Documentation:Nightly:Registration:RegistrationLibrary:RegLib C12 - Revision history

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

2019-11-27T02:34:02Z

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

Meier: /* Description */

2014-06-24T20:14:32Z

Description

Meier: /* Description */

2014-06-24T20:10:28Z

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Meier at 20:04, 24 June 2014

2014-06-24T20:04:27Z

Meier: /* Description */

2013-08-28T18:31:19Z

Description

Meier at 18:28, 28 August 2013

2013-08-28T18:28:46Z

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

2013-06-30T19:02:54Z

Download (from NAMIC MIDAS)

Meier at 19:02, 30 June 2013

2013-06-30T19:02:02Z

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

2013-06-30T18:56:57Z

Download (from NAMIC MIDAS)

Meier at 18:55, 30 June 2013

2013-06-30T18:55:40Z

@@ Line 53: / Line 53: @@
 #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 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.
-'''[[Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C12a|Click here for older version (4.3.1)]]'''
+'''[[Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C12a|Click here for alternate version, demonstrating the use of nested transforms (isolating nonrigid portion)]]'''
 == Modules used ==

@@ 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.
-'''[[RegistrationLibrary:RegLib_C12a|Click here for older version (4.3.1)]]'''
+'''[[Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C12a|Click here for older version (4.3.1)]]'''
 == Modules used ==

@@ Line 17: / Line 17: @@
 We have a pre-operative MRI and an intra-operative CT. We wish to align the MRI to the CT to aid in guiding the surgical intervention. Tumor visibility is much better on the MRI, hence a properly registered MRI can help locate the tumor during the intervention. <br>
 '''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.
 == Modules used ==

@@ Line 16: / Line 16: @@
 == Description ==
 We have a pre-operative MRI and an intra-operative CT. We wish to align the MRI to the CT to aid in guiding the surgical intervention. Tumor visibility is much better on the MRI, hence a properly registered MRI can help locate the tumor during the intervention. <br>
-'''Approach'':
+'''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.
 == Modules used ==
 * [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]

@@ Line 19: / Line 19: @@
 == 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=103479 '''RegLib_12.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 35 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=103749 '''RegLib_12.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 35 MB). </small>]
 *[http://slicer.kitware.com/midas3/download/?items=103748 '''RegLib_C12_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 68 MB). </small>]

@@ Line 1: / Line 1: @@
 [[Documentation/Nightly/Registration/RegistrationLibrary|Back to Registration Library]] <br>
-== Slicer Registration Library Case #12:  Liver Tumor Cryoablation ==
+= Slicer Registration Library Case #12:  Liver Tumor Cryoablation =
-=== Input ===
+== Input ==
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
 |[[Image:RegLib_C12_Thumb1.png|150px|lleft|this is a pre-op CT + contrast reference image. All images are aligned into this space]]
@@ Line 14: / Line 14: @@
 |}
-=== Slicer4 Modules used ===
+== Modules used ==
 * [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
@@ Line 23: / Line 23: @@
 == Video Screencasts ==
-#[[Media:RegLib_C12.mov|Movie/screencast showing registration Case #12]]
+#[[Media:RegLib_C12.mov|Movie/'''screencast showing registration Case #12''']]
-===Objective / Background ===
+==Objective / Background ==
 We seek to align a pre-operative MRI with a contrast enhanced CT for surgical guidance.
-=== Keywords ===
+== Keywords ==
 MRI, CT, IGT, intra-operative, liver, cryoablation, change detection, non-rigid registration
-===Input Data===
+==Input Data==
 *reference/fixed :  pr-op CT, 0.95 x 0.95 x 5 mm voxel size
 *moving:  intra-op MRI, 0.78 x 0.78 x 2.5 mm  axial,
-=== Procedures ===
+== 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 87: / Line 87: @@
 ##click: Apply
-=== Registration Results===
+== Registration Results <small>(click to enlarge) </small>==
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
 |[[Image:RegLib_C12_unregistered.gif|300px|left|unregistered MRI & CT]]