BRAINSFit prostate registration - Revision history

PeterBehringer: /* Current status */

2015-05-18T23:39:17Z

Current status

2015-05-18T23:39:01Z

Things to do

2015-05-18T23:38:15Z

Things to do

2015-05-18T14:56:58Z

2015-05-15T15:08:22Z

Goal

2015-05-15T15:06:10Z

Goal

2015-05-13T15:52:50Z

Standing SimpleITK issues

2015-05-13T15:52:22Z

Standing SimpleITK issues

2015-05-09T19:30:53Z

Goal

2015-05-09T19:30:21Z

Goal

@@ Line 197: / Line 197: @@
 SimpleITK registration code on github: [https://github.com/PeterBehringer/SimpleITKtraining/blob/master/BRAINSFit_to_sitk_MMI.py here]
-'''Latest update: Mai 9, 2015'''
+'''Latest update: Mai 18, 2015'''
 ==Things to do==

@@ Line 200: / Line 200: @@
 ==Things to do==
-* Set ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS to 1 as described here http://comments.gmane.org/gmane.comp.lib.itk.user/44256
+* Set ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS to 1 as described [http://comments.gmane.org/gmane.comp.lib.itk.user/44256 here]
 * Write message to ITK mailing list, cc Nicholas Tustin: ask for regularization of the BSpline displacement field
 * look at DICE comparison between Slicer3 and Slicer4 to quantify the problem

@@ Line 200: / Line 200: @@
 ==Things to do==
-* Set Thread to 1 to in Slicer4
+* Set ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS to 1 as described here http://comments.gmane.org/gmane.comp.lib.itk.user/44256
 * Write message to ITK mailing list, cc Nicholas Tustin: ask for regularization of the BSpline displacement field
 * look at DICE comparison between Slicer3 and Slicer4 to quantify the problem

← Older revision		Revision as of 14:56, 18 May 2015
Line 198:		Line 198:

	'''Latest update: Mai 9, 2015'''		'''Latest update: Mai 9, 2015'''
		+
		+	==Things to do==
		+	* Set Thread to 1 to in Slicer4
		+	* Write message to ITK mailing list, cc Nicholas Tustin: ask for regularization of the BSpline displacement field
		+	* look at DICE comparison between Slicer3 and Slicer4 to quantify the problem
		+	* displace the masks and run with Slicer3 and Slicer4 to quantify the impact of the mask in the registration result

	==Things that are working==		==Things that are working==

@@ Line 1: / Line 1: @@
 =Goal=
-We are developing registration module in Slicer version 4 (which is using ITKv4) for deformable registration of prostate MRI using [BRAINSFit https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSFit]
+We are developing registration module in Slicer version 4 (which is using ITKv4) for deformable registration of prostate MRI using [https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSFit BRAINSFit]
 This Slicer4/ITKv4 registration tool should be functional, accurate and fast (i.e., comparable with the functionality we had in Slicer3/ITKv3, which has been evaluated previously [1]). We worked on implementing BRAINSFit registration in SimpleITK but due to several issues (see [http://www.na-mic.org/Wiki/index.php/BRAINSFit_prostate_registration#Standing_SimpleITK_issues here]) we are considering a C++ implementation that uses ITKv3 libraries and can be integrated in the latest Slicer versions.

@@ Line 224: / Line 224: @@
 ==Standing SimpleITK issues==
 * no API for consistent initialization of the metric seed
-**  The ITKv4 ImageRegistrationMethod random sampling utilizes a fixed seed
+**  The ITKv4 ImageRegistrationMethod random sampling utilizes a fixed seed ([https://github.com/InsightSoftwareConsortium/ITK/blob/03f28bb2e0c4b3d00f1ceeb772b342746c89e148/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.hxx#L903-L967 here])
+*

@@ Line 3: / Line 3: @@
 We are developing registration module in Slicer version 4 (which is using ITKv4) for deformable registration of prostate MRI.
-We want to develop a prostate registration tool in Slicer4/ITKv4. This Slicer4/ITKv4 registration tool should be functional, accurate and fast (i.e., comparable with the functionality we had in Slicer3/ITKv3, which has been evaluated previously [1]). We worked on implementing BRAINSFit registration in SimpleITK but due to several issues (see [http://www.na-mic.org/Wiki/index.php/BRAINSFit_prostate_registration#Standing_SimpleITK_issues here]) we are considering a C++ implementation that uses ITKv3 libraries but can be used in Slicer 4.4.
+We want to develop a prostate registration tool in Slicer4/ITKv4. This Slicer4/ITKv4 registration tool should be functional, accurate and fast (i.e., comparable with the functionality we had in Slicer3/ITKv3, which has been evaluated previously [1]). We worked on implementing BRAINSFit registration in SimpleITK but due to several issues (see [http://www.na-mic.org/Wiki/index.php/BRAINSFit_prostate_registration#Standing_SimpleITK_issues here]) we are considering a C++ implementation that uses ITKv3 libraries and can be integrated in the latest Slicer versions.
 =Details on the registration approach=