_C28_reg.gif|200px|registered (after flipping axis and cropping volume)]]
+[[Image:RegLib_C28_reg.gif|400px|registered (after flipping axis and cropping volume)]] registered <br>
 ===Download ===

@@ Line 39: / Line 39: @@
 ###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
+###select the "L4_intact" node and drag it inside/on top of the "Xf0_AxialFlip" node
 ##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
@@ Line 46: / Line 47: @@
 ###change the number to -1. Hit Enter.
 ###you should see the image flip in the sagittal and coronal slice views
 ##Input Surface: S02_femur
@@ Line 60: / Line 94: @@
 ##the surfaces for the two femur models should now align in basic position and orientation
 #for additional details see tutorial downloads below
-−
 === Registration Results===
 [[Image:RegLib C05 AGif reg.gif|200px|femur surface models before/after registration]]

Projects:RegistrationLibrary:RegLib C28 - Revision history

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

Meier: /* Acknowledgments */

Meier: /* Acknowledgments */

Meier: /* Acknowledgments */

Meier at 16:56, 24 March 2011

Meier: /* Download */

Meier: /* Registration Results */

Meier at 16:36, 24 March 2011

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…'