Difference between revisions of "Documentation:Nightly:Registration:RegistrationLibrary:RegLib C40"
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== Input == | == Input == | ||
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" | {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" | ||
| − | |[[Image: | + | |[[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:RegArrow_NonRigid.png|100px|lleft]] | ||
| − | |[[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 | |fixed image/target | ||
| Line 17: | Line 17: | ||
== Download (from NAMIC MIDAS) == | == 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> | <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= | + | *[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= | + | *[http://slicer.kitware.com/midas3/download/?items=119691 '''RegLib_C40_full.mrb''']<br><small>(input data + results, Slicer mrb file. 100 MB). </small> |
== Description == | == Description == | ||
| Line 25: | Line 25: | ||
=== Keywords === | === Keywords === | ||
micro-CT, deformation modeling | micro-CT, deformation modeling | ||
| + | |||
| + | == Video Screencasts == | ||
| + | #[[Media:RegLib_C40.mov|Movie/screencast showing registration steps]] | ||
== Procedure == | == Procedure == | ||
| Line 41: | Line 44: | ||
##Output: Slicer Linear transform: set to None | ##Output: Slicer Linear transform: set to None | ||
##Output: Slicer BSpline transform: create new, rename to "Xf2_BSpline" or similar | ##Output: Slicer BSpline transform: create new, rename to "Xf2_BSpline" or similar | ||
| − | ##Output Image Volume: create new, rename to "sample2_Xf2 | + | ##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 | ##Registration Parameters: increase ''Number Of Samples'' to 300,000; ''Number of Grid Subdivisions'': 5,5,5 | ||
##Leave all other settings at default | ##Leave all other settings at default | ||
| Line 50: | Line 53: | ||
[[Image:RegLib_C40_registered_Affine.gif|300px]] after affine alignment. Note the residual shape differences (click to enlarge) <br> | [[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_C40_registered_BSpline.gif|300px]] after nonrigid BSpline registration (click to enlarge) <br> | ||
| − | [[Image: | + | [[Image:RegLib_C40_DeformationOnly.gif|300px]]| visualization of the nonrigid deformation component only <br> |
| + | |||
| + | ==Acknowledgments == | ||
| + | Registration problem and dataset kindly provided by Alessandra Patera from the [http://www.ethz.ch/index_EN Swiss Federal Institute of Technology (ETHZ)] in collaboration with the [http://www.empa.ch/ Swiss Federal Laboratories for Material Science and Technology (EMPA)]. | ||
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Latest revision as of 21:02, 2 October 2013
Home < Documentation:Nightly:Registration:RegistrationLibrary:RegLib C40Contents
Slicer Registration Library Case #40:
micro-CT of material wood sample
Input
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|
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| fixed image/target | moving image |
Modules used
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.
- RegLib_C40.mrb
(input data only, Slicer mrb file. 40 MB) - 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
Video Screencasts
Procedure
- Affine Registration: open the 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 Volumes module and in the Display tab, select "green" and "magenta" as the respective colormaps for the two volumes.
- Nonrigid Registration: open the 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"
- 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
baseline and follow-up before registration (click to enlarge)
after affine alignment. Note the residual shape differences (click to enlarge)
after nonrigid BSpline registration (click to enlarge)
| visualization of the nonrigid deformation component only
Acknowledgments
Registration problem and dataset kindly provided by Alessandra Patera from the Swiss Federal Institute of Technology (ETHZ) in collaboration with the Swiss Federal Laboratories for Material Science and Technology (EMPA).
