Documentation:Nightly:Registration:RegistrationLibrary:RegLib C12a - Revision history

Grundlett: Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:23:10Z

Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Meier: /* Procedures */

2014-06-24T21:02:06Z

Procedures

Meier at 21:00, 24 June 2014

2014-06-24T21:00:14Z

Meier: /* Procedures */

2014-06-24T20:31:20Z

Procedures

Meier at 20:28, 24 June 2014

2014-06-24T20:28:35Z

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

2014-06-24T20:21:00Z

Download (from NAMIC MIDAS)

Meier at 20:16, 24 June 2014

2014-06-24T20:16:00Z

Meier: /* Description */

2014-06-24T20:10:43Z

Description

Meier: moved RegistrationLibrary:RegLib C12a to Documentation:Nightly:Registration:RegistrationLibrary:RegLib C12a

2014-06-24T20:09:51Z

moved RegistrationLibrary:RegLib C12a to Documentation:Nightly:Registration:RegistrationLibrary:RegLib C12a

Meier: /* Description */

2014-06-24T20:08:53Z

Description

@@ Line 57: / Line 57: @@
 #select the ''Dilate'' tool and click ''Apply'' 3-4 times to extend the mask area
 #repeat for both masks
-#In the  [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 ''Editor'' module], use the ''Dilate'' function to expand the outline by 2-3 pixels (click on ''Apply'' button 2-3 times)
+#In the  [[Modules:Editor-Documentation-3.6|''Editor'' module]], use the ''Dilate'' function to expand the outline by 2-3 pixels (click on ''Apply'' button 2-3 times)
 #save dilated labelmasks under new name (e.g. CT_mask.nrrd)
 *'''Phase II: MR-CTpre registration''' (Affine)

@@ Line 106: / Line 106: @@
 ##click: Apply
 *'''Phase V: Nested Transforms'''
-##We now have the 2 main transforms: "Xf1_Affine" and "Xf2_BSplineOnly". Together they form the full alignment.
+#We now have the 2 main transforms: "Xf1_Affine" and "Xf2_BSplineOnly". Together they form the full alignment.
 ##drag the volume "MRI_Xf1" volume into the transform "Xf2_BSplineOnly". You should see the views update immediately.
 ##to generate a resampled version, you can apply the same function as for the affine transform, i.e. right-click + ''Harden Transform''
@@ Line 113: / Line 113: @@
 ###reload the original volume "MRI"
 ###place it inside the "Xf1_Affine" transform
-###place the entire "Xf1_Affine" struct (including the MRI volume within) onto the "Xf2_BSplineOnly" transform. Your structure should now look like this: [[Image:RegLib_C12_NestedTransforms.png|100px|left|nested transforms]]
+###place the entire "Xf1_Affine" struct (including the MRI volume within) onto the "Xf2_BSplineOnly" transform. Your structure should now look like the image on the right: [[Image:RegLib_C12_NestedTransforms.png|200px|right|nested transforms]]
 ###again to resample select "Harden Transform". Note that while hardening a linear (e.g. Affine) transform can be done without resampling, the hardening of nonlinear transforms like a BSpline '''does''' require a resampling. Hence you will notice a slight delay before the "MRI" node is placed back onto the main level.
 ###note that currently only limited combinations of Affine + BSpline nesting are supported, e.g. you cannot (yet) nest multiple BSplines together using this function.
 *'''Phase VI: Transform Visualizer'''
-##significant additions to visualize transforms have been added recently.
+#significant additions to visualize transforms have been added recently.
 #open the  [[Documentation/Nightly/Modules/Transforms|''Transforms'' module]]
 ##under ''Active Transforms'', select "Xf2_BSplineOnly"
@@ Line 124: / Line 124: @@
 ##under the ''Colors'' tab you can control the color coding, and under the ''Advanced'' tab you can control  size & density, range, icon etc. of the glyphs
 ##see the demo screencasts above for examples on how to visualize the transform
 ##note that to visualize a deformation effectively, it should not contain an linear (rigid, affine) portion, because that quickly dominates the field and makes deformations hard to see. That's the main motivation for separating the affine and BSpline transforms the way we did in the above workflow.
 == Registration Results <small>(click to enlarge) </small>==

@@ Line 44: / Line 44: @@
 == Procedures ==
-Note that the approach below is different from the original version: here we want to isolate the nonrigid part of the registration from the affine portion, so that we can visualize the deformation only. See the original version above if the main interest is the final aligned image.
+Note that the approach below is different from the original version: here we want to isolate the nonrigid part of the registration from the affine portion, so that we can visualize the deformation only. See the '''[[Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C12|original version]]''' if the main interest is the final aligned image.
 *'''Phase I: Build Masks'''
 : Note: for illustration the example set contains 2 masks: one with only the liver and one also including spleen and kidney (Mask2).  As shown in the results below, the liver-only mask is insufficiently constraining the registration, yielding a result that at first glance looks ok for the liver, but has significant misalignment in the remaining abdominal area. Hence it is advisable to stabilize the registration further by including more structures with good contrast in both images (Spleen, Kidney).
@@ Line 75: / Line 76: @@
 ##click: Apply; runtime < 1 min (MacPro QuadCore 2.4GHz)
 ##this should generate a first alignment.
-*'''Phase III: Nonrigid Registration'''
+*'''Phase III: Prepare for Nonrigid Registration: create Affine aligned volume'''
 #open the  [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
 ##''Fixed Image Volume'': CT
-##''Moving Image Volume'': MRI
+##''Moving Image Volume'': MRI_Xf1
 ##Output Settings:
-###''Slicer BSpline Transform": create new transform, rename to "Xf2_BSpline"
+###''Slicer BSpline Transform": create new transform, rename to "Xf2_BSplineOnly"
 ###''Slicer Linear Transform'': none
-###''Output Image Volume'': create new volume,  rename to "MRI_Xf2"
+###''Output Image Volume'': none (we use the new dynamic visualization of BSpline transforms to view the result)
 ##''Initialization'':
-###''Initialization Transform'': select  "Xf1_Affine" created in Phase II above
+###''Initialization Transform'': None (remember that MRI_Xf1 is already in the affine-aligned space)
 ###''Initialization Transform Mode'': Off
 ##''Registration Phases'': check boxes for ''BSpline'' only
@@ Line 92: / Line 102: @@
 ##''Mask Option'': select ''ROI'' button
 ###''(ROI)Masking input fixed'': CT_mask
-###''(ROI)Masking input moving'': MRI_mask
+###''(ROI)Masking input moving'': MRI_mask_Xf1 (remember to use the aligned mask, not the original one)
 ##Leave all other settings at default
 ##click: Apply
 == Registration Results <small>(click to enlarge) </small>==

@@ Line 44: / Line 44: @@
 == Procedures ==
 *'''Phase I: Build Masks'''
 : Note: for illustration the example set contains 2 masks: one with only the liver and one also including spleen and kidney (Mask2).  As shown in the results below, the liver-only mask is insufficiently constraining the registration, yielding a result that at first glance looks ok for the liver, but has significant misalignment in the remaining abdominal area. Hence it is advisable to stabilize the registration further by including more structures with good contrast in both images (Spleen, Kidney).

@@ Line 1: / Line 1: @@
 [[Documentation/Nightly/Registration/RegistrationLibrary|Back to Registration Library]] <br>
-= Slicer Registration Library Case #12a:  Liver Tumor Cryoablation (alternat version using nested transforms)  =
+= Slicer Registration Library Case #12a:  Liver Tumor Cryoablation (alternate version using nested transforms)  =
 == Input ==
@@ Line 28: / Line 28: @@
 == Video Screencasts ==
-#[[Media:RegLib_C12.mov|Movie/'''screencast showing registration Case #12''']]
+#[[Media:RegLib_C12a_1_Registration.mov|Movie/'''screencast showing registration (affine + BSpline) for Case #12a''']]
 ==Objective / Background ==

@@ Line 25: / Line 25: @@
 == 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=103748 '''RegLib_C12a.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 36 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=142765 '''RegLib_C12a.mrb''': includes raw data + masks + transforms <small>(Slicer mrb file. 34 MB). </small>]
 == Video Screencasts ==

@@ Line 18: / Line 18: @@
 '''Approach''': we seek a non-rigid registration of the MRI to the CT. Because contrast and image content are very different, we must first build masks to guide the registration process onto the structures of interest. We then obtain the registration in 2 steps: we first compute an affine registration to test stability and feasibility of our masks. Once successful we use this registration as starting point for a BSpline non-rigid transform.<br>
-'''[[RegistrationLibrary:RegLib_C12|Click here for newer version using dynamic visualization of nonrigid transforms]]'''
+'''[[Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C12|Click here for newer version using dynamic visualization of nonrigid transforms]]'''
 == Modules used ==

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