Difference between revisions of "Projects:RegistrationLibrary:RegLib C17"

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==<small>v3.6.3</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case #17: <br>Kidney pre-op MR to intra-op CT==
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==<small>v3.6.3</small> [[Image:Slicer_cvers_banner.png|70px|This case is complete and up to date for version 3.6.3]] Slicer Registration Library Case #17: Kidney pre-op MR to intra-op CT==
 
=== Input ===
 
=== Input ===
 
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
 
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
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=== Modules ===
 
=== Modules ===
*[http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit '''BRAINSfit''']
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*[https://www.slicer.org/wiki/Modules:BRAINSFit '''BRAINSfit''']
*for mask generation: ''Draw'' tool in the [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor]  and/or [http://www.slicer.org/slicerWiki/index.php/Modules:FastMarchingSegmentation-Documentation-3.6 Fast-Marching Segmentation],  
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*for mask generation: ''Draw'' tool in the [https://www.slicer.org/wiki/Modules:Editor-Documentation-3.6 Editor]  and/or [https://www.slicer.org/wiki/Modules:FastMarchingSegmentation-Documentation-3.6 Fast-Marching Segmentation],  
  
 
=== Keywords ===
 
=== Keywords ===
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*fixed: intra-operative CT, oblique,  0.58 x 0.58 x 3  mm voxel size, dimensions 512 x 512 x 20
 
*fixed: intra-operative CT, oblique,  0.58 x 0.58 x 3  mm voxel size, dimensions 512 x 512 x 20
 
*moving: opre-operative MRI lique,  1.2 x 1.2 x 4  mm voxel size, dimensions 320 x 240 x 64
 
*moving: opre-operative MRI lique,  1.2 x 1.2 x 4  mm voxel size, dimensions 320 x 240 x 64
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=== Download ===
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*Data
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**[[Media:RegLib_C17_Data.zip‎|'''Registration Library Case 17: Kidney MR-CT''' <small> (Data,Presets, Solution, zip file 11 MB) </small>]]
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*Presets
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**[[Media:RegLib_C17_Presets.mrml‎|'''Registration Library Case 17: Parameter Presets (Slicer 3.6.3)''' <small> (.mrml file 16 kB) </small>]]
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**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
  
 
===Registration Challenges===
 
===Registration Challenges===
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=== Procedures===
 
=== Procedures===
*''Phase 1'': obtain masks for kidney ROI
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*'''Phase 1''': obtain masks for kidney ROI
#Use the ''Draw'' tool in the [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor]  and/or use the [http://www.slicer.org/slicerWiki/index.php/Modules:FastMarchingSegmentation-Documentation-3.6 Fast-Marching Segmentation] module to obtain segmentations of the kidney in both CT and MR image. In the example dataset, you can find those segementations as files "Probe1CT_seg.nrrd" and "MRl_seg.nrrd"  
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#Use the ''Draw'' tool in the [https://www.slicer.org/wiki/Modules:Editor-Documentation-3.6 Editor]  and/or use the [https://www.slicer.org/wiki/Modules:FastMarchingSegmentation-Documentation-3.6 Fast-Marching Segmentation] module to obtain segmentations of the kidney in both CT and MR image. In the example dataset, you can find those segementations as files "Probe1CT_seg.nrrd" and "MRl_seg.nrrd"  
#See the  [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training tutorials]  for the Editor and and segmentation methods for details on how to obtain an efficient segmentation.
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#See the  [https://www.slicer.org/wiki/Slicer_3.6:Training tutorials]  for the Editor and and segmentation methods for details on how to obtain an efficient segmentation.
*''Phase 2'': obtain initial manual alignment
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*'''Phase 2''': obtain initial manual alignment
**Details in the [http://www.slicer.org/slicerWiki/index.php/Slicer3.6:Training  manual registration tutorial] and also in the [http://www.slicer.org/slicerWiki/index.php/Slicer-3-6-FAQ#How_do_I_initialize.2Falign_images_with_very_different_orientations_and_no_overlap.3F Slicer FAQ]
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**Details in the [https://www.slicer.org/wiki/Slicer3.6:Training  manual registration tutorial] and also in the [https://www.slicer.org/wiki/Slicer-3-6-FAQ#How_do_I_initialize.2Falign_images_with_very_different_orientations_and_no_overlap.3F Slicer FAQ]
#go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 Data module]
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#go to the [https://www.slicer.org/wiki/Modules:Data-Documentation-3.6 Data module]
 
#right click on the "Scene" mode and select ''Insert New Transform''. In the MRML edit field below, rename it to "Xf0_manual" or similar
 
#right click on the "Scene" mode and select ''Insert New Transform''. In the MRML edit field below, rename it to "Xf0_manual" or similar
 
#In the ''Data'' module, drag the "MRI" image volume inside the"Xf0_manual" node
 
#In the ''Data'' module, drag the "MRI" image volume inside the"Xf0_manual" node
 
#Select the views so that the MR and CT volumes are displayed in the slice views
 
#Select the views so that the MR and CT volumes are displayed in the slice views
#Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module] and adjust the translation and rotation sliders to adjust the current position. To get a finer degree of control, enter smaller numbers for the translation limits and enter rotation angles numerically in increments of a few degrees at a time
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#Go to the [https://www.slicer.org/wiki/Modules:Transforms-Documentation-3.6 Transforms module] and adjust the translation and rotation sliders to adjust the current position. To get a finer degree of control, enter smaller numbers for the translation limits and enter rotation angles numerically in increments of a few degrees at a time
*''Phase 3'': automated rigid/affine alignment
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*'''Phase 3''': automated rigid/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
 
##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: "Probe1CT", moving image: "MRI"
 
##fixed image: "Probe1CT", moving image: "MRI"
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##Mask Processing: check ''ROI'' box, ''Input Fixed Mask'' select CT segmentation created in Phase 1 above. For  ''Input Moving Mask'' select MRI segmentation created in Phase 1 above.
 
##Mask Processing: check ''ROI'' box, ''Input Fixed Mask'' select CT segmentation created in Phase 1 above. For  ''Input Moving Mask'' select MRI segmentation created in Phase 1 above.
 
##Click Apply
 
##Click Apply
#return to the  [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 Data module] and drag the MRI 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 MRI inside/outside the different registration transforms to compare the alignment
 
#to obtain a resampled volume: move MRI 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 MRI inside Xform of choice and then right-click on the volume and select ''Harden Transforms''. Save MRI under new name.
  
 
=== Registration Results===
 
=== Registration Results===
[[Image:RegLib_C17_unregistered.gif||400px|original  unregistered]]
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[[Image:RegLib_C17_unregistered.gif||400px|original  unregistered]] original  unregistered <br>
[[Image:RegLib_C17_manualInit.gif||400px|after manual initial alignment]]
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[[Image:RegLib_C17_manualInit.gif||400px|after manual initial alignment]] after manual initial alignment<br>
[[Image:RegLib_C17_Rigid.gif||400px|after rigid registration]]
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[[Image:RegLib_C17_Rigid.gif||400px|after rigid registration]] after rigid registration  <br>
[[Image:RegLib_C17_Affine.gif||400px|after affine registration]]
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[[Image:RegLib_C17_Affine.gif||400px|after affine registration]] after affine registration  <br>
 
 
=== Download ===
 
*Data
 
**[[Media:RegLib_C17_Data.zip‎|'''Registration Library Case 17: Kidney MR-CT''' <small> (Data,Presets, Solution, zip file 11 MB) </small>]]
 
*Presets
 
**[[Media:RegLib_C17_Presets.mrml‎|'''Registration Library Case 17: Parameter Presets (Slicer 3.6.3)''' <small> (.mrml file 16 kB) </small>]]
 
**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
 

Latest revision as of 17:36, 10 July 2017

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v3.6.3 This case is complete and up to date for version 3.6.3 Slicer Registration Library Case #17: Kidney pre-op MR to intra-op CT

Input

this is the fixed reference 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: intra-operative CT moving image: per-operative MRI

Modules

Keywords

CT, MRI, abdominal, image-guided therapy, IGT, tumor ablation

Input Data

  • fixed: intra-operative CT, oblique, 0.58 x 0.58 x 3 mm voxel size, dimensions 512 x 512 x 20
  • moving: opre-operative MRI lique, 1.2 x 1.2 x 4 mm voxel size, dimensions 320 x 240 x 64

Download

Registration Challenges

  • intra-operative CT is acquired with limited FOV and very oblique position
  • intra-operative CT contains artifacts from surgical needles
  • both datasets have strong voxel anisotropy
  • the region of interest (kidney) is small compared to the FOV, i.e. there is substantial "distracting" image content

Key Strategies

  • manual alignment to obtain initial pose
  • rough segmentation of both kidneys to mask "distracting" image content
  • gradual increase in registration DOF.

Procedures

  • Phase 1: obtain masks for kidney ROI
  1. Use the Draw tool in the Editor and/or use the Fast-Marching Segmentation module to obtain segmentations of the kidney in both CT and MR image. In the example dataset, you can find those segementations as files "Probe1CT_seg.nrrd" and "MRl_seg.nrrd"
  2. See the tutorials for the Editor and and segmentation methods for details on how to obtain an efficient segmentation.
  1. go to the Data module
  2. right click on the "Scene" mode and select Insert New Transform. In the MRML edit field below, rename it to "Xf0_manual" or similar
  3. In the Data module, drag the "MRI" image volume inside the"Xf0_manual" node
  4. Select the views so that the MR and CT volumes are displayed in the slice views
  5. Go to the Transforms module and adjust the translation and rotation sliders to adjust the current position. To get a finer degree of control, enter smaller numbers for the translation limits and enter rotation angles numerically in increments of a few degrees at a time
  • Phase 3: automated rigid/affine 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: "Probe1CT", moving image: "MRI"
    3. Initialize with previous transform: select "Xf0_manual" from Phase 1 above
    4. Initialize Transform Mode: leave at default = OFF
    5. check Include Rigid registration Phase box. For affine also check ScaleVersor3D and Affine
    6. Output: under Slicer Linear Transform, select new and rename to "Xf1_Rigid" or "Xf2_Affine" or similar
    7. Registration Parameters: set "Number of Samples" to 100,000 at least
    8. Mask Processing: check ROI box, Input Fixed Mask select CT segmentation created in Phase 1 above. For Input Moving Mask select MRI segmentation created in Phase 1 above.
    9. Click Apply
  2. return to the Data module and drag the MRI inside/outside the different registration transforms to compare the alignment
  3. to obtain a resampled volume: move MRI inside Xform of choice and then right-click on the volume and select Harden Transforms. Save MRI under new name.

Registration Results

original unregistered original unregistered
after manual initial alignment after manual initial alignment
after rigid registration after rigid registration
after affine registration after affine registration