Projects:RegistrationLibrary:RegLib C40 - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T17:13:36Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Meier: /* Procedures */

2011-03-31T22:26:28Z

Procedures

Meier: /* Procedures */

2011-03-31T22:26:07Z

Procedures

Meier at 22:15, 31 March 2011

2011-03-31T22:15:25Z

Meier at 22:13, 31 March 2011

2011-03-31T22:13:53Z

Meier: /* Registration Results */

2011-03-31T22:06:59Z

Registration Results

Meier: /* Registration Results */

2011-03-31T22:05:39Z

Registration Results

Meier at 22:05, 31 March 2011

2011-03-31T22:05:05Z

Meier at 22:03, 31 March 2011

2011-03-31T22:03:14Z

Meier at 21:57, 31 March 2011

2011-03-31T21:57:33Z

@@ Line 18: / Line 18: @@
 === Modules ===
 '''Slicer 3.6.1''' recommended modules:
-*[http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]
+*[https://www.slicer.org/wiki/Modules:BRAINSFit BrainsFit]
-*[http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume-Documentation-3.6 Resampling Module]
+*[https://www.slicer.org/wiki/Modules:ResampleVolume-Documentation-3.6 Resampling Module]
 ===Objective / Background ===
@@ Line 49: / Line 49: @@
 ::The original images are 350MB each and not included in the example set, since for the purpose of registration the subsampled smaller versions are equivalent. We subsample to the sizes below:
 #Load original images
-#Go to [http://www.slicer.org/slicerWiki/index.php/Modules:Volumes-Documentation-3.6 ''Volumes''] module
+#Go to [https://www.slicer.org/wiki/Modules:Volumes-Documentation-3.6 ''Volumes''] module
 ##select ''Info'' tab and record the voxel size and overall dimensions. For this case we have  0.35x0.35x1 mm voxel size and an 1024x1024x200 voxel volume. To reduce this to 256x256 in plane resolution we will increase the voxel size to , 1.4x1.4x1 mm
-#go to [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume-Documentation-3.6 ''Resample Scalar Volume''] module
+#go to [https://www.slicer.org/wiki/Modules:ResampleVolume-Documentation-3.6 ''Resample Scalar Volume''] module
 ##for ''Spacing'' enter 1.41112,1.41112,1 (4 times the original inplane voxel size; through plane we leave unchanged.)
 ##for Interpolation leave linear (default).
 ##''Input volume'': select original image volume (e/g/ 20a_wood) , ''Output Volume'': select "create new" , then select "Rename" and rename to "20a_wood_sub2" or similar
 ##Click ''Apply''
-##Go back to the [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 ''Data''] module.
+##Go back to the [https://www.slicer.org/wiki/Modules:Data-Documentation-3.6 ''Data''] module.
 ##you can now delete the original 350MB volume: right click on the node in the tree and select ''Delete Node''
 *'''Phase I:  Register Rigid/Affine'''
-#open [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit ''BrainsFit''] module
+#open [https://www.slicer.org/wiki/Modules:BRAINSFit ''BrainsFit''] module
 #set the parameters below or, if loaded, use presets (''Parameter Set''): BRAINSfit1_Affine
 ##Fixed: "88a_sub2", Moving: "20a_sub2"
@@ Line 71: / Line 71: @@
 ##Click ''Apply''. Registration should take <1 min.
 ##Note: we're not selecting a resampled volume at this point, because the affine transform is only an intermediate step. It is recommended for the first time to do the affine and nonrigid portions separately, so that potential failure of the affine portion can be recognized. If you're confident about the affine step, you can combine both Phase I & II here into a single step. In that case choose the output selections from phase II below.
-#When complete, the algorithm will automatically place the moving volume inside the newly created transformation node. To see this go to the  [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 ''Data''] module.
+#When complete, the algorithm will automatically place the moving volume inside the newly created transformation node. To see this go to the  [https://www.slicer.org/wiki/Modules:Data-Documentation-3.6 ''Data''] module.
 #set to link the 3 slice views
 #Set the fixed image (88a) as background and the moving image (20a) as foreground.
 #use the fade slider to pan between the two images and evaluate the registration quality. To see the original unregistered position, drag the moving image (20a) back out of the transform node (drag on top of "scene" node.
 *'''Phase III:  Register norigid BSpline'''
-#open [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit ''BrainsFit''] module
+#open [https://www.slicer.org/wiki/Modules:BRAINSFit ''BrainsFit''] module
 #open Registration : ''BrainsFit'' module (presets: BRAINSfit3_BSpline_9x9x9
 ##Input Parameters: same as above:Fixed: "88a_sub2", Moving: "20a_sub2"
@@ Line 93: / Line 93: @@
 *'''Phase IV: (optional not included in example dataset)  Resample Original (full size) images''
 #load the full resolution image
-#go to the  [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ''ResampleScalarVectorDWIVolume''] module
+#go to the  [https://www.slicer.org/wiki/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ''ResampleScalarVectorDWIVolume''] module
 ##''Input Volume'': select original full size image (20a_wood)
 ##''Reference Volume": select original full size reference (88a_wood)

@@ Line 98: / Line 98: @@
 ##''Output Volume'': select "Create New Volume" , then "Rename" to "20a_wood_Xf3" or similar
 ##''Transform Parameters'' under ''Transform Node'' select the above final BSpline transform "Xf2_BSpline_9x9x9"
-##''Transforms Order'': make sure that ''output-to-input''' is checked and ''Bulk Transform'' is off
+##''Transforms Order'': make sure that '''output-to-input''' is checked and ''Bulk Transform'' is off
 ##Select desired interpolation type (linear or ws)
 ##Click Apply

@@ Line 91: / Line 91: @@
 ##Leave all other settings at default
 ##Click ''Apply''. Registration should take ~2 min. Note: main optimizer is parallelized; i.e. multi-core CPU systems will benefit greatly in speed.
 === Registration Results===

@@ Line 33: / Line 33: @@
 *subsampled reference/fixed : micro CT , 1.41x1.41x1 mm voxel size, 256x256x200
 *subsampled moving : micro CT , 1.41x1.41x1 mm voxel size, 256x256x200
 === Overall Strategy ===
@@ Line 98: / Line 105: @@
 |}
 ===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)].

@@ Line 22: / Line 22: @@
 ===Objective / Background ===
-We seek a low-DOF nonrigid registration to assess structural changes in the microstructure of the test sample.
+We seek a low-DOF nonrigid registration to assess structural changes in the microstructure of the test sample. In particular the goal is to characterize the hygromechanical behavior of wood under specific environmental conditions.
 === Keywords ===
 micro CT, serial imaging,  change assessment
@@ Line 104: / Line 104: @@
 **[[Media:RegLib_C40_Presets.mrml‎|'''RegLib_C40_Presets''' Presets for BRAINSFIT registration <small> (.mrml file 16 kB) </small>]]'''
 **[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
+===Acknowledgments ===
 <!--
 comment
 -->

@@ Line 86: / Line 86: @@
 === Registration Results===
 {| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
 |[[Image:RegLib_C40_unreg.gif|400px|center|unregistered]]

@@ Line 6: / Line 6: @@
 === Input ===
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLibC40_Thumb1.png|150px|lleft|sample 1]]
+|[[Image:RegLib_C40_Thumb1.png|150px|lleft|sample 1]]
 |[[Image:RegArrow_NonRigid.png|100px|lleft]]
-|[[Image:RegLibC40_Thumb2.png|150px|lleft|sample 2]]
+|[[Image:RegLib_C40_Thumb2.png|150px|lleft|sample 2]]
 |-
 |fixed image 1/target<br>microCT sample 1

@@ Line 40: / Line 40: @@
 === Procedures ===
 *'''Phase 0:  Subsample to reduce memory usage (not included in example dataset)'''
+::The original images are 350MB each and not included in the example set, since for the purpose of registration the subsampled smaller versions are equivalent. We subsample to the sizes below:
 *'''Phase I:  Register Rigid/Affine'''
 #open Registration : ''BrainsFit'' module (presets: BRAINSfit2_Affine