Documentation:Nightly:Registration:RegistrationLibrary:RegLib C40 - Revision history

Meier: /* Download (from NAMIC MIDAS) */

2013-10-02T21:02:35Z

Download (from NAMIC MIDAS)

Meier: /* Procedure */

2013-10-02T21:02:05Z

Procedure

Meier at 21:01, 2 October 2013

2013-10-02T21:01:30Z

Meier at 21:00, 2 October 2013

2013-10-02T21:00:46Z

Meier: /* Input */

2013-10-02T20:57:23Z

Input

Meier: /* Registration Results */

2013-10-02T20:57:10Z

Registration Results

Meier: Created page with 'Back to Registration Library = Slicer Registration Library Case #40:
micro-CT of material wood sample = == Input ==…'

2013-10-02T20:54:08Z

Created page with 'Back to Registration Library = Slicer Registration Library Case #40: micro-CT of material wood sample = == Input ==…'

New page

[[Documentation/Nightly/Registration/RegistrationLibrary|Back to Registration Library]]
= Slicer Registration Library Case #40: micro-CT of material wood sample =
== Input ==
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C42_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_C42_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_C40.mrb'''] (input data only, Slicer mrb file. 40 MB) 
*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C40_full.mrb'''] (input data + results, Slicer mrb file. 100 MB). 

== Description ==
We have 2 micro-CT scans of a material (wood) sample under different environmental conditions (e.g. moisture). We seek to use a nonrigid registration to capture and model the structural changes (deformations) that occur when conditions change. We register the two volumes to eachother and then interpret the deformation in this registration as a surrogate of the change that occurred.

=== Keywords ===
micro-CT, deformation modeling

== Procedure ==
#'''Affine Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']] module.
##''Fixed Image Volume'': "sample1"
##''Moving Volume'': "sample2"
##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.
#'''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 "sample2_Xf2"; ''Pixel Type'': "unsigned 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_C40_unregistered.gif|300px]] baseline and follow-up before registration (click to enlarge) 
[[Image:RegLib_C40_registered_Affine.gif|300px]] after affine alignment. Note the residual shape differences (click to enlarge) 
[[Image:RegLib_C40_registered_BSpline.gif|300px]] after nonrigid BSpline registration (click to enlarge) 
[[Image:RegLib_C42_DeformationOnly.gif|300px]]| visualization of the nonrigid deformation component only

@@ Line 17: / Line 17: @@
 == Download (from NAMIC MIDAS) ==
 <small>''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. ''</small>
-*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C40.mrb'''] <br><small>(input data only, Slicer mrb file. 40 MB) </small><br>
+*[http://slicer.kitware.com/midas3/download/?items=119692 '''RegLib_C40.mrb'''] <br><small>(input data only, Slicer mrb file. 40 MB) </small><br>
-*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C40_full.mrb''']<br><small>(input data + results, Slicer mrb file. 100 MB). </small>
+*[http://slicer.kitware.com/midas3/download/?items=119691 '''RegLib_C40_full.mrb''']<br><small>(input data + results, Slicer mrb file. 100 MB). </small>
 == Description ==

@@ Line 51: / Line 51: @@
 [[Image:RegLib_C40_registered_BSpline.gif|300px]] after nonrigid BSpline registration (click to enlarge) <br>
 [[Image:RegLib_C40_DeformationOnly.gif|300px]]| visualization of the nonrigid deformation component only <br>
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 comment
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@@ Line 50: / Line 50: @@
 [[Image:RegLib_C40_registered_Affine.gif|300px]] after affine alignment. Note the residual shape differences (click to enlarge) <br>
 [[Image:RegLib_C40_registered_BSpline.gif|300px]] after nonrigid BSpline registration (click to enlarge) <br>
-[[Image:RegLib_C42_DeformationOnly.gif|300px]]| visualization of the nonrigid deformation component only <br>
+[[Image:RegLib_C40_DeformationOnly.gif|300px]]| visualization of the nonrigid deformation component only <br>
 <!--
 comment
 -->

@@ Line 44: / Line 44: @@
 ##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 "sample2_Xf2"; ''Pixel Type'': "unsigned short"
+##Output Image Volume:  create new, rename to "sample2_Xf2"
 ##Registration Parameters: increase ''Number Of Samples'' to 300,000; ''Number of Grid Subdivisions'': 5,5,5
 ##Leave all other settings at default

@@ Line 25: / Line 25: @@
 === Keywords ===
 micro-CT, deformation modeling
 == Procedure ==

@@ Line 3: / Line 3: @@
 == Input ==
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C42_Thumb1.png|150px|lleft|this is the fixed reference image. All images are aligned into this space]]
+|[[Image:RegLib_C40_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_C42_Thumb2.png|150px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]]
+|[[Image:RegLib_C40_Thumb2.png|150px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]]
 |-
 |fixed image/target