Difference between revisions of "Projects:RegistrationLibrary:RegLib C20b"

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=== Modules ===
 
=== Modules ===
*'''Slicer 3.6.3''' recommended modules: [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit '''BrainsFit'''],
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*'''Slicer 3.6.3''' recommended modules: [https://www.slicer.org/wiki/Modules:BRAINSFit '''BrainsFit'''],
  
 
===Objective / Background ===
 
===Objective / Background ===
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===Download ===
 
===Download ===
 
*Data
 
*Data
**[[Media:RegLib_C20_Data.zip‎‎|'''RegLib C20 example data set; incl Presets and solutions <small> (zip file 116 MB) </small>]]
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**[[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_C20_Presets.mrml‎ |'''Registration Presets'''<small> (.mrml files 16kB) </small>]]
 
**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
 
**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
  
 
=== Registration Results===
 
=== Registration Results===
[[Image:RegLib_C20_Rigid.gif|300px|rigid]]rigid<br>
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[[Image:RegLib_C20b_Rigid.gif|300px|rigid]]rigid<br>
[[Image:RegLib_C20_Affine.gif|300px|affine alignment]]affine alignment<br>
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[[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>
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[[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>
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[[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>
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[[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>
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[[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>
  
  
 
=== Procedures===
 
=== Procedures===
 
*'''Phase 1''': rigid alignment
 
*'''Phase 1''': rigid alignment
#Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit '''BRAINSfit'''] module
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#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:
 
##select Presets "Xf1_Rigid" or "Xf2_Affine" or set the parameters as given below:
 
##fixed image: "CT_1", moving image: "CT_2"
 
##fixed image: "CT_1", moving image: "CT_2"
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##leave rest at defaults
 
##leave rest at defaults
 
##Click Apply
 
##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
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#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
 
*'''Phase 2''': affine alignment
#Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit '''BRAINSfit'''] module
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#Go to the [https://www.slicer.org/wiki/Modules:BRAINSFit '''BRAINSfit'''] module
 
##same as Phase 1 above, except:
 
##same as Phase 1 above, except:
 
##''Initialize with previous transform'': select "Xf1_Rigid" from phase 1 above
 
##''Initialize with previous transform'': select "Xf1_Rigid" from phase 1 above
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##Number of Grid Subdivisions: 9,9,5  or 11,11,7
 
##Number of Grid Subdivisions: 9,9,5  or 11,11,7
 
##Click Apply
 
##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
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#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.
 
#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
 
*'''Phase 4''': Resample PET
#Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 '''ResampleScalarVectorDWIVolume'''] module
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#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"
 
##''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 Node'': select  "Xf3_BSpline" created in phase 3 above

Latest revision as of 18:07, 10 July 2017

Home < Projects:RegistrationLibrary:RegLib C20b

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Back to Registration Use-case Inventory

v3.6.3 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

this is the fixed PET/CT image. All images are aligned into this space lleft this is the moving image. The transform is calculated by matching this to the reference image
fixed image/target moving image

Versions

For the Slicer 4.1 version of this case see here

Modules

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

Registration Results

rigidrigid
affine alignmentaffine alignment
BSpline registration of full volumes. 9 x 9 x 5 gridBSpline registration of full volumes. 9 x 9 x 5 grid
PET overlay ; BSpline registration of full volumes. 9 x 9 x 5 gridPET overlay ; BSpline registration of full volumes. 9 x 9 x 5 grid
BSpline registration of full volumes. 11 x 11 x 7 gridBSpline registration of full volumes. 11 x 11 x 7 grid
PET overlay ; BSpline registration of full volumes. 11 x 11 x 7 gridPET overlay ; BSpline registration of full volumes. 11 x 11 x 7 grid


Procedures

  • Phase 1: rigid alignment
  1. Go to the BRAINSfit module
    1. select Presets "Xf1_Rigid" or "Xf2_Affine" or set the parameters as given below:
    2. fixed image: "CT_1", moving image: "CT_2"
    3. Initialize with previous transform: select "Off"
    4. Initialize Transform Mode: check box for use MomentsAlign
    5. check Include Rigid registration Phase box.
    6. Output: under Slicer Linear Transform, select new and rename to "Xf1_Rigid" or similar
    7. Registration Parameters: set "Number of Samples" to 200,000 at least
    8. leave rest at defaults
    9. Click Apply
  2. return to the Data module and drag the CT_2 inside/outside the different registration transforms to compare the alignment
  • Phase 2: affine alignment
  1. Go to the BRAINSfit module
    1. same as Phase 1 above, except:
    2. Initialize with previous transform: select "Xf1_Rigid" from phase 1 above
    3. Initialize Transform Mode: check box for Off
    4. Output: under Slicer Linear Transform, select new and rename to "Xf2_Affine" or similar
  • Phase 3: BSpline alignment
    1. same as Phase 2 above, except:
    2. Initialize with previous transform: select "Xf2_Affine" from phase 2 above
    3. Output: under Slicer BSpline Transform, select new and rename to "Xf3_BSpline" or similar
    4. Output Image Volume: select new and rename to "CT_2_Xf3" or similar
    5. Registration Parameters: set "Number of Samples" to 250,000 at least
    6. Number of Grid Subdivisions: 9,9,5 or 11,11,7
    7. Click Apply
  1. return to the Data module and drag the CT_2 inside/outside the different registration transforms to compare the alignment
  2. 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
  1. Go to the ResampleScalarVectorDWIVolume module
    1. Input Volume: PET_2 ; Reference Volume: PET_1 ; Output Volume: create new, rename to "PET_2_Xf3"
    2. Transform Node: select "Xf3_BSpline" created in phase 3 above
    3. Transform Order: check box for "output-to-input"
    4. 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.