Difference between revisions of "Documentation:Nightly:Registration:RegistrationLibrary:RegLib C21"

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(Created page with 'Back to Registration Library <br> = Slicer Registration Library Case #21: Align knee MRI of two different subjects = =…')
 
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#'''Compute Rigid Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
 
#'''Compute Rigid Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
 
##''Input Images: Fixed Image Volume'': MRI_58
 
##''Input Images: Fixed Image Volume'': MRI_58
−
##'''Input Images: Moving Image Volume'': MRI_64
+
##''Input Images: Moving Image Volume'': MRI_64
 
##''Output Settings'':  
 
##''Output Settings'':  
−
###''Slicer Linear Transform'' (create new transform, rename to: "Xf1_Rigid")
+
###''Slicer Linear Transform'': (create new transform, rename to: "Xf1_Rigid")
−
###''Output Image Volume'' none (we need no resampled volume at this stage, only the transform)
+
###''Output Image Volume'': none (we need no resampled volume at this stage, only the transform)
 
##''Registration Phases'':  select/check ''Rigid''  
 
##''Registration Phases'':  select/check ''Rigid''  
 
##''Main Parameters'':  
 
##''Main Parameters'':  
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##check the result
 
##check the result
 
###Place "MRI_58" in the background and "MRI_64" in the foreground
 
###Place "MRI_58" in the background and "MRI_64" in the foreground
−
###switch to the [[Documentation/Nightly/Modules/Data|''Data'' module]], locate the "MRI_64" node, and drag it onto the newly created "Xf1_Affine" node.
+
###switch to the [[Documentation/Nightly/Modules/Data|''Data'' module]], locate the "MRI_64" node, and drag it onto the newly created "Xf1_Rigid" node.
 
###fade between background and foreground to judge the alignment.
 
###fade between background and foreground to judge the alignment.
−
###for better visibility, you can change the colormaps of the two volumes, as used in the examples shown here. Switch to the [[Documentation/Nightly/Modules/Volumes|''Volumes'' #'''Compute Affine Registration''': return to the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
+
###for better visibility, you can change the colormaps of the two volumes, as used in the examples shown here. Switch to the [[Documentation/Nightly/Modules/Volumes|''Volumes'' module]], select "MRI_58" and then select "Green" from the ''Lookup Table'' menu. Similarly select "Cyan" for "MRI_64".
 +
#'''Compute Affine Registration''': return to the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
 
##''Input Images: Fixed Image Volume'': MRI_58
 
##''Input Images: Fixed Image Volume'': MRI_58
−
##'''Input Images: Moving Image Volume'': MRI_64
+
##''Input Images: Moving Image Volume'': MRI_64
 
##''Output Settings'':  
 
##''Output Settings'':  
−
###''Slicer Linear Transform'' (create new transform, rename to: "Xf2_Affine")
+
###''Slicer Linear Transform'': (create new transform, rename to: "Xf2_Affine")
−
###''Output Image Volume'' none (we need no resampled volume at this stage, only the transform)
+
###''Output Image Volume'': none (we need no resampled volume at this stage, only the transform)
 
##''Initialization'':  for the ''Initialization transform'' select the "Xf1_Rigid" transform created above.  
 
##''Initialization'':  for the ''Initialization transform'' select the "Xf1_Rigid" transform created above.  
 
##''Initialize Transform Mode'': switch to ''Off''
 
##''Initialize Transform Mode'': switch to ''Off''
−
##''Registration Phases'':  '''un'''check ''Rigid'' and select ''Rigid+Scale" and ''Affine'' only
+
##''Registration Phases'':  '''un'''check ''Rigid'' and select ''Rigid+Scale'' and ''Affine'' only
 
##''Main Parameters'':  
 
##''Main Parameters'':  
 
###leave ''Number Of Samples'' to 200,000
 
###leave ''Number Of Samples'' to 200,000
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###fade between background and foreground to judge the alignment.
 
###fade between background and foreground to judge the alignment.
 
###for better visibility, you can change the colormaps of the two volumes, as used in the examples shown here. Switch to the [[Documentation/Nightly/Modules/Volumes|''Volumes'' module]], select "MRI_58" and then select "Green" from the ''Lookup Table'' menu. Similarly select "Cyan" for "MRI_64".  
 
###for better visibility, you can change the colormaps of the two volumes, as used in the examples shown here. Switch to the [[Documentation/Nightly/Modules/Volumes|''Volumes'' module]], select "MRI_58" and then select "Green" from the ''Lookup Table'' menu. Similarly select "Cyan" for "MRI_64".  
−
#'''Apply transform to PET:''' We have now computed the registration transform, but we still need to apply this transform to the PET image. The preferred way to do this is without resampling the image, i.e. by applying the linear transform to the spatieal orientation information in the image header. You can of course also create a resampled version, like the MRI_Xf1 output volume produced above.
+
#'''Compute BSpline Registration''': return to the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
−
##Go to the [[Documentation/Nightly/Modules/Data|''Data'']] module
+
##''Input Images: Fixed Image Volume'': MRI_58
−
###Find the original PET image, labeled as "PET"
+
##''Input Images: Moving Image Volume'': MRI_64
−
###drag the "PET" node '''onto''' the transform node, labeled "Xf1_Affine". You should see a small + appear next to the transform node. When you click it you should see the "PET" image now residing inside the transform. If you have the PET image in one of the Slice views, it should show you now the aligned position of the PET image.
+
##''Output Settings'':
−
###apply the transform: right click on the "PET" image and from the pop-up menu, select ''Harden Transform''. This will apply the transform '''without resampling''' and move it back to the main hierarchy level.  
+
###''Slicer BSpline Transform'': Create and rename new. Rename to "MRI_64_Xf3"
−
###double click on the PET node and rename it to something like "PET_registered" or "PET_XF1applied" 3etc. to document that this image has now a transform applied to it.
+
###''Slicer Linear Transform'': set to ''none''
−
##Click on the Save icon and save the new "PET" image under a new name.
+
###''Output Image Volume'': Create and rename new. Rename to "MRI_64_Xf3"
 +
##''Initialization'':  for the ''Initialization transform'' select the "Xf1_Affine" transform created above.  
 +
##''Initialize Transform Mode'': switch to ''Off''
 +
##''Registration Phases'':  '''un'''check ''Rigid+Scale'' and ''Affine'' and select ''BSpline'' only
 +
##''Main Parameters'':
 +
###increase ''Number Of Samples'' to 400,000
 +
###set ''B-Spline Grid Size'' to 5,5,3
 +
##Leave all other settings at default
 +
##click: ''Apply''; runtime for this will be more than 1 minute, depending on CPU.
 +
##check the result
 +
###Place "MRI_58" in the background and "MRI_64_Xf3" in the foreground
 +
#Apply and save transforms
 +
##To apply the rigid and affine transforms you need not resample the volume. Simply drag the MRI_64 volume into the transform node (Xf1_Rigid or Xf2_Affine), and then right click on the "MRI_64" volume node and from the pop-up menu, select ''Harden Transform''. This will apply the transform '''without resampling''' and move it back to the main hierarchy level. '''Note that now you have a reoriented volume although the name is the same. It is advisable to immediately rename the node to document this fact. Then save it as a new file under a new name.'''
 +
##To apply the nonrigid transform resampling is required. You already have a resampled volume "MRI_64_Xf3" from above. This uses linear interpolation and float as default. You can change these settings under the ''Advanced Output Settings'' tab. For this example "short" as Pixel Type and "Windowed Sinc" is recommended. To obtain a new resampled copy without repeating the whole registration step, use the [[Documentation/Nightly/Modules/BRAINSResample|''BRAINSResample'' module]]
  
 
==Registration Results==
 
==Registration Results==

Revision as of 15:28, 19 August 2013

Home < Documentation:Nightly:Registration:RegistrationLibrary:RegLib C21

Back to Registration Library

Slicer Registration Library Case #21: Align knee MRI of two different subjects

Input

this is the fixed MRI reference image. lleft this is the moving image, to be aligned with the reference MRI on the left
fixed image/target
MRI 		moving image
MRI


Modules used

Download (from NAMIC MIDAS)

Keywords

MRI, knee, inter-subject, nonrigid

Procedure

It is possible to perform all 3 steps of rigid, affine and BSpline registration in a single pass within the General Registration (BRAINS) module, but to better show/judge progress we perform each separately and feed the results of one the the next step. Hence we first run a rigid registration, then use that to compute an affine registration, and finally use the affine as starting point for a BSpline registration. For the last one we will need to generate a quick mask to prevent aliasing artifacts in the image from influencing the result. The masks are available in the download set.

  1. Compute Rigid Registration: open the General Registration (BRAINS) module
    1. Input Images: Fixed Image Volume: MRI_58
    2. Input Images: Moving Image Volume: MRI_64
    3. Output Settings:
      1. Slicer Linear Transform: (create new transform, rename to: "Xf1_Rigid")
      2. Output Image Volume: none (we need no resampled volume at this stage, only the transform)
    4. Registration Phases: select/check Rigid
    5. Main Parameters:
      1. increase Number Of Samples to 200,000
    6. Leave all other settings at default
    7. click: Apply; runtime < 1 min.
    8. check the result
      1. Place "MRI_58" in the background and "MRI_64" in the foreground
      2. switch to the Data module, locate the "MRI_64" node, and drag it onto the newly created "Xf1_Rigid" node.
      3. fade between background and foreground to judge the alignment.
      4. for better visibility, you can change the colormaps of the two volumes, as used in the examples shown here. Switch to the Volumes module, select "MRI_58" and then select "Green" from the Lookup Table menu. Similarly select "Cyan" for "MRI_64".
  2. Compute Affine Registration: return to the General Registration (BRAINS) module
    1. Input Images: Fixed Image Volume: MRI_58
    2. Input Images: Moving Image Volume: MRI_64
    3. Output Settings:
      1. Slicer Linear Transform: (create new transform, rename to: "Xf2_Affine")
      2. Output Image Volume: none (we need no resampled volume at this stage, only the transform)
    4. Initialization: for the Initialization transform select the "Xf1_Rigid" transform created above.
    5. Initialize Transform Mode: switch to Off
    6. Registration Phases: uncheck Rigid and select Rigid+Scale and Affine only
    7. Main Parameters:
      1. leave Number Of Samples to 200,000
    8. Leave all other settings at default
    9. click: Apply; runtime < 1 min.
    10. check the result
      1. Place "MRI_58" in the background and "MRI_64" in the foreground
      2. switch to the Data module, locate the "MRI_64" node, and drag it onto the newly created "Xf1_Affine" node.
      3. fade between background and foreground to judge the alignment.
      4. for better visibility, you can change the colormaps of the two volumes, as used in the examples shown here. Switch to the Volumes module, select "MRI_58" and then select "Green" from the Lookup Table menu. Similarly select "Cyan" for "MRI_64".
  3. Compute BSpline Registration: return to the General Registration (BRAINS) module
    1. Input Images: Fixed Image Volume: MRI_58
    2. Input Images: Moving Image Volume: MRI_64
    3. Output Settings:
      1. Slicer BSpline Transform: Create and rename new. Rename to "MRI_64_Xf3"
      2. Slicer Linear Transform: set to none
      3. Output Image Volume: Create and rename new. Rename to "MRI_64_Xf3"
    4. Initialization: for the Initialization transform select the "Xf1_Affine" transform created above.
    5. Initialize Transform Mode: switch to Off
    6. Registration Phases: uncheck Rigid+Scale and Affine and select BSpline only
    7. Main Parameters:
      1. increase Number Of Samples to 400,000
      2. set B-Spline Grid Size to 5,5,3
    8. Leave all other settings at default
    9. click: Apply; runtime for this will be more than 1 minute, depending on CPU.
    10. check the result
      1. Place "MRI_58" in the background and "MRI_64_Xf3" in the foreground
  4. Apply and save transforms
    1. To apply the rigid and affine transforms you need not resample the volume. Simply drag the MRI_64 volume into the transform node (Xf1_Rigid or Xf2_Affine), and then right click on the "MRI_64" volume node and from the pop-up menu, select Harden Transform. This will apply the transform without resampling and move it back to the main hierarchy level. Note that now you have a reoriented volume although the name is the same. It is advisable to immediately rename the node to document this fact. Then save it as a new file under a new name.
    2. To apply the nonrigid transform resampling is required. You already have a resampled volume "MRI_64_Xf3" from above. This uses linear interpolation and float as default. You can change these settings under the Advanced Output Settings tab. For this example "short" as Pixel Type and "Windowed Sinc" is recommended. To obtain a new resampled copy without repeating the whole registration step, use the BRAINSResample module

Registration Results

RegLib C21 Unregistered.png before registration (click to enlarge)
RegLib C21 Rigid.png after rigid registration (click to enlarge)
RegLib C21 Affine.png after affine registration (click to enlarge)
RegLib C21 BSpline.png after BSpline registration (click to enlarge)
RegLib C21 registered.gif animated gif showing the progression of all 3 steps(click to enlarge)


Acknowledgments

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