Projects:RegistrationLibrary:RegLib C47 - Revision history

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

2017-07-10T18:07:15Z

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

Meier: /* Download */

2012-05-09T20:54:16Z

Download

Meier at 20:53, 9 May 2012

2012-05-09T20:53:37Z

Meier: /* Registration Results */

2012-05-09T20:52:31Z

Registration Results

Meier: /* Registration Results */

2012-05-09T20:52:05Z

Registration Results

Meier: /* Procedures */

2012-05-09T20:50:39Z

Procedures

Meier: /* Procedures */

2012-05-09T20:49:50Z

Procedures

Meier: /* Procedures */

2012-05-09T20:48:19Z

Procedures

Meier: /* Discussion: Registration Challenges */

2012-05-09T20:47:18Z

Discussion: Registration Challenges

Meier at 20:46, 9 May 2012

2012-05-09T20:46:42Z

Show changes

@@ Line 16: / Line 16: @@
 === Slicer4 Modules used ===
-*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BrainsFit]'''
+*[https://www.slicer.org/wiki/Documentation/4.1/Modules/BRAINSFit BrainsFit]'''
 ===Objective / Background ===
@@ Line 40: / Line 40: @@
 *'''Phase I: MR-CTpre registration'''
 #Following the concept of manual registration, we create an initial transform that roughly aligns the MR to the pre-op CT.
-#open  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]''' module
+#open  [https://www.slicer.org/wiki/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]''' module
 ##''Input Images''
 ###''Fixed Image Volume'': CT_intraop
@@ Line 51: / Line 51: @@
 ##Leave all other settings at default
 ##click: ''Apply''
-#switch to the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Data Data module]
+#switch to the  [https://www.slicer.org/wiki/Documentation/4.1/Modules/Data Data module]
 ##click on the "MRI_intra" node, and drag it onto the transform node "Xf1_MRI-CT_Affine" created above
 #this should yield a rough alignment as shown in the result section below. We will use this to initialize a more refined nonrigid registration
 *'''Phase II:  nonrigid registration'''
-#open  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]'''module
+#open  [https://www.slicer.org/wiki/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]'''module
 ##''Input Images'':
 ###''Fixed Image Volume'': CT_intraop

@@ Line 22: / Line 22: @@
 ===Download ===
-*[[Media:RegLib_C47_Data.zip|'''download input image data'''  <small> (Input Data, NRRD images,  zip file 42 MB) </small>]]
+*[[Media:RegLib_C47_Data.zip|'''download RegLib_C47 input image data'''  <small> (NRRD images, transforms, Slicer Scene File,  zip file 52 MB) </small>]]
 === Keywords ===

@@ Line 20: / Line 20: @@
 ===Objective / Background ===
 We seek to align a pre-operative MRI with the intra-operative CT for surgical guidance.
 === Keywords ===
@@ Line 85: / Line 88: @@
 |}
 === Acknowledgments ===
 Thanks to Dr.Stuart Silverman and Dr. Nobuhiko Hata for sharing this case.

@@ Line 70: / Line 70: @@
 ##click: ''Apply''
-=== Registration Results===
+=== Registration Results (click to enlarge) ===
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
 |[[Image:RegLib_C47_unregistered.gif|300px|left|unregistered MRI & CT]]

@@ Line 78: / Line 78: @@
 |after linear (affine) registration
 |-
-|[[Image:RegLib_C47_BSPline.gif|300px|left|after nonrigid registration]]
+|[[Image:RegLib_C47_BSpline.gif|300px|left|after nonrigid registration]]
 |after nonrigid registration
 |-

@@ Line 50: / Line 50: @@
 #switch to the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Data Data module]
 ##click on the "MRI_intra" node, and drag it onto the transform node "Xf1_MRI-CT_Affine" created above
-##this should yield a rough alignment as shown in the result section below. We will use this to initialize a more refined nonrigid registration
+#this should yield a rough alignment as shown in the result section below. We will use this to initialize a more refined nonrigid registration
 *'''Phase II:  nonrigid registration'''
 #open  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]'''module
@@ Line 61: / Line 61: @@
 ###''Output Image Volume'' create new volume, rename to "MRI_Xf2"
 ##''Initialization'':
-##''Initialization transform'': select "" created in phase 1 above
+###''Initialization transform'': select "" created in phase 1 above
-##''Initialize Transform Mode'': Off
+###''Initialize Transform Mode'': Off
 ##''Registration Phases'':  select/check ''BSpline'' only
 ##''Main Parameters'':
-##''Number Of Samples'': 200,000
+###''Number Of Samples'': 200,000
-## ''B-Spline Grid Size'': 7,7,5
+### ''B-Spline Grid Size'': 7,7,5
 ##Leave all other settings at default
 ##click: ''Apply''

@@ Line 42: / Line 42: @@
 ###''Moving Image Volume'': MRI_preop
 ##''Output Settings'':
-###''Slicer BSpline Transform'' none
+###''Slicer BSpline Transform'': none
-###''Slicer Linear Transform'' (create new transform, rename to: "Xf1_MRI-CT_Affine")
+###''Slicer Linear Transform'': (create new transform, rename to: "Xf1_MRI-CT_Affine")
-###''Output Image Volume'' none
+###''Output Image Volume'': none
 ##''Registration Phases'':  select/check ''Rigid'' , ''Rigid+Scale'', ''Affine''
 ##Leave all other settings at default
@@ Line 53: / Line 53: @@
 *'''Phase II:  nonrigid registration'''
 #open  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]'''module
-##''Input Images''
+##''Input Images'':
 ###''Fixed Image Volume'': CT_intraop
 ###''Moving Image Volume'': MRI_preop
 ##''Output Settings'':
-###''Slicer BSpline Transform''  (create new transform, rename to: "Xf2_MRI-CT_BSpline")
+###''Slicer BSpline Transform'': (create new transform, rename to: "Xf2_MRI-CT_BSpline")
-###''Slicer Linear Transform'' none
+###''Slicer Linear Transform'': none
 ###''Output Image Volume'' create new volume, rename to "MRI_Xf2"
-##''Initialization''
+##''Initialization'':
 ##''Initialization transform'': select "" created in phase 1 above
-##'''Initialize Transform Mode'': Off
+##''Initialize Transform Mode'': Off
 ##''Registration Phases'':  select/check ''BSpline'' only
-##''Main Parameters''
+##''Main Parameters'':
 ##''Number Of Samples'': 200,000
 ## ''B-Spline Grid Size'': 7,7,5

@@ Line 32: / Line 32: @@
 *strong differences in image contrast between MRI & CT
 *we have strongly anisotropic voxel sizes with much less through-plane resolution
-*[[Projects:RegistrationLibrary:RegLib_C47 there is a related example for pre-operative contrast CT to MRI here]]
+*[[Projects:RegistrationLibrary:RegLib_C12|there is a related example for pre-operative contrast CT to MRI in Library Case #12]]
 === Procedures ===
 *'''Phase I: MR-CTpre registration'''