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==Slicer Registration Librar Case 15: Brain MR Alignment along AC-PC line==
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[[Projects:ARRASuplements|Back to ARRA main page]] <br>
{| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
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[[Projects:RegistrationDocumentation|Back to Registration main page]] <br>
|[[Image:RLib15_FiducialsI.png|150px|lleft|this is a set of reference landmarks. The transform is derived from these fiducials.]]  
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[[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br>
|[[Image:Arrow_left_gray.jpg|100px|lleft]]  
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|[[Image:RLib15_MRI.png|150px|lleft|this is the moving image to which the calculated transform is applied.]]
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|align="left"|LEGEND<br><small><small>
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==<small>v3.6.1</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case #15: <br>Brain MR Alignment along AC-PC line==
[[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>
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=== Input ===
[[Image:Button_green_moving.jpg|20px|lleft]]  this indicates the moving image that determines the registration transform.  <br>
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{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
[[Image:Button_purple_mask.jpg|20px|lleft]] this indicates images that serve as masks, i.e. they focus the active registration onto a specific area.<br>
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|[[Image:RegLib_C15_Fiducials.png|150px|lleft|this is the fixed reference image. All images are aligned into this space]]  
[[Image:Button_blue_tag.jpg|20px|lleft]] this indicates images that passively move into the reference space, i.e. they have the transform applied but do not contribute to the calculation of the transform.
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|[[Image:RegArrow_Rigid.png|100px|lleft]]  
</small></small>
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|[[Image:RegLib_C15_MRI.png‎|150px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]]
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|[[Image:Button_red_fixed.jpg|40px|lleft]]  T1 SPGR
 
|[[Image:Button_purple_mask.jpg|40px|lleft]]  mask
 
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|[[Image:Button_green_moving.jpg|40px|lleft]] T2 FLAIR
 
|[[Image:Button_blue_tag.jpg|40px|lleft]] segmentation
 
 
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|1mm isotropic<br> 256 x 256 x 146<br>RAS
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|fixed image/target
|1mm isotropic<br> 256 x 256 x 146<br>RAS
 
 
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|1.2mm isotropic<br> 256 x 256 x 116<br>RAS
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|moving image
|1.2mm isotropic<br> 256 x 256 x 116<br>RAS
 
 
|}
 
|}
===Objective / Background ===
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=== Modules ===
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*[https://www.slicer.org/wiki/Modules:ACPCTransform-Documentation-3.6 '''AC-PC Transform''']
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*[https://www.slicer.org/wiki/Modules:Fiducials-Documentation-3.6 Fiducials]
  
 
=== Keywords ===
 
=== Keywords ===
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===Input Data===
 
===Input Data===
*[[Image:Button_green_moving_white.jpg|20px]] moving: T1 MPRAGE 1.2x1.2x1.2 mm voxel size, sagittal, RAS orientation.
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*moving: T1 MPRAGE 1x1x1 mm voxel size
  
 
===Registration Challenges===
 
===Registration Challenges===
*
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*A dedicated module for AC-PC alignment is used.
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*the only difficulty lies with accurate placement of the AC-PC fiducials. Depending on image resolution and contrast these can be difficult to find.
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*midline fiducials should be easily obtainable from axial and coronal views. 3 midline fiducials suffice; more is recommended for a more robust solution.
 
===Key Strategies===
 
===Key Strategies===
*
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* this is a special case of fiducial-based alignment. Instead of aligning two sets of fiducial pairs, only one set of fiducials is aligned with a predefined orientation: The plane defined by the midline fiducials is aligned to be vertical in coronal/axial views, and the line defined by the AC-PC line is rotated to be horizontal in a sagittal view.
  
 
=== Registration Results===
 
=== Registration Results===
[[Image:RegLib_C02_Unreg_AnimGif.gif||500px|Unregistered Data + segmentation labelmap]]
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[[Image:RegLib_C15_ACPC_AnimGif.gif||500px|original and aligned MRI]]
  
 
=== Download ===
 
=== Download ===
*[[Media:RegLib_C02_DATA.zip‎|'''Registration Library Case 02: MSBrain intra-subject multi-contrast: FLAIR+lesion segmentation to SPGR + mask''' <small> (Data,Presets, Solution, zip file 27 MB) </small>]]
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*Data
*download/view guided video tutorial
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**[[Media:RegLib_C15_Data.zip‎|'''Registration Library Case 15: Brain alignment along AC-PC Line''' <small> (Data,Presets, Solution, zip file 21 MB) </small>]]
*download power point tutorial
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*Presets
*[[Media:RegInstr_RegUC-001.txt‎|download step-by step text instructions (text only)]]
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**[[Media:RegLib_C15_Presets.mrml‎|'''Registration Library Case 15: Presets for AC-PC module ''' <small> (.mrml file 172 kB) </small>]]
 
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**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
 
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*Documentation
[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
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**[[Media:RegLib_C15_Tutorial_ACPCAlignment.ppt‎|'''Registration Library Case 15: step-by step tutorial''' <small> (PowerPoint file 3.2 MB) </small>]]

Latest revision as of 18:05, 10 July 2017

Home < Projects:RegistrationLibrary:RegLib C15

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v3.6.1 Slicer3-6Announcement-v1.png Slicer Registration Library Case #15:
Brain MR Alignment along AC-PC line

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 moving image

Modules

Keywords

MRI, brain, head, anterior commissure, posterior commissure, AC-PC Line, Talairach, fiducial alignment

Input Data

  • moving: T1 MPRAGE 1x1x1 mm voxel size

Registration Challenges

  • A dedicated module for AC-PC alignment is used.
  • the only difficulty lies with accurate placement of the AC-PC fiducials. Depending on image resolution and contrast these can be difficult to find.
  • midline fiducials should be easily obtainable from axial and coronal views. 3 midline fiducials suffice; more is recommended for a more robust solution.

Key Strategies

  • this is a special case of fiducial-based alignment. Instead of aligning two sets of fiducial pairs, only one set of fiducials is aligned with a predefined orientation: The plane defined by the midline fiducials is aligned to be vertical in coronal/axial views, and the line defined by the AC-PC line is rotated to be horizontal in a sagittal view.

Registration Results

original and aligned MRI

Download