Documentation/Nightly/RegistrationVideoTutorials - Revision history

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

2019-11-27T02:15:40Z

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

Meier: /* Fiducial Based Registration: How can I register two volumes with manually selected landmarks? */

2014-08-29T22:02:49Z

Fiducial Based Registration: How can I register two volumes with manually selected landmarks?

Meier: /* Fiducial Based Registration: How can I register two volumes with manually selected landmarks? */

2014-08-29T22:01:33Z

Fiducial Based Registration: How can I register two volumes with manually selected landmarks?

Meier at 21:59, 29 August 2014

2014-08-29T21:59:07Z

Meier: /* Slicer Registration Training Videos */

2014-08-29T21:55:50Z

Slicer Registration Training Videos

Meier: /* Registration Masking: How do I quickly generate a mask for use in registration? */

2013-10-02T16:31:50Z

Registration Masking: How do I quickly generate a mask for use in registration?

Meier: /* Registration Masking: How do I quickly generate a mask for use in registration? */

2013-09-04T17:01:01Z

Registration Masking: How do I quickly generate a mask for use in registration?

Meier: /* Registration Masking: How do I quickly generate a mask for use in registration? */

2013-09-04T17:00:41Z

Registration Masking: How do I quickly generate a mask for use in registration?

Meier: /* Registration Masking: How do I quickly generate a mask for use in registration? */

2013-09-04T16:59:22Z

Registration Masking: How do I quickly generate a mask for use in registration?

Meier: /* Slicer Registration Training Videos */

2013-06-27T18:12:47Z

Slicer Registration Training Videos

@@ Line 24: / Line 24: @@
 #[[Media:HowToInstallDeformationFieldVisualizer.mov|'''Install & use Deformation Field Visualizer Extension''' (3 min, 20MB)]]: For visualizing deformation (BSpline) fields the '''SlicerRT''' extension provides an extensive interactive tool that renders the deformation field as both slice projections and 3D models. Movie shows how to install & use. You will need a recent Slicer build,i.e. June 2013 or after.
 == Fiducial Based Registration: How can I register two volumes with manually selected landmarks? ==
-There are two fiducial registration tools available within Slicer. The default is within the Registration menu, and an alternative version is found in the SlicerIGT extension as "Fiducial Registration Wizard". A detailed case example using both tools is available in the [http://wiki.slicer.org/slicerWiki/index.php/Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C48 Case 48 in the Registration Case Library]. A brief screencast on selecting landmarks and running either tools are also here:
+There are two fiducial registration tools available within Slicer. The default is within the Registration menu, and an alternative version is found in the SlicerIGT extension as "Fiducial Registration Wizard". A detailed case example using both tools is available in the [[Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C48|Case 48 in the Registration Case Library]]. A brief screencast on selecting landmarks and running either tools are also here:
 #[[Media:RegLib_C48_FiducialRegistration.mov|'''fiducial-based registration''']]
 #[[Media:RegLib_C48_FiducialRegistration_IGT.mov|'''alternative tool: using SlicerIGT's fiducial-based registration''']] (shows extension download and module execution only, for the landmark selection see movie above)

@@ Line 24: / Line 24: @@
 #[[Media:HowToInstallDeformationFieldVisualizer.mov|'''Install & use Deformation Field Visualizer Extension''' (3 min, 20MB)]]: For visualizing deformation (BSpline) fields the '''SlicerRT''' extension provides an extensive interactive tool that renders the deformation field as both slice projections and 3D models. Movie shows how to install & use. You will need a recent Slicer build,i.e. June 2013 or after.
 == Fiducial Based Registration: How can I register two volumes with manually selected landmarks? ==
-There are two fiducial registration tools available within Slicer. The default is within the Registration menu, and an alternative version is found in the SlicerIGT extension as "Fiducial Registration Wizard". A detailed case example using both tools is available in the Documentation:[[Documentation/Nightly/Registration/RegLib_C48| Case 48 in the Registration Case Library]]. A brief screencast on selecting landmarks and running either tools are also here:
+There are two fiducial registration tools available within Slicer. The default is within the Registration menu, and an alternative version is found in the SlicerIGT extension as "Fiducial Registration Wizard". A detailed case example using both tools is available in the [http://wiki.slicer.org/slicerWiki/index.php/Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C48 Case 48 in the Registration Case Library]. A brief screencast on selecting landmarks and running either tools are also here:
 #[[Media:RegLib_C48_FiducialRegistration.mov|'''fiducial-based registration''']]
 #[[Media:RegLib_C48_FiducialRegistration_IGT.mov|'''alternative tool: using SlicerIGT's fiducial-based registration''']] (shows extension download and module execution only, for the landmark selection see movie above)

@@ Line 24: / Line 24: @@
 #[[Media:HowToInstallDeformationFieldVisualizer.mov|'''Install & use Deformation Field Visualizer Extension''' (3 min, 20MB)]]: For visualizing deformation (BSpline) fields the '''SlicerRT''' extension provides an extensive interactive tool that renders the deformation field as both slice projections and 3D models. Movie shows how to install & use. You will need a recent Slicer build,i.e. June 2013 or after.
 == Fiducial Based Registration: How can I register two volumes with manually selected landmarks? ==
-There are two fiducial registration tools available within Slicer. The default is within the Registration menu, and an alternative version is found in the SlicerIGT extension as "Fiducial Registration Wizard". A detailed case example using both tools is available in the [[Documentation/Nightly/Registration/RegistrationLibrary/RegLib_C48| Case 48 in the Registration Case Library]]. A brief screencast on selecting landmarks and running either tools are also here:
+There are two fiducial registration tools available within Slicer. The default is within the Registration menu, and an alternative version is found in the SlicerIGT extension as "Fiducial Registration Wizard". A detailed case example using both tools is available in the Documentation:[[Documentation/Nightly/Registration/RegLib_C48| Case 48 in the Registration Case Library]]. A brief screencast on selecting landmarks and running either tools are also here:
 #[[Media:RegLib_C48_FiducialRegistration.mov|'''fiducial-based registration''']]
 #[[Media:RegLib_C48_FiducialRegistration_IGT.mov|'''alternative tool: using SlicerIGT's fiducial-based registration''']] (shows extension download and module execution only, for the landmark selection see movie above)

@@ Line 23: / Line 23: @@
 Visualizing complex datasets is one of 3DSlicer's great strengths.  There are several tools/methods you can use to assess the result of a registration. The most common ones are shown below:
 #[[Media:HowToInstallDeformationFieldVisualizer.mov|'''Install & use Deformation Field Visualizer Extension''' (3 min, 20MB)]]: For visualizing deformation (BSpline) fields the '''SlicerRT''' extension provides an extensive interactive tool that renders the deformation field as both slice projections and 3D models. Movie shows how to install & use. You will need a recent Slicer build,i.e. June 2013 or after.
-=== Fiducial Based Registration: How can I register two volumes with manually selected landmarks? ==
+== Fiducial Based Registration: How can I register two volumes with manually selected landmarks? ==
-There are two fiducial registration tools available within Slicer. The default is within the Registration menu, and an alternative version is found in the SlicerIGT extension as "Fiducial Registration Wizard":
+There are two fiducial registration tools available within Slicer. The default is within the Registration menu, and an alternative version is found in the SlicerIGT extension as "Fiducial Registration Wizard". A detailed case example using both tools is available in the [[Documentation/Nightly/Registration/RegistrationLibrary/RegLib_C48| Case 48 in the Registration Case Library]]. A brief screencast on selecting landmarks and running either tools are also here:
-[[Media:RegLib_C48_FiducialRegistration_IGT.mov|'''(screencast on downloading and running the SlicerIGT extension)''']]
+#[[Media:RegLib_C48_FiducialRegistration.mov|'''fiducial-based registration''']]

← Older revision		Revision as of 21:55, 29 August 2014
Line 23:		Line 23:
	Visualizing complex datasets is one of 3DSlicer's great strengths. There are several tools/methods you can use to assess the result of a registration. The most common ones are shown below:		Visualizing complex datasets is one of 3DSlicer's great strengths. There are several tools/methods you can use to assess the result of a registration. The most common ones are shown below:
	#[[Media:HowToInstallDeformationFieldVisualizer.mov\|'''Install & use Deformation Field Visualizer Extension''' (3 min, 20MB)]]: For visualizing deformation (BSpline) fields the '''SlicerRT''' extension provides an extensive interactive tool that renders the deformation field as both slice projections and 3D models. Movie shows how to install & use. You will need a recent Slicer build,i.e. June 2013 or after.		#[[Media:HowToInstallDeformationFieldVisualizer.mov\|'''Install & use Deformation Field Visualizer Extension''' (3 min, 20MB)]]: For visualizing deformation (BSpline) fields the '''SlicerRT''' extension provides an extensive interactive tool that renders the deformation field as both slice projections and 3D models. Movie shows how to install & use. You will need a recent Slicer build,i.e. June 2013 or after.
		+	=== Fiducial Based Registration: How can I register two volumes with manually selected landmarks? ==
		+	There are two fiducial registration tools available within Slicer. The default is within the Registration menu, and an alternative version is found in the SlicerIGT extension as "Fiducial Registration Wizard":
		+	[[Media:RegLib_C48_FiducialRegistration_IGT.mov\|'''(screencast on downloading and running the SlicerIGT extension)''']]

@@ Line 14: / Line 14: @@
 #[[Media:QuickMask_all.mov|'''All of the above'''  (21 min)]]: Joint video showing all of the above steps in succession.
 #[[Media:RegLib_C09_2_SwissSkullStripper.mov|'''New: SwissSkullStripper''']] : this is a new extension module that can generate quick and fairly accurate skull stripping masks. Movie shows installation and use
 == Registration Masking: How accurate should my mask be ? ==

@@ Line 13: / Line 13: @@
 #[[Media:QuickMask_07_upsampling.mov|'''Upsample label map''' (2 min)]]: This is the post-editing counterpart to the subsampling above. Once you complete the manual editing, resample the labelmap back to its original resolution. Includes smoothing techniques.
 #[[Media:QuickMask_all.mov|'''All of the above'''  (21 min)]]: Joint video showing all of the above steps in succession.
-#[[Media:RegLib_C09_2_SwissSkullStripper.mov|New: installation and use of the "SwissSkullStripper" for generating a T1 mask]]
+#[[Media:RegLib_C09_2_SwissSkullStripper.mov|'''New: SwissSkullStripper''': this is a new extension module that can generate quick and fairly accurate skull stripping masks. Movie shows installation and use]]
 == Registration Masking: How accurate should my mask be ? ==

← Older revision		Revision as of 18:12, 27 June 2013
Line 17:		Line 17:
	A highly accurate segmentation can be counter-productive when used as a mask in registration. If it follows the main edges of the structure of interest (e.g. brain surface) exactly, then that edge is excluded from actively driving the registration. The result will be an incorrect excessive amount of expansion or shrinkage near the edge. We therefore recommend to dilate your mask a few pixels beyond the edges. The video below shows the difference:		A highly accurate segmentation can be counter-productive when used as a mask in registration. If it follows the main edges of the structure of interest (e.g. brain surface) exactly, then that edge is excluded from actively driving the registration. The result will be an incorrect excessive amount of expansion or shrinkage near the edge. We therefore recommend to dilate your mask a few pixels beyond the edges. The video below shows the difference:
	#[[Media:BSplineWithDilatedMask.mov\|'''B-spline registration with masking: original + dilated''' (5 min)]]		#[[Media:BSplineWithDilatedMask.mov\|'''B-spline registration with masking: original + dilated''' (5 min)]]
		+
		+	== Registration Validation How do I check / visualize a registration result ? ==
		+	Visualizing complex datasets is one of 3DSlicer's great strengths. There are several tools/methods you can use to assess the result of a registration. The most common ones are shown below:
		+	#[[Media:HowToInstallDeformationFieldVisualizer.mov\|'''Install & use Deformation Field Visualizer Extension''' (3 min, 20MB)]]: For visualizing deformation (BSpline) fields the '''SlicerRT''' extension provides an extensive interactive tool that renders the deformation field as both slice projections and 3D models. Movie shows how to install & use. You will need a recent Slicer build,i.e. June 2013 or after.