Modules:BRAINSFit - Revision history

Grundlett: Text replacement - "https?:\/\/(?:www|wiki)\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1 "

2019-11-27T13:15:08Z

Text replacement - "https?:\/\/(?:www|wiki)\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1 "

Meier: /* Example Applications: from the Registration Library */

2011-06-16T13:55:44Z

Example Applications: from the Registration Library

Meier: /* Example Applications: from the Registration Library */

2011-06-16T13:54:55Z

Example Applications: from the Registration Library

Meier at 13:54, 16 June 2011

2011-06-16T13:54:34Z

Meier: /* Experimental results from the registration library */

2011-06-16T13:48:35Z

Experimental results from the registration library

Hjmjohnson: /* Module Name */

2011-01-14T18:07:14Z

Module Name

Matsuij: /* Use Cases, Examples */

2011-01-13T20:51:53Z

Use Cases, Examples

Matsuij: /* Use Cases, Examples */

2011-01-13T20:50:31Z

Use Cases, Examples

Matsuij: /* Use Cases, Examples */

2011-01-13T20:06:52Z

Use Cases, Examples

Mscully at 22:30, 29 December 2010

2010-12-29T22:30:27Z

@@ Line 52: / Line 52: @@
 |Program version || 3.0.0
 |-
-|Program documentation-url || http://wiki.slicer.org/slicerWiki/index.php/Modules:BRAINSFit
+|Program documentation-url || https://www.slicer.org/wiki/Modules:BRAINSFit
-|-
+|- |}
 Insight/Examples/Registration/ImageRegistration8.cxx

@@ Line 23: / Line 23: @@
 |-
 |[[Image:RegLib_C29_thumb4.png|160px|lleft||Registration Library Case 29: DTI nonrigid|link=http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C29]]
-|http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C29 Diffusion MRI/DTI]
+|[http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C29 Diffusion MRI/DTI]
 |}
 * And many more, see the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''Slicer Registration Library''']

@@ Line 16: / Line 16: @@
 === Example Applications:  from the Registration Library ===
 {|
-|[[Image::RegLib_C02_Thumb.png|60px|lleft|Registration Library Case 02: Brain Affine|link=http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C02]]
+|[[Image:RegLib_C02_Thumb.png|160px|lleft|Registration Library Case 02: Brain Affine|link=http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C02]]
 |[http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C02 Affine Intra Subject Brain]
 |-
-|[[Image:RegLib_C14_Thumb_MRI.png|60px|lleft|Registration Library Case 14: PET|link=http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C14]]
+|[[Image:RegLib_C14_Thumb_MRI.png|160px|lleft|Registration Library Case 14: PET|link=http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C14]]
 |[http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C14 PET Brain]
 |-
-|[[Image:RegLib_C29_thumb4.png|60px|lleft||Registration Library Case 29: DTI nonrigid|link=http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C29]]
+|[[Image:RegLib_C29_thumb4.png|160px|lleft||Registration Library Case 29: DTI nonrigid|link=http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C29]]
 |http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C29 Diffusion MRI/DTI]
 |}

@@ Line 15: / Line 15: @@
 === Example Applications:  from the Registration Library ===
-[[Image:RegLib_C02_Thumb.png|Registration Library Case 02: Brain Affine]]
+{|
-[[Image:RegLib_C14_Thumb_MRI.png|Registration Library Case 14: PET]]
+|[[Image::RegLib_C02_Thumb.png|60px|lleft|Registration Library Case 02: Brain Affine|link=http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C02]]
-[[Image:RegLib_C29_thumb4.png|Registration Library Case 29: DTI nonrigid]]
+|[http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C02 Affine Intra Subject Brain]
+|-
-*[http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C02 Affine Intra Subject Brain]
+|[[Image:RegLib_C14_Thumb_MRI.png|60px|lleft|Registration Library Case 14: PET|link=http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C14]]
-*[http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C14 PET Brain]
+|[http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C14 PET Brain]
-*[http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C29 Diffusion MRI/DTI]
+|-
 * And many more, see the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''Slicer Registration Library''']
   (you can sort the table by method)

@@ Line 14: / Line 14: @@
-=== Experimental results from the registration library ===
+=== Example Applications:  from the Registration Library ===
-http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C02
+*[http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C02 Affine Intra Subject Brain]
+*[http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C14 PET Brain]
-http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C14
+*[http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C29 Diffusion MRI/DTI]
+* And many more, see the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''Slicer Registration Library''']
--- And several more from:
+ (you can sort the table by method)
 == General Information ==

@@ Line 12: / Line 12: @@
 |  [[Image:After.png|thumb|280px|AfterRegistration]]
 |}
 == General Information ==

@@ Line 195: / Line 195: @@
 --histogramMatch \
 </pre>
-To start with the best possible initial alignment we use --initializeTransformMode but we are't working with human heads so we can't pick useCenterOfHead. Instead we pick useMomentsAlign which does a reasonable job of selecting the centers of mass.
+To start with the best possible initial alignment we use --initializeTransformMode but we are't working with human heads so we can't pick useCenterOfHeadAlign. Instead we pick useMomentsAlign which does a reasonable job of selecting the centers of mass.
 <pre>
 --initializeTransformMode useMomentsAlign \

@@ Line 88: / Line 88: @@
 --histogramMatch \
 </pre>
-To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHead, which detects the center of head even with varying amounts of neck or shoulders present.
+To start with the best possible initial alignment we use --initializeTransformMode. We're working with human heads so we pick useCenterOfHeadAlign, which detects the center of head even with varying amounts of neck or shoulders present.
 <pre>
---initializeTransformMode useCenterOfHead \
+--initializeTransformMode useCenterOfHeadAlign \
 </pre>
 ROI masks normally improve registration but we haven't generated any so we turn on --maskProcessingMode ROIAUTO.
@@ Line 113: / Line 113: @@
 --transformType Rigid \
 --histogramMatch \
---initializeTransformMode useCenterOfHead \
+--initializeTransformMode useCenterOfHeadAlign \
 --maskProcessingMode ROIAUTO \
 --ROIAutoDilateSize 3 \

@@ Line 69: / Line 69: @@
 This module is especially appropriate for these use cases:
-* Use Case 1: Same Subject: Longitudinal
+* '''''Use Case 1: Same Subject: Longitudinal'''''
 For this use case we're registering a baseline T1 scan with a follow-up T1 scan on the same subject a year later.  The two images are again available in the Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/TestData directory as testT1.nii.gz and testT1Longitudinal.nii.gz
@@ Line 124: / Line 124: @@
 |}
-* Use Case 2: Same Subject: MultiModal
+* '''''Use Case 2: Same Subject: MultiModal'''''
 For this use case we're registering a T1 scan with a T2 scan collected in the same sesson.  The two images are again available in the Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/TestData directory as testT1.nii.gz and testT2.nii.gz
@@ Line 176: / Line 176: @@
 |}
-* Use Case 3: Mouse Registration
+* '''''Use Case 3: Mouse Registration'''''
 Here we'll register brains from two different mice together.  The fixed and moving mouse brains used in this example are available in the Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/TestData directory.