Difference between revisions of "Documentation:Nightly:Registration:RegistrationLibrary:RegLib C03"

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== Procedure ==
 
== Procedure ==
 
This assumes you have the following: 1) a T2 reference image, 2) a DTI baseline image and  3) the DTI volume (both obtained from the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation module]). If you do not have a baseline image, generate a scalar Trace image from the DTI, using the ''Diffusion Tensor Scalar Measurements'' module:
 
This assumes you have the following: 1) a T2 reference image, 2) a DTI baseline image and  3) the DTI volume (both obtained from the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation module]). If you do not have a baseline image, generate a scalar Trace image from the DTI, using the ''Diffusion Tensor Scalar Measurements'' module:
#open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
+
#'''Compute Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
 
##''Input Images: Fixed Image Volume'': T2
 
##''Input Images: Fixed Image Volume'': T2
 
##'''Input Images: Moving Image Volume'': DTI_baseline
 
##'''Input Images: Moving Image Volume'': DTI_baseline
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##Leave all other settings at default
 
##Leave all other settings at default
 
##click: ''Apply''; runtime < 1 min.
 
##click: ''Apply''; runtime < 1 min.
#Resample DTI: We have now computed the registration transform, but the output volume produced above is a registered version of the baseline, which we need for validation only. To get the actual DTI registered we now apply this transform to the tensor image.
+
#'''Resample DTI:''' We have now computed the registration transform, but the output volume produced above is a registered version of the baseline, which we need for validation only. To get the actual DTI registered we now apply this transform to the tensor image.
 
##Open the [[Documentation/Nightly/Modules/ResampleDTIVolume|''Resample DTI Volume'']] module (found under: All Modules) (Do not resample a tensor image with other modules, this one must be used to correctly transform the tensor data)
 
##Open the [[Documentation/Nightly/Modules/ResampleDTIVolume|''Resample DTI Volume'']] module (found under: All Modules) (Do not resample a tensor image with other modules, this one must be used to correctly transform the tensor data)
 
###Input Volume: select DTI
 
###Input Volume: select DTI

Revision as of 16:07, 13 May 2013

Home < Documentation:Nightly:Registration:RegistrationLibrary:RegLib C03

Back to Registration Library

Slicer Registration Library Case #3: Diffusion Weighted Image Volume: align with structural reference MRI

Input

this is the fixed T2 reference image. All images are aligned into this space lleft this is the DTI Baseline scan, to be registered with the T2 this is the DTI tensor image, in the same orientation as the DTI Baseline
fixed image 1/target
T2
moving image 2a
DTI baseline
moving image 2b
DTI tensor

Objective / Background

Goal is to align the DTI image with the structural reference T2 scan that provides accuracte anatomical reference.

Modules used

Alternate Versions

Download (from NAMIC MIDAS)

Video Screencasts

  1. Movie/screencast showing registration+resampling for Case #03

Procedure

This assumes you have the following: 1) a T2 reference image, 2) a DTI baseline image and 3) the DTI volume (both obtained from the Diffusion Tensor Estimation module). If you do not have a baseline image, generate a scalar Trace image from the DTI, using the Diffusion Tensor Scalar Measurements module:

  1. Compute Registration: open the General Registration (BRAINS) module
    1. Input Images: Fixed Image Volume: T2
    2. 'Input Images: Moving Image Volume: DTI_baseline
    3. Output Settings:
      1. Slicer BSpline Transform (create new transform, rename to: "Xf1_DTbase-T2_BSpline")
      2. Slicer Linear Transform none
      3. Output Image Volume (create new volume, rename to: "DTIbaseline_Xf1"
    4. Registration Phases: select/check Rigid , Rigid+Scale, Affine, BSpline
    5. Main Parameters:
      1. increase Number Of Samples to 300,000
      2. set B-Spline Grid Size to 7,7,5 (we have lower resolution in the IS-direction (z), hence we set a smaller (5) grid size there)
    6. Leave all other settings at default
    7. click: Apply; runtime < 1 min.
  2. Resample DTI: We have now computed the registration transform, but the output volume produced above is a registered version of the baseline, which we need for validation only. To get the actual DTI registered we now apply this transform to the tensor image.
    1. Open the Resample DTI Volume module (found under: All Modules) (Do not resample a tensor image with other modules, this one must be used to correctly transform the tensor data)
      1. Input Volume: select DTI
      2. Output Volume: select create new Diffusion Tensor Volume,and rename it to DTI_Xf1
      3. Reference Volume: select T2
      4. Transform Parameters: select transform node "Xf1_DTI-T2_BSpline", for Deformation Field: none ; check the displacement checkbox
      5. Leave all other settings at defaults
      6. Click Apply; runtime ~ 2 min.
    2. set T2 as background and new DTI_Xf1 volume as foreground
    3. fade between back- and foreground to see DTI overlay onto the T2 image. Note that you can also fade via holding the OPTION+CMD keys (mac) + dragging left mouse.

Registration Results (animated gifs, click to enlarge & play)

RegLib C03 baseline unregistered.gif baseline & T2 before registration
RegLib C03 baseline registered.gif baseline to T2 after affine+nonrigid alignment
RegLib C03 DTI registered.gif DTI and T2 before & after registration

Keywords

MRI, brain, head, intra-subject, DTI, DWI

Discussion: Key Strategies

  • the strong EPI-based distortions of the DTI image make nonrigid registration necessary
  • initial alignment & overlap is sufficient so that no "initialization" methods are necessary and registration can succeed without.
  • contrast & initial pose are similar enough for registration to succeed without any masking. However the DTI estimation procedure does provide an optional mask that is usually very helpful in registering cases with more "distracting" image content. For an example see the extended version of this case here.
  • the DTI in this example is isotropic and hence can be resampled directly. If the DTI contains strong anisotropy of ratios 1:3 or greater, reorienting the DTI can lead to strong artifacts (e.g. in axial direction appear as blue cast in the color orientation view). In that case it is necessary to resample the DWI in the original orientation to an isotropic size before reorienting. It may also be advisable to first reorient the DWI and perform the DTI estimation afterwards.

Acknowledgments