Difference between revisions of "Projects:RegistrationLibrary:RegLib C47"

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m (Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/")
 
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=== Slicer4 Modules used ===
 
=== Slicer4 Modules used ===
−
*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BrainsFit]'''
+
*[https://www.slicer.org/wiki/Documentation/4.1/Modules/BRAINSFit BrainsFit]'''
  
 
===Objective / Background ===
 
===Objective / Background ===
 
We seek to align a pre-operative MRI with the intra-operative CT for surgical guidance.
 
We seek to align a pre-operative MRI with the intra-operative CT for surgical guidance.
 +
 +
===Download ===
 +
*[[Media:RegLib_C47_Data.zip|'''download RegLib_C47 input image data'''  <small> (NRRD images, transforms, Slicer Scene File,  zip file 52 MB) </small>]]
  
 
=== Keywords ===
 
=== Keywords ===
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*strong differences in image contrast between MRI & CT
 
*strong differences in image contrast between MRI & CT
 
*we have strongly anisotropic voxel sizes with much less through-plane resolution
 
*we have strongly anisotropic voxel sizes with much less through-plane resolution
−
*[[Projects:RegistrationLibrary:RegLib_C47 there is a related example for pre-operative contrast CT to MRI here]]
+
*[[Projects:RegistrationLibrary:RegLib_C12|there is a related example for pre-operative contrast CT to MRI in Library Case #12]]
 +
 
 
=== Procedures ===
 
=== Procedures ===
 
*'''Phase I: MR-CTpre registration'''
 
*'''Phase I: MR-CTpre registration'''
 
#Following the concept of manual registration, we create an initial transform that roughly aligns the MR to the pre-op CT.  
 
#Following the concept of manual registration, we create an initial transform that roughly aligns the MR to the pre-op CT.  
−
#open  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]''' module  
+
#open  [https://www.slicer.org/wiki/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]''' module  
 
##''Input Images''
 
##''Input Images''
 
###''Fixed Image Volume'': CT_intraop
 
###''Fixed Image Volume'': CT_intraop
 
###''Moving Image Volume'': MRI_preop
 
###''Moving Image Volume'': MRI_preop
 
##''Output Settings'':  
 
##''Output Settings'':  
−
###''Slicer BSpline Transform'' none  
+
###''Slicer BSpline Transform'': none  
−
###''Slicer Linear Transform'' (create new transform, rename to: "Xf1_MRI-CT_Affine")
+
###''Slicer Linear Transform'': (create new transform, rename to: "Xf1_MRI-CT_Affine")
−
###''Output Image Volume'' none
+
###''Output Image Volume'': none
 
##''Registration Phases'':  select/check ''Rigid'' , ''Rigid+Scale'', ''Affine''
 
##''Registration Phases'':  select/check ''Rigid'' , ''Rigid+Scale'', ''Affine''
 
##Leave all other settings at default
 
##Leave all other settings at default
 
##click: ''Apply''
 
##click: ''Apply''
−
#switch to the  [http://www.slicer.org/slicerWiki/index.php/Modules:Data Data module]  
+
#switch to the  [https://www.slicer.org/wiki/Documentation/4.1/Modules/Data Data module]  
 
##click on the "MRI_intra" node, and drag it onto the transform node "Xf1_MRI-CT_Affine" created above
 
##click on the "MRI_intra" node, and drag it onto the transform node "Xf1_MRI-CT_Affine" created above
−
##this should yield a rough alignment as shown in the result section below. We will use this to initialize a more refined nonrigid registration  
+
#this should yield a rough alignment as shown in the result section below. We will use this to initialize a more refined nonrigid registration  
 
*'''Phase II:  nonrigid registration'''
 
*'''Phase II:  nonrigid registration'''
−
#open  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]'''module  
+
#open  [https://www.slicer.org/wiki/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]'''module  
−
##''Input Images''
+
##''Input Images'':
 
###''Fixed Image Volume'': CT_intraop
 
###''Fixed Image Volume'': CT_intraop
 
###''Moving Image Volume'': MRI_preop
 
###''Moving Image Volume'': MRI_preop
 
##''Output Settings'':  
 
##''Output Settings'':  
−
###''Slicer BSpline Transform'' (create new transform, rename to: "Xf2_MRI-CT_BSpline")  
+
###''Slicer BSpline Transform'': (create new transform, rename to: "Xf2_MRI-CT_BSpline")  
−
###''Slicer Linear Transform'' none
+
###''Slicer Linear Transform'': none
 
###''Output Image Volume'' create new volume, rename to "MRI_Xf2"
 
###''Output Image Volume'' create new volume, rename to "MRI_Xf2"
−
##''Initialization''
+
##''Initialization'':
−
##''Initialization transform'': select "" created in phase 1 above
+
###''Initialization transform'': select "" created in phase 1 above
−
##'''Initialize Transform Mode'': Off
+
###''Initialize Transform Mode'': Off
 
##''Registration Phases'':  select/check ''BSpline'' only
 
##''Registration Phases'':  select/check ''BSpline'' only
−
##''Main Parameters''
+
##''Main Parameters'':
−
##''Number Of Samples'': 200,000
+
###''Number Of Samples'': 200,000
−
## ''B-Spline Grid Size'': 7,7,5
+
### ''B-Spline Grid Size'': 7,7,5
 
##Leave all other settings at default
 
##Leave all other settings at default
 
##click: ''Apply''
 
##click: ''Apply''
  
−
=== Registration Results===
+
=== Registration Results (click to enlarge) ===
 
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
 
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
 
|[[Image:RegLib_C47_unregistered.gif|300px|left|unregistered MRI & CT]]  
 
|[[Image:RegLib_C47_unregistered.gif|300px|left|unregistered MRI & CT]]  
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|after linear (affine) registration
 
|after linear (affine) registration
 
|-
 
|-
−
|[[Image:RegLib_C47_BSPline.gif|300px|left|after nonrigid registration]]  
+
|[[Image:RegLib_C47_BSpline.gif|300px|left|after nonrigid registration]]  
 
|after nonrigid registration
 
|after nonrigid registration
 
|-
 
|-
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|}
 
|}
  
−
===Download ===
 
−
*[[Media:RegLib_C47_Data.zip|'''download input image data'''  <small> (Input Data, NRRD images,  zip file 42 MB) </small>]]
 
  
 
=== Acknowledgments ===
 
=== Acknowledgments ===
 
Thanks to Dr.Stuart Silverman and Dr. Nobuhiko Hata for sharing this case.
 
Thanks to Dr.Stuart Silverman and Dr. Nobuhiko Hata for sharing this case.

Latest revision as of 18:07, 10 July 2017

Home < Projects:RegistrationLibrary:RegLib C47

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updated for v4.1 Slicer4 RegLibLogo.png
Slicer Registration Library Case #47: Liver Tumor Cryoablation

Input

this is the intra-op CT reference image. All images are aligned into this space lleft this is the pre-op MRI we seek to align with the intra-op CT
fixed image/target moving image

Slicer4 Modules used

Objective / Background

We seek to align a pre-operative MRI with the intra-operative CT for surgical guidance.

Download

Keywords

MRI, CT, IGT, intra-operative, liver, cryoablation, change detection, non-rigid registration

Input Data

  • reference/fixed : pr-op CT, 0.95 x 0.95 x 5 mm voxel size
  • moving: intra-op MRI, 0.78 x 0.78 x 2.5 mm axial,

Discussion: Registration Challenges

Procedures

  • Phase I: MR-CTpre registration
  1. Following the concept of manual registration, we create an initial transform that roughly aligns the MR to the pre-op CT.
  2. open General Registraion (BRAINS) module
    1. Input Images
      1. Fixed Image Volume: CT_intraop
      2. Moving Image Volume: MRI_preop
    2. Output Settings:
      1. Slicer BSpline Transform: none
      2. Slicer Linear Transform: (create new transform, rename to: "Xf1_MRI-CT_Affine")
      3. Output Image Volume: none
    3. Registration Phases: select/check Rigid , Rigid+Scale, Affine
    4. Leave all other settings at default
    5. click: Apply
  3. switch to the Data module
    1. click on the "MRI_intra" node, and drag it onto the transform node "Xf1_MRI-CT_Affine" created above
  4. this should yield a rough alignment as shown in the result section below. We will use this to initialize a more refined nonrigid registration
  • Phase II: nonrigid registration
  1. open General Registraion (BRAINS)module
    1. Input Images:
      1. Fixed Image Volume: CT_intraop
      2. Moving Image Volume: MRI_preop
    2. Output Settings:
      1. Slicer BSpline Transform: (create new transform, rename to: "Xf2_MRI-CT_BSpline")
      2. Slicer Linear Transform: none
      3. Output Image Volume create new volume, rename to "MRI_Xf2"
    3. Initialization:
      1. Initialization transform: select "" created in phase 1 above
      2. Initialize Transform Mode: Off
    4. Registration Phases: select/check BSpline only
    5. Main Parameters:
      1. Number Of Samples: 200,000
      2. B-Spline Grid Size: 7,7,5
    6. Leave all other settings at default
    7. click: Apply

Registration Results (click to enlarge)

unregistered MRI & CT
 unregistered MRI & CT
after linear (affine) registration
 after linear (affine) registration
after nonrigid registration
 after nonrigid registration
comparing kidney alignment at different registration stages
 comparing kidney alignment at different registration stages


Acknowledgments

Thanks to Dr.Stuart Silverman and Dr. Nobuhiko Hata for sharing this case.

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