Documentation:Nightly:Registration:RegistrationLibrary:RegLib C44 - Revision history

Meier: /* Input */

2013-10-01T18:14:06Z

Input

Meier: /* Input */

2013-10-01T18:13:55Z

Input

Meier: /* Procedure / Pipeline */

2013-10-01T17:02:23Z

Procedure / Pipeline

Meier: /* Registration Results */

2013-10-01T17:01:03Z

Registration Results

Meier: /* Registration Results */

2013-10-01T17:00:16Z

Registration Results

Meier: /* Registration Results */

2013-10-01T16:58:47Z

Registration Results

Meier: /* Procedure / Pipeline */

2013-10-01T16:57:26Z

Procedure / Pipeline

Meier: /* Procedure / Pipeline */

2013-10-01T16:57:11Z

Procedure / Pipeline

Meier: /* Procedure / Pipeline */

2013-10-01T16:56:13Z

Procedure / Pipeline

Meier at 16:55, 1 October 2013

2013-10-01T16:55:04Z

@@ Line 4: / Line 4: @@
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
 |[[Image:RegLib_C44_Thumb1.png|150px|lleft|this is the main fixed reference image. All images are ev. aligned into this space]]
-|[[Image:RegArrow_Nonrigid.png|70px|lleft]]
+|[[Image:RegArrow_NonRigid.png|70px|lleft]]
 |[[Image:RegLib_C44_Thumb2.png|150px|lleft|this is the moving image]]
 |-

@@ Line 4: / Line 4: @@
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
 |[[Image:RegLib_C44_Thumb1.png|150px|lleft|this is the main fixed reference image. All images are ev. aligned into this space]]
-|[[Image:RegArrow_Affine.png|70px|lleft]]
+|[[Image:RegArrow_Nonrigid.png|70px|lleft]]
 |[[Image:RegLib_C44_Thumb2.png|150px|lleft|this is the moving image]]
 |-

@@ Line 69: / Line 69: @@
 ##click apply
 #'''Deformation Visualization''':  [[Media:RegLib_C44_3_Deformation.mov|Movie/screencast showing this step]]
-##if you have not yet installed the [[Documentation/Nightly/Modules/DeformationFieldVisualizer| ''Deformation Field Visualizer'']] extension, see [[here]] for a movie clip on how to install it.
+##if you have not yet installed the [[Documentation/Nightly/Modules/DeformationFieldVisualizer| ''Deformation Field Visualizer'']] extension, [[Documentation/Nightly/RegistrationVideoTutorials#Registration_Validation__How_do_I_check_.2F_visualize_a_registration_result_.3F|see here]] for a movie clip on how to install it.
 ##we first generate a smaller version of our image to save memory:
 ###open the '''Resize Image (BRAINS)''' module (under Registration)

@@ Line 86: / Line 86: @@
 == Registration Results==
 [[Image:RegLib_C44_unregistered.gif|400px|original unregistered]] unregistered <br>
 [[Image:RegLib_C44_registered_noMask.gif|400px|registered (nonrigid w/o masking)]] registered  (nonrigid w/o masking)<br>
 [[Image:RegLib_C44_registered_withMask.gif|400px|registered (nonrigid+masking)]] registered (nonrigid+masking)<br>
 [[Image:RegLib_C44_deformOnly.gif|400px|deformation only of vhf]] registered deformation only of vhf<br>
 [[Image:RegLib_C44_DeformationGrid.png|400px|deformation grid]] deformation visualized by grid image overlay <br>
 == Acknowledgments ==
 Original CT from the [https://mri.radiology.uiowa.edu/visible_human_datasets.html '''Visible Human Project'''] shared by the University of Iowa.

@@ Line 86: / Line 86: @@
 == Registration Results==
 [[Image:RegLib_C44_unregistered.gif|400px|original unregistered]] unregistered <br>
 [[Image:RegLib_C44_registered_noMask.gif|400px|registered (nonrigid w/o masking)]] registered  (nonrigid w/o masking)<br>
 [[Image:RegLib_C44_registered_withMask.gif|400px|registered (nonrigid+masking)]] registered (nonrigid+masking)<br>
 [[Image:RegLib_C44_deformOnly.gif|400px|deformation only of vhf]] registered deformation only of vhf<br>
 [[Image:RegLib_C44_DeformationGrid.png|400px|deformation grid]] deformation visualized by grid image overlay <br>
 == Acknowledgments ==
 Original CT from the [https://mri.radiology.uiowa.edu/visible_human_datasets.html '''Visible Human Project'''] shared by the University of Iowa.

@@ Line 71: / Line 71: @@
 ##if you have not yet installed the [[Documentation/Nightly/Modules/DeformationFieldVisualizer| ''Deformation Field Visualizer'']] extension, see [[here]] for a movie clip on how to install it.
 ##we first generate a smaller version of our image to save memory:
-###open the '''Resize Image (BRAINS)'''module (under Registration)
+###open the '''Resize Image (BRAINS)''' module (under Registration)
 ###''Image To Warp'': select "vhf"
 ###''Output Image'': create new, rename to "vhf_small" or similar

@@ Line 33: / Line 33: @@
 == Procedure / Pipeline ==
-#'''Mask generation''': open the [[Documentation/Nightly/Modules/Editor|''Editor'' module]]. [[Media:RegLib_C44_1_Masking.mov|Movie/screencast showing this step]]
+#'''Mask generation''': open the [[Documentation/Nightly/Modules/Editor|''Editor'']] module. [[Media:RegLib_C44_1_Masking.mov|Movie/screencast showing this step]]
 ##"Master Volume": select ''vhm''
 ##A new labelmap "vhm-label" will be created
@@ Line 48: / Line 48: @@
 ##repeat the above for "vhf".
 ##save the two segmentations.
-#'''Affine Registration''': open the  [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]. [[Media:RegLib_C44_2_Registration.mov|Movie/screencast showing this step]]
+#'''Affine Registration''': open the  [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']] module. [[Media:RegLib_C44_2_Registration.mov|Movie/screencast showing this step]]
 ##''Fixed Image Volume'': vhm
 ##''Moving Volume'': vhf

@@ Line 33: / Line 33: @@
 == Procedure / Pipeline ==
-#'''Mask generation''': open the [[Documentation/Nightly/Modules/Editor|''Editor'' module]]
+#'''Mask generation''': open the [[Documentation/Nightly/Modules/Editor|''Editor'' module]]. [[Media:RegLib_C44_1_Masking.mov|Movie/screencast showing this step]]
 ##"Master Volume": select ''vhm''
 ##A new labelmap "vhm-label" will be created
@@ Line 40: / Line 40: @@
 ##Adjust the lower threshold (slider bar) until most of the bone is highlighted,just before speckle noise starts to become included e.g. somewhere around an intensity value of 80. Leave the upper threshold unchanged at the max.
 ##Click Apply
-##Morphologically clean the segmentation:
+##clean the segmentation:
 ##Select the "Identify Islands" editor effect. [[Image:IdentifyIslandsEffectIcon.png|30px]] This will identify all continuous areas that are disconnected from each other. Click "Apply"
 ##you should see the bones of the arms being assigned a different label value & color. We can now delete them with one click:
@@ Line 48: / Line 48: @@
 ##repeat the above for "vhf".
 ##save the two segmentations.
-#'''Affine Registration''': open the  [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]
+#'''Affine Registration''': open the  [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]. [[Media:RegLib_C44_2_Registration.mov|Movie/screencast showing this step]]
-###''Fixed Image Volume'': vhm
+##''Fixed Image Volume'': vhm
-###''Moving Volume'': vhf
+##''Moving Volume'': vhf
-###check boxes for ''Include Rigd registr. phase'' , ''Include ScaleVersor3D'', ''include Affine''
+##check boxes for ''Include Rigd registr. phase'' , ''Include ScaleVersor3D'', ''include Affine''
-###''Slicer Linear Transform'': select "create new transform", rename to "Xf1_Affine" or similar
+##''Slicer Linear Transform'': select "create new transform", rename to "Xf1_Affine" or similar
-###leave rest at defaults. Click ''Apply''
+##leave rest at defaults. Click ''Apply''
-###registration should take ~ 10 secs.
+##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.
+##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)
+##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)
-#'''Affine Registration (masked)''': open the  [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]
+#'''Nonrigid Registration (masked)''': open the  [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]. [[Media:RegLib_C44_2_Registration.mov|Movie/screencast showing this step]]
-##Go to the [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]
+##''Fixed Image Volume'': vhm ''Moving'': vhf
 ##Registration phases: from ''Initialize with previously generated transform', select "Xf1_Affine" node created before.
 ##Registration phases: uncheck boxes for rigid, scale and affine and check box for  ''BSpline''
@@ Line 69: / Line 68: @@
 ##Leave all other settings at default
 ##click apply
-#'''Deformation Visualization''': open the
+#'''Deformation Visualization''':  [[Media:RegLib_C44_2_Deformation.mov|Movie/screencast showing this step]]
 ##if you have not yet installed the [[Documentation/Nightly/Modules/DeformationFieldVisualizer| ''Deformation Field Visualizer'']] extension, see [[here]] for a movie clip on how to install it.
 ##we first generate a smaller version of our image to save memory:
 ###open the [[Documentation/Nightly/Modules/BRAINSResize| ''Resize Image (BRAINS)'']] module (under Registration)
-##''Image To Warp'': select "vhf"
+###''Image To Warp'': select "vhf"
-##''Output Image'': create new, rename to "vhf_small" or similar
+###''Output Image'': create new, rename to "vhf_small" or similar
-##''Pixel Type'': select "short"
+###''Pixel Type'': select "short"
-##''Scale Factor'': leave at 2.0
+###''Scale Factor'': leave at 2.0
-##click ''Apply''
+###click ''Apply''
-#open the [[Documentation/Nightly/Modules/DeformationFieldVisualizer| ''Transform Visualizer'']]  module (under: All Modules)
+##open the [[Documentation/Nightly/Modules/DeformationFieldVisualizer| ''Transform Visualizer'']]  module (under: All Modules)
-##Deformation: select "Xf2_BSpline"
+###Deformation: select "Xf2_BSpline"
-##Reference Image: select "vhf_small" generated above
+###Reference Image: select "vhf_small" generated above
-##Visualization mode: click on "Grid Slice"
+###Visualization mode: click on "Grid Slice"
-##Grid Slice Options: Slice: red; Spacing: 20mm
+###Grid Slice Options: Slice: red; Spacing: 20mm
-##Click Apply. you should see the deformation field overlay. Adjust slice, spacing etc. to taste.
+###Click Apply. you should see the deformation field overlay. Adjust slice, spacing etc. to taste.
 == Registration Results==