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= v3.6.3 [[Image:Slicer_cvers_banner.png|70px|This case is complete and up to date for version 3.6.3]] Slicer Registration Library Case #21: Intra-subject knee MRI =
=== Input ===
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C21_Thumb1.png|150px|lleft|this is the fixed PET/CT image. All images are aligned into this space]]
|[[Image:RegArrow_NonRigid.png|100px|lleft]]
|[[Image:RegLib_C21_Thumb2.png|150px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]]
|-
|fixed image/target
|
|moving image
|}

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

===Objective / Background ===
atlas building, priors, cartilage segmentation
=== Keywords ===
knee, MRI

===Input Data===
*reference/fixed : subject 58 MRI: 0.47 x 0.47 x 1.55 mm , 256 x 256 x 60; sagittal
*moving: subject 64 MRI: 0.55 x 0.55 x 1.5 mm , 256 x 256 x 60; sagittal

===Download ===
*Data
**[[Media:RegLib_C21_Data.zip‎‎|'''RegLib C20 example data set; incl Presets and solutions (zip file 116 MB) ]]
**[[Media:RegLib_C21_Presets.mrml‎ |'''Registration Presets''' (.mrml files 16kB) ]]
**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]

=== Registration Results===
[[Image:RegLib_C21_unregistered.gif|300px|rigid]]rigid 
[[Image:RegLib_C21_Rigid.gif|300px|rigid]]rigid 
[[Image:RegLib_C21_Affine.gif|300px|affine alignment]]affine alignment 
[[Image:RegLib_C21_BSpline.gif‎|300px|BSpline registration of full volumes. 9 x 9 x 5 grid]]BSpline registration of full volumes. 9 x 9 x 5 grid 

=== Procedures===
*'''Phase 1''': rigid alignment
#Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit '''BRAINSfit'''] module
##select Presets "Xf1_Rigid" or set the parameters as given below:
##fixed image: "58_MRI", moving image: "64_MRI"
##''Initialize with previous transform'': select "Off"
##''Initialize Transform Mode'': check box for ''use MomentsAlign''
##check ''Include Rigid registration Phase'' box.
##Output: under ''Slicer Linear Transform'', select new and rename to "Xf1_Rigid" or similar
##Registration Parameters: set "Number of Samples" to 150,000 at least
##leave rest at defaults
##Click Apply
*'''Phase 2''': affine alignment
#Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit '''BRAINSfit'''] module
##same as Phase 1 above, except:
##''Initialize with previous transform'': select "Xf1_Rigid" from phase 1 above
##''Initialize Transform Mode'': check box for ''Off''
##check ''Include ScaleVersor" , "Include ScaleSkewVersor" and "Include Affine" registration Phase box.
##Registration Parameters: set "Number of Samples" to 200,000 at least
##Output: under ''Slicer Linear Transform'', select new and rename to "Xf2_Affine" or similar
*'''Phase 3''': Masking
#Before allowing nonrigid deformations we must mask the aliasing present:
##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor module].
##Select 58_MRI as ''Master Volume'', choose the threshold tool and threshold at intensity ~68 to separate from the background.
##Select the ''Brush'' tool and cut connections between the aliasing portions and the rest of the image
##Select ''Island Tool'' and remove aliasing portions
##Select ''Dilate'' tool to fill holes
##Save. Repeat for the 64_MRI volume
*'''Phase 4''': BSpline alignment
#Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit '''BRAINSfit'''] module
##''Initialize with previous transform'': select "Xf2_Affine" from phase 2 above
##Output: under ''Slicer BSpline Transform'', select new and rename to "Xf3_BSpline" or similar
##Output Image Volume: select new and rename to "64_MRI_Xf3" or similar
##Registration Parameters: set "Number of Samples" to 300,000 at least
##Number of Grid Subdivisions: 7,7,5
##Maximum B-Spline Displacement: set to 5 [mm]
##Masking: check ''ROI'' box, Input Fixed Mask: "58_MRI-label", Input Moving Mask: "64_MRI-label" generated in Phase 3 above.
##Click Apply
#Note to compare the different registrations: to see the Rigid or Affine registrations, drag the 64_MRI volume inside/onto the respective transform node. To see the BSpline registrations, select the "64_MRI_Xf3" volume as fore- or background.



=== Discussion: Registration Challenges ===
*inter-subject registration: content differences are large, as are relative limb positions
*aliasing: both MRIs have aliasing with part of the anatomy wrapping around to the other edge of the image. This needs to be masked for detailed registration

=== Discussion: Key Strategies ===
*to calculate the transform, we use the images with the most accurate geometric representation and the smallest expected change, i.e. we align the follow-up CT to the baseline CT and then apply the transforms to the PET image.
*because of the non-rigid differences due to posture and breathing we will need to apply a 2-step registration with an affine alignment followed by a BSpline.

@@ Line 29: / Line 29: @@
 ===Download ===
 *Data
-**[[Media:RegLib_C21_Data.zip‎‎|'''RegLib C20 example data set; incl Presets and solutions <small> (zip file 116 MB) </small>]]
+**[[Media:RegLib_C21_Data.zip‎‎|'''RegLib C20 example data set; incl Presets and solutions <small> (zip file 9.6 MB) </small>]]
 **[[Media:RegLib_C21_Presets.mrml‎ |'''Registration Presets'''<small> (.mrml files 16kB) </small>]]
 **[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]

@@ Line 16: / Line 16: @@
 === 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 42: / Line 42: @@
 === Procedures===
 *'''Phase 1''': rigid alignment
-#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 Presets "Xf1_Rigid"  or set the parameters as given below:
 ##fixed image: "58_MRI", moving image: "64_MRI"
@@ Line 53: / Line 53: @@
 ##Click Apply
 *'''Phase 2''': affine alignment
-#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
 ##same as Phase 1 above, except:
 ##''Initialize with previous transform'': select "Xf1_Rigid" from phase 1 above
@@ Line 62: / Line 62: @@
 *'''Phase 3''': Masking
 #Before allowing nonrigid deformations we must mask the aliasing present:
-##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].
 ##Select 58_MRI as ''Master Volume'', choose the threshold tool and threshold at intensity ~68 to separate from the background.
 ##Select the ''Brush'' tool and cut connections between the aliasing portions and the rest of the image
@@ Line 69: / Line 69: @@
 ##Save. Repeat for the 64_MRI volume
 *'''Phase 4''': BSpline alignment
-#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
 ##''Initialize with previous transform'': select "Xf2_Affine" from phase 2 above
 ##Output: under ''Slicer BSpline Transform'', select new and rename to "Xf3_BSpline" or similar

Projects:RegistrationLibrary:RegLib C21 - Revision history

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

Meier: /* Download */

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…'