Meier at 13:42, 4 October 2013

2013-10-04T13:42:45Z

Meier: Created page with 'Back to Registration Library = Slicer Registration Library Case #37:
Intra-subject Brain MRI: assessment of brain …'

2013-10-04T13:42:04Z

Created page with 'Back to Registration Library = Slicer Registration Library Case #37: Intra-subject Brain MRI: assessment of brain …'

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[[Documentation/Nightly/Registration/RegistrationLibrary|Back to Registration Library]]
= Slicer Registration Library Case #37: Intra-subject Brain MRI: assessment of brain tumor resection =
== Input ==
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C37_Thumb1.png|150px|lleft|this is the fixed reference image. All images are aligned into this space]]
|[[Image:RegArrow_NonRigid.png|100px|lleft]]
|[[Image:RegLib_C37_Thumb2.png|150px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]]
|-
|fixed image/target
|
|moving image
|}

== Modules used ==
*[[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]

== Download (from NAMIC MIDAS) ==
''Why 2 sets of files? The "input data" mrb includes only the unregistered data to try the method yourself from start to finish. The full dataset includes intermediate files and results (transforms, resampled images etc.). If you use the full dataset we recommend to choose different names for the images/results you create yourself to distinguish the old data from the new one you generated yourself. ''
*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C37.mrb'''] (input data only, Slicer mrb file. 12 MB) 
*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C37_full.mrb'''] (input data + results, Slicer mrb file. 36 MB). 

== Description ==
This is a typical case of change assessment.

=== Keywords ===
MRI, brain, head, intra-subject, T1, brain tumor, surgery follow-up, change assessment

== Procedure ==
Shown below is a workflow stepping through multiple registrations of increasing DOF (degrees of freedom). All steps can be combined into one, we execute them separately here to allow tracking the differences in the registration result.
#'''Rigid Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']] module.
##''Fixed Image Volume'': "Autism_T1_4yrs"
##''Moving Volume'': "Autism_T1_2yrs"
##Registration phases: check boxes for ''Rigid" ,"Scale", "Affine"
##''Slicer Linear Transform'': select "create new transform", rename to "Xf1_Affine" or similar
##leave rest at defaults. Click ''Apply''
##registration should take ~ 10 secs.
#'''Affine Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']] module.
##''Fixed Image Volume'': "Autism_T1_4yrs"
##''Moving Volume'': "Autism_T1_2yrs"
##Registration phases: check boxes for ''Rigid" ,"Scale", "Affine"
##''Slicer Linear Transform'': select "create new transform", rename to "Xf1_Affine" or similar
##leave rest at defaults. Click ''Apply''
##registration should take ~ 10 secs.
##use fade slider to verify alignment; compare with result snapshots shown below. Alignment will not be perfect but should be better than before.
##note: you can also change the colormaps for the fixed and moving volumes to better judge the alignment: go to the [[Documentation/Nightly/Modules/Volumes| ''Volumes'']] module and in the ''Display'' tab, select "green" and "magenta" as the respective colormaps for the two volumes (vhf, vhm)
#'''Nonrigid Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']].
##''Fixed/Moving Image Volume'': as above
##Registration phases: uncheck boxes for rigid, scale and affine and check box for ''BSpline''
##Output: Slicer Linear transform: set to None
##Output: Slicer BSpline transform: create new, rename to "Xf2_BSpline" or similar
##Output Image Volume: create new, rename to "Autism_T1_2yrs_Xf2"; ''Pixel Type'': "short"
##Registration Parameters: increase ''Number Of Samples'' to 300,000; ''Number of Grid Subdivisions'': 5,5,5
##Leave all other settings at default
##click apply

== Registration Results==
[[Image:RegLib_C37_unregistered.gif|300px]] baseline and follow-up before registration (click to enlarge) 
[[Image:RegLib_C37_registered_Rigid.gif|300px]] after Rigid alignment. Note the residual shape differences (click to enlarge) 
[[Image:RegLib_C37_registered_Affine.gif|300px]] after Affine registration (click to enlarge) 
[[Image:RegLib_C37_registered_BSpline.gif|300px]]| after nonrigid BSpline registration (click to enlarge) 
[[Image:RegLib_C37_registered_BSplineMasked.gif|300px]]| after nonrigid BSpline registration with masking (click to enlarge)

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 [[Documentation/Nightly/Registration/RegistrationLibrary|Back to Registration Library]]
 = Slicer Registration Library Case #37: <br>Intra-subject Brain MRI:  assessment of brain tumor resection =
 == Input ==
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"

Documentation:Nightly:Registration:RegistrationLibrary:RegLib C37 - Revision history

Meier at 13:42, 4 October 2013

Meier: Created page with 'Back to Registration Library = Slicer Registration Library Case #37: Intra-subject Brain MRI: assessment of brain …'

Meier: Created page with 'Back to Registration Library = Slicer Registration Library Case #37:
Intra-subject Brain MRI: assessment of brain …'