Difference between revisions of "Projects:RegistrationLibrary:RegLib C14"

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[[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br>
 
[[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br>
  
==<small>v3.6.1</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case #14: <br>Intra-subject Brain PET-MRI with MRI orientation adjustment ==
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==Slicer Registration Use Case Exampe #14: Intra-subject Brain PET-MRI with MRI orientation adjustment ==
=== Input ===
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{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
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{| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
 
|[[Image:RegLib_C14_Thumb_MRI.png|100px|lleft|this is the fixed reference image. All images are aligned into this space]]  
 
|[[Image:RegLib_C14_Thumb_MRI.png|100px|lleft|this is the fixed reference image. All images are aligned into this space]]  
 
|[[Image:Arrow_left_gray.jpg|100px|lleft]]  
 
|[[Image:Arrow_left_gray.jpg|100px|lleft]]  
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|[[Image:RegLib_C14_Thumb_PET.png|100px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]]
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|align="left"|LEGEND<br>
 
[[Image:Button_red_fixed.jpg|20px|lleft]]  this indicates the reference image that is fixed and does not move. All other images are aligned into this space and resolution<br>
 
[[Image:Button_red_fixed.jpg|20px|lleft]]  this indicates the reference image that is fixed and does not move. All other images are aligned into this space and resolution<br>
 
[[Image:Button_green_moving.jpg|20px|lleft]]  this indicates the moving image that determines the registration transform.  <br>
 
[[Image:Button_green_moving.jpg|20px|lleft]]  this indicates the moving image that determines the registration transform.  <br>
 
|-
 
|-
|fixed image/target
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|[[Image:Button_red_fixed.jpg|40px|lleft]] MRI
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|
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|[[Image:Button_green_moving.jpg|40px|lleft]] PET
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|-
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|MRI: <small> coronal T1w <br>256 x 256 x 79<br>0.86 x 0.86 x 2.5 mm
 
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|
|moving image
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|PET: <small> axial, fluorodeoxyglucose<br>128 x 128 x 35<br>      4.29  x 4.29 x 4.25 mm  </small>
 
|}
 
|}
 
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===Objective / Background ===
===Objective / Background ===
 
 
Image fusion.
 
Image fusion.
 
=== Keywords ===
 
=== Keywords ===
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===Input Data===
 
===Input Data===
*reference/fixed : baseline MRI: 0.97  x 0.97 x 3.27 mm ,  PET: 4.7 x 4.7 x 3.3 mm
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*[[Image:Button_red_fixed_white.jpg|20px]]reference/fixed : baseline MRI: 0.97  x 0.97 x 3.27 mm ,  PET: 4.7 x 4.7 x 3.3 mm
*moving: PET: 4.1 x 4.1 x 5 mm
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*[[Image:Button_green_moving_white.jpg|20px]] moving: PET: 4.1 x 4.1 x 5 mm
**axial, fluorodeoxyglucose<br>128 x 128 x 35<br>      4.29  x 4.29 x 4.25 mm  </small>
 
**coronal T1w <br>256 x 256 x 79<br>0.86 x 0.86 x 2.5 mm
 
  
 
=== Registration Results===
 
=== Registration Results===
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===Download ===
 
===Download ===
*Data:
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*'''[[Media:RegLib_C14_BrainPET-MRI.zip‎ ‎‎|download full tutorial  set  <small> (Data+intermediate results+presets+tutorial, zip file 17 MB) </small>]]'''
*[[Media:RegLib_C14_Data.zip‎‎‎|download example '''data''' set  <small> (Data+intermediate results+presets, zip file 17 MB) </small>]]
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*'''[[Media:RegLib_C14_BrainPET-MRI_Data.zip‎‎|download example data set <small> (Data only, zip file 16 MB) </small>]]'''
*Presets
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*'''[[Media:RegLib_C14_Tutorial_BrainPET-MRI.ppt|download step-by-step tutorial  <small> (PowerPoint 1.2 MB) </small>]]'''
**[[Media:RegLib_C14_Presets_BFit.mrml‎‎|download registration parameter '''presets (BRAINSfit)''' <small> (Data only, zip file 8 kB) </small>]]
 
**[[Media:RegLib_C14_RegistrationPresets.mrml‎‎|download registration parameter '''presets (Slicer v3.5)''' <small> (Data only, zip file 20 kB) </small>]]
 
**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
 
*Documentation
 
**'''[[Media:RegLib_C14_Tutorial_BrainPET-MRI.ppt|download step-by-step tutorial  <small> (PowerPoint 1.2 MB) </small>]]'''
 
**'''[[Media:RegLib_C14_Tutorial_BrainPET-MRI.pdf|download step-by-step tutorial  <small> (PDF  MB) </small>]]'''
 
  
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[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
  
 
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Revision as of 13:27, 13 October 2010

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Slicer Registration Use Case Exampe #14: Intra-subject Brain PET-MRI with MRI orientation adjustment

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 LEGEND

lleft this indicates the reference image that is fixed and does not move. All other images are aligned into this space and resolution
lleft this indicates the moving image that determines the registration transform.

lleft MRI lleft PET
MRI: coronal T1w
256 x 256 x 79
0.86 x 0.86 x 2.5 mm
PET: axial, fluorodeoxyglucose
128 x 128 x 35
4.29 x 4.29 x 4.25 mm

Objective / Background

Image fusion.

Keywords

PET-MRI, brain, intra-subject, image fusion

Input Data

  • Button red fixed white.jpgreference/fixed : baseline MRI: 0.97 x 0.97 x 3.27 mm , PET: 4.7 x 4.7 x 3.3 mm
  • Button green moving white.jpg moving: PET: 4.1 x 4.1 x 5 mm

Registration Results

Download

Link to User Guide: How to Load/Save Registration Parameter Presets


Discussion: Registration Challenges

  • the original DICOM files of the MRI have image orientation data stripped. Hence the volume does not load in correct orientation and needs to be adjusted
  • the two series have different voxel sizes
  • image content and resolution in PET is low

Discussion: Key Strategies

  • we use the Volumes module to adjust the MRI voxel size based on the info in the DICOM header
  • we use the Transforms module to reorient the MRI along the proper axes
    • the aspect ratio we correct via the "Volumes" module. The correct slice thickness we obtain from the DICOM header via the browser displayed when selecting "Add Volume"
    • the "Transforms" module is used to correct orientation. We enter manual rotations of 90 and 180 degrees around the LR (left-right) and IS (inferior-superior) axes, respectively
    • the corrected MRI volume is resampled in the Data module via "harden transforms"
  • Register Images is used to automatically align the PET with the MRI. We choose mutual information ("MI") as the criterion and a 5% sampling rate. We request an affine transform to correct for small distortion differences between the PET and the MRI

Acknowledgments

Our thanks to the University of Western Ontario for providing this example case.