Projects:RegistrationLibrary:RegLib C20b - Revision history

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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 #20: Intra-subject whole-body PET-CT =
=== Input ===
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C20_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_C20_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
|}
=== Versions ===
'''[[Projects:RegistrationLibrary:RegLib_C20|For the Slicer 4.1 version of this case see here]]'''

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

===Objective / Background ===
Change assessment.
=== Keywords ===
PET-CT, whole-body, change assessment

===Input Data===
*reference/fixed : baseline '''CT''': 0.98 x 0.98 x 5 mm , 512 x 512 x 149; '''PET''': 4.1 x 4.1 x 5 mm , 168 x 168 x 149
*moving: '''CT''': 0.98 x 0.98 x 5 mm , 512 x 512 x 149; '''PET''': 4.1 x 4.1 x 5 mm , 168 x 168 x 149

===Download ===
*Data
**[[Media:RegLib_C20_Data.zip‎‎|'''RegLib C20 example data set; incl Presets and solutions (zip file 116 MB) ]]
**[[Media:RegLib_C20_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_C20_Rigid.gif|300px|rigid]]rigid 
[[Image:RegLib_C20_Affine.gif|300px|affine alignment]]affine alignment 
[[Image:RegLib_C20_BSpline1.gif‎|300px|BSpline registration of full volumes. 9 x 9 x 5 grid]]BSpline registration of full volumes. 9 x 9 x 5 grid 
[[Image:RegLib_C20_BSpline1_PET.gif‎‎| 300px|PET overlay ; BSpline registration of full volumes. 9 x 9 x 5 grid]]PET overlay ; BSpline registration of full volumes. 9 x 9 x 5 grid 
[[Image:RegLib_C20_BSpline2.gif‎|300px|BSpline registration of full volumes. 11 x 11 x 7 grid]]BSpline registration of full volumes. 11 x 11 x 7 grid 
[[Image:RegLib_C20_BSpline2_PET.gif‎‎| 300px|PET overlay ; BSpline registration of full volumes. 11 x 11 x 7 grid]]PET overlay ; BSpline registration of full volumes. 11 x 11 x 7 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 "Xf2_Affine" or set the parameters as given below:
##fixed image: "CT_1", moving image: "CT_2"
##''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 200,000 at least
##leave rest at defaults
##Click Apply
#return to the [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 Data module] and drag the CT_2 inside/outside the different registration transforms to compare the alignment
*'''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''
##Output: under ''Slicer Linear Transform'', select new and rename to "Xf2_Affine" or similar
*'''Phase 3''': BSpline alignment
##same as Phase 2 above, except:
##''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 "CT_2_Xf3" or similar
##Registration Parameters: set "Number of Samples" to 250,000 at least
##Number of Grid Subdivisions: 9,9,5 or 11,11,7
##Click Apply
#return to the [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 Data module] and drag the CT_2 inside/outside the different registration transforms to compare the alignment
#to obtain a resampled volume: move CT_2 inside Xform of choice and then right-click on the volume and select ''Harden Transforms''. Save MRI under new name.
*'''Phase 4''': Resample PET
#Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 '''ResampleScalarVectorDWIVolume'''] module
##''Input Volume'': PET_2 ; ''Reference Volume'': PET_1 ; ''Output Volume'': create new, rename to "PET_2_Xf3"
##''Transform Node'': select "Xf3_BSpline" created in phase 3 above
##''Transform Order'': check box for "output-to-input"
##Click Apply



=== Discussion: Registration Challenges ===
*accuracy is the critical criterion here. We need the registration error (residual misalignment) to be smaller than the change we want to measure/detect. Agreement on what constitutes good alignment can therefore vary greatly.
*because of the large FOV we have strong non-rigid deformations from differences in patient/limb positions etc.
*images are large volumes (>100 MB total)
*2 images pairs have to be aligned, i.e. the calculated transform must be applied to the second (PET) image.
=== 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 32: / Line 32: @@
 *Data
 **[[Media:RegLib_C20b_Data.zip‎‎|'''RegLib C20 example data set; incl Presets and solutions <small> (zip file 116 MB) </small>]]
-**[[Media:RegLib_C20b_Presets.mrml‎ |'''Registration Presets'''<small> (.mrml files 16kB) </small>]]
+**[[Media:RegLib_C20_Presets.mrml‎ |'''Registration Presets'''<small> (.mrml files 16kB) </small>]]
 **[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]

@@ Line 31: / Line 31: @@
 ===Download ===
 *Data
-**[[Media:RegLib_C20_Data.zip‎‎|'''RegLib C20 example data set; incl Presets and solutions <small> (zip file 116 MB) </small>]]
+**[[Media:RegLib_C20b_Data.zip‎‎|'''RegLib C20 example data set; incl Presets and solutions <small> (zip file 116 MB) </small>]]
-**[[Media:RegLib_C20_Presets.mrml‎ |'''Registration Presets'''<small> (.mrml files 16kB) </small>]]
+**[[Media:RegLib_C20b_Presets.mrml‎ |'''Registration Presets'''<small> (.mrml files 16kB) </small>]]
 **[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
 === Registration Results===
-[[Image:RegLib_C20_Rigid.gif|300px|rigid]]rigid<br>
+[[Image:RegLib_C20b_Rigid.gif|300px|rigid]]rigid<br>
-[[Image:RegLib_C20_Affine.gif|300px|affine alignment]]affine alignment<br>
+[[Image:RegLib_C20b_Affine.gif|300px|affine alignment]]affine alignment<br>
-[[Image:RegLib_C20_BSpline1.gif‎|300px|BSpline registration of full volumes. 9 x 9 x 5 grid]]BSpline registration of full volumes. 9 x 9 x 5 grid<br>
+[[Image:RegLib_C20b_BSpline1.gif‎|300px|BSpline registration of full volumes. 9 x 9 x 5 grid]]BSpline registration of full volumes. 9 x 9 x 5 grid<br>
-[[Image:RegLib_C20_BSpline1_PET.gif‎‎| 300px|PET overlay ; BSpline registration of full volumes. 9 x 9 x 5 grid]]PET overlay ; BSpline registration of full volumes. 9 x 9 x 5 grid<br>
+[[Image:RegLib_C20b_BSpline1_PET.gif‎‎| 300px|PET overlay ; BSpline registration of full volumes. 9 x 9 x 5 grid]]PET overlay ; BSpline registration of full volumes. 9 x 9 x 5 grid<br>
-[[Image:RegLib_C20_BSpline2.gif‎|300px|BSpline registration of full volumes. 11 x 11 x 7 grid]]BSpline registration of full volumes. 11 x 11 x 7 grid<br>
+[[Image:RegLib_C20b_BSpline2.gif‎|300px|BSpline registration of full volumes. 11 x 11 x 7 grid]]BSpline registration of full volumes. 11 x 11 x 7 grid<br>
-[[Image:RegLib_C20_BSpline2_PET.gif‎‎| 300px|PET overlay ; BSpline registration of full volumes. 11 x 11 x 7 grid]]PET overlay ; BSpline registration of full volumes. 11 x 11 x 7 grid <br>
+[[Image:RegLib_C20b_BSpline2_PET.gif‎‎| 300px|PET overlay ; BSpline registration of full volumes. 11 x 11 x 7 grid]]PET overlay ; BSpline registration of full volumes. 11 x 11 x 7 grid <br>

@@ Line 18: / Line 18: @@
 === 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 46: / Line 46: @@
 === 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 "Xf2_Affine" or set the parameters as given below:
 ##fixed image: "CT_1", moving image: "CT_2"
@@ Line 56: / Line 56: @@
 ##leave rest at defaults
 ##Click Apply
-#return to the  [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 Data module] and drag the CT_2 inside/outside the different registration transforms to compare the alignment
+#return to the  [https://www.slicer.org/wiki/Modules:Data-Documentation-3.6 Data module] and drag the CT_2 inside/outside the different registration transforms to compare the alignment
 *'''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 71: / Line 71: @@
 ##Number of Grid Subdivisions: 9,9,5  or 11,11,7
 ##Click Apply
-#return to the  [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 Data module] and drag the CT_2 inside/outside the different registration transforms to compare the alignment
+#return to the  [https://www.slicer.org/wiki/Modules:Data-Documentation-3.6 Data module] and drag the CT_2 inside/outside the different registration transforms to compare the alignment
 #to obtain a resampled volume: move CT_2 inside Xform of choice and then right-click on the volume and select ''Harden Transforms''. Save MRI under new name.
 *'''Phase 4''': Resample PET
-#Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 '''ResampleScalarVectorDWIVolume'''] module
+#Go to the [https://www.slicer.org/wiki/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 '''ResampleScalarVectorDWIVolume'''] module
 ##''Input Volume'': PET_2  ; ''Reference Volume'': PET_1 ; ''Output Volume'':  create new, rename to "PET_2_Xf3"
 ##''Transform Node'': select  "Xf3_BSpline" created in phase 3 above

Projects:RegistrationLibrary:RegLib C20b - Revision history

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

Meier at 19:20, 7 June 2012

Meier at 19:17, 7 June 2012

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…'