Projects:RegistrationLibrary:RegLib C07 - Revision history

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

2017-07-10T17:44:21Z

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

Meier: /* Procedures */

2012-08-13T15:35:44Z

Procedures

Meier: /* Download */

2012-08-13T15:35:07Z

Download

Meier: /* Procedures */

2012-08-13T15:34:42Z

Procedures

Meier: /* Procedures */

2012-08-13T15:33:38Z

Procedures

Meier: /* Procedures */

2012-08-13T15:32:51Z

Procedures

Meier: /* Procedures */

2012-08-13T15:21:55Z

Procedures

Meier at 15:21, 13 August 2012

2012-08-13T15:21:12Z

Meier at 14:39, 19 August 2011

2011-08-19T14:39:04Z

Meier: /* Input */

2011-08-19T14:37:00Z

Input

@@ 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:N4ITKBiasFieldCorrection-Documentation-3.6 N4ITKBiasFieldCorrection module]
+**[https://www.slicer.org/wiki/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 N4ITKBiasFieldCorrection module]
-**[http://www.slicer.org/slicerWiki/index.php/Modules:CropVolume-Documentation-3.6 Crop Volume module]
+**[https://www.slicer.org/wiki/Modules:CropVolume-Documentation-3.6 Crop Volume module]
 ===Objective / Background ===

@@ Line 61: / Line 61: @@
 #repeat above for the other image: "Day42_axial"
 *'''Phase II:  Affine Alignment'''
-#go to the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit module]
+#go to the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BRAINSfit module]
 ##Select  ''Fixed Image'' = Day01_axial_n4 and ''Moving Image'' as "Day42_axial_n4"
 ##Output Settings: ''Slicer Linear Transform'': create new linear transform , then rename to "Xf1_Affine" or similar
@@ Line 69: / Line 69: @@
 ##compare results with those shown below
 *'''Phase II:  BSpline Alignment Level 1'''
-#go to the  [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BRAINSfit module]
+#go to the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BRAINSfit module]
 ##Select  ''Fixed Image'' = Day01_axial_n4 and ''Moving Image'' as "Day42_axial_n4"
 ##Initialization Transform: select "Xf1_Affine" (generated above) from the dropdown menu

@@ Line 34: / Line 34: @@
 *Data
 **[[Media:RegLib_C07_Data.zip‎ ‎|'''RegLib_C07_Data''' : original image series, result transforms and images, presets, Slicer Scene  <small> (zip file 18 MB) </small>]]'''
-**[[Media:RegLib_C07_Presets.mrml ‎|'''Parameter Presets''  <small> (.mrml text  file 20 kB file 20 kB) </small>]]'''
+**Slicer 3.6 only: [[Media:RegLib_C07_Presets.mrml ‎|'''Parameter Presets''  <small> (.mrml text  file 20 kB file 20 kB) </small>]]'''
 [[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]

@@ Line 84: / Line 84: @@
 *'''Phase III:  Cropping'''
 #for a more refined alignment of the prostate only we first crop both images to the ROI only
-#go to the [http://www.slicer.org/slicerWiki/index.php/Modules:CropVolume-Documentation-3.6 Crop Volume module]
+#go to the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Crop_Volume Crop Volume module]
 ##''Input Volume'', select "Day_01_axial_n4"
 ##''ROI'': select "New ROI"
@@ Line 96: / Line 96: @@
 *'''Phase IV:  BSpline Alignment Level 2'''
 #you can now perform a second refined alignment on the cropped volumes only
-#first resample the cropped volume with the initial BSpline above. Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ResampleScalarVectorDWIVolume module]
+#first resample the cropped volume with the initial BSpline above. Go to the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ResampleScalarVectorDWIVolume ResampleScalarVectorDWIVolume module]
 ##Select your ""Day42_cropped" volume as input volume and the above "Xf2_BSpline" as input transform
 ##select "Day01_cropped" as reference

@@ Line 53: / Line 53: @@
 *'''Phase I: Bias field correction'''
 #load reference image and one moving image from the series
-#open [http://www.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 N4ITKBiasFieldCorrection module]
+#open [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/N4ITKBiasFieldCorrection N4ITKBiasFieldCorrection module]
 ##select "Day01_axial" as input image, create new "Day1_axial_N4" output image
 ##set ''Iterations'' to 90,60,40

@@ Line 61: / Line 61: @@
 #repeat above for the other image: "Day42_axial"
 *'''Phase II:  Affine Alignment'''
-#go to [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit module]
+#go to the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit module]
 ##Select  ''Fixed Image'' = Day01_axial_n4 and ''Moving Image'' as "Day42_axial_n4"
-##check boxes to include "rigid","scale", "skew" and "affine" registration phases
+##Output Settings: ''Slicer Linear Transform'': create new linear transform , then rename to "Xf1_Affine" or similar
-##increase''Number Of Samples'' to 300,000
+##Registration Phases: check boxes to include "rigid","scale", "skew" and "affine" registration phases (all except last box for BSpline)
-##create new output transform from  ''Slicer Linear Transform'' menu, rename to "Xf1_Affine" or similar
+##''Main Parameters'': increase ''Number Of Samples'' to 300,000
-##click ''Apply''
+##leave rest at defaults and click ''Apply''
 ##compare results with those shown below
 *'''Phase II:  BSpline Alignment Level 1'''
-#go to [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit module]
+#go to the  [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BRAINSfit module]
 ##Select  ''Fixed Image'' = Day01_axial_n4 and ''Moving Image'' as "Day42_axial_n4"
-##check boxes to include "BSpline" registration phase only
+##Initialization Transform: select "Xf1_Affine" (generated above) from the dropdown menu
-##increase''Number Of Samples'' to 300,000
+##Registration Phases: uncheck all boxes and turn on "BSpline" only
-##create new output transform from  ''Slicer BSpline Transform'' menu, rename to "Xf2_BSpline" or similar
+##Output Settings:
-##create new output volume from  ''Output Image Volume'' menu, rename to "Day42_n4_Xf2_BSpline" or similar
+###''Slicer BSpline Transform'' : create new transform, then rename to "Xf2_BSpline" or similar
-##set BSpline Grid size: ''Number of Grid Subdivisions" to 5,5,3
+### ''Output Image Volume'' : create new output volume, then rename to "Day42_n4_Xf2_BSpline" or similar
 ##click ''Apply''
 ##compare results with those shown below
@@ Line 100: / Line 103: @@
 ##click ''Apply''
 ##compare alignment of cropped volumes with results shown below
-#go back to [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit module]
+#go back to the  [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BRAINSfit module]
 ##you can now run a second BSpline with "Day01_cropped" as fixed and "Day42_cropped_Xf2" as moving volume
 ##set BSpline grid to 5,5,5

@@ Line 3: / Line 3: @@
 [[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br>
-==<small>v3.6.3</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case #07: Prostate MRI follow-up ==
+== <small>updated for '''v4.1'''</small> [[Image:Slicer4_RegLibLogo.png|150px]]  Slicer Registration Library Case #07: Prostate MRI follow-up ==
 === Input ===

@@ Line 17: / Line 17: @@
 === Modules ===
-*'''Slicer 3.6.1 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]'''
+*'''Slicer 3.6.1 recommended modules:
 ===Objective / Background ===
@@ Line 27: / Line 30: @@
 *reference/fixed : axial MRI 256x256x36 ,0.7 x 0.7 x 4mm voxel size
 *moving: axial MRI 256x256x20 ,0.8 x 0.8 x 5mm voxel size
 === Notes / Overall Strategy ===
@@ Line 120: / Line 129: @@
 |}
 === Acknowledgments ===
 Images from the [http://prostatemrimagedatabase.com Prostate MR Image Database] (patient 1, exam 1).

@@ Line 9: / Line 9: @@
 |[[Image:RegLib_C07_Thumb1.png|150px|lleft|this is the fixed reference image. All images are aligned into this space]]
 |[[Image:RegArrow_NonRigid.png|100px|lleft]]
-|[[Image:RegLib_C07_Thumb2.gif|150px|lleft|this is the time series of 2D images to be registered with the reference]]
+|[[Image:RegLib_C07_Thumb2.png|150px|lleft|this is the time series of 2D images to be registered with the reference]]
 |-
 |fixed:prostate MRI<br>day 1