Slicer3:LinearRegistrationUseCases - Revision history

Gcasey: moved Slicer3:Registration to Slicer3:LinearRegistrationUseCases: Make room for a top-level page to point to all the registration modules

2010-01-14T15:10:18Z

moved Slicer3:Registration to Slicer3:LinearRegistrationUseCases: Make room for a top-level page to point to all the registration modules

Aylward at 00:09, 31 July 2008

2008-07-31T00:09:57Z

Aylward at 22:40, 30 July 2008

2008-07-30T22:40:34Z

Aylward at 11:10, 30 July 2008

2008-07-30T11:10:59Z

Aylward at 11:02, 30 July 2008

2008-07-30T11:02:07Z

Marianna at 22:37, 19 May 2008

2008-05-19T22:37:18Z

Marianna: 1 revision

2008-05-15T17:56:45Z

1 revision

Pieper: /* T1 to Average Gradient Affine Registration */

2008-04-10T13:27:49Z

T1 to Average Gradient Affine Registration

New page

Slicer 3 includes linear and nonlinear registration tools built as command line modules. On this page we are working to collect a variety of example data sets which test the boundary cases in order to optimize the registration performance and accuracy.

See also [[ITK_Registration_Optimization#Algorithmic_Requirements_and_Use_Cases | additional use cases collected for nonlinear registration optimization]].

__TOC__

----

= T2 to FA Affine Registration =

[[Image:T2-FA-registration-slicer2-2008-04-08.png|thumb|right|250px|Results using slicer2]]

[[Image:T2-fa-registration-2008-04-08.png|thumb|right|250px|Results using slicer3 as of 2008-04-07]]

* Input Volumes
** [[media:T2 Aligned.nrrd]] (Sagittal)
** [[media:FA-slicer3-2008-04-08.nrrd]] (Rotated Axial)

* Reference 'Gold Standard'
** Slicer2 calculation using Mattes MI Affine (also uses ITK implementation)
** Result transform:
0.998582 0.0548244 0.00874164 1.86596
-0.051956 0.957673 0.0339914 -12.8223
-0.00506141 -0.00847398 0.994165 16.2862
0 0 0 1

* Software
** Slicer3 svn trunk 2008-04-07

* Parameters
** Defaults

* Method
** Use T2 as fixed, FA as moving
** Create new output transform and output volume (no input transform)
** In data module drag FA volume under the newly calculated transform
** In Transform Module select the output transform and click Invert

* Results 2008-04-07
** Output volume appears to be all 0
** Output transform looks correct, see image to the right.

0.924175 0.0524361 0.0617505 -0.457981
0.0453017 0.99089 0.0283234 -8.79902
-0.0525653 -0.0657896 1.11031 18.5389
-0 0 -0 1

----

= T1 to Average Gradient Affine Registration =

[[Image:Debrecen-slicer2-affine.png|thumb|right|250px|Results using slicer2]]

[[Image:Derecen-slicer3-affine.png|thumb|right|250px|Results using slicer3 as of 2008-04-10]]

* Input Volumes
** Provided by András Jakab, University of Debrecen Medical School and Health Science Center
** [http://cooler.underground.hu/docs/imaging/send/extract_brain_3dt1_manual_volume.nrrd]
** [http://cooler.underground.hu/docs/imaging/send/AVGgradient.nrrd]

* Reference 'Gold Standard'
** Slicer2 calculation using Mattes MI Affine (also uses ITK implementation)
** Result transform:
0.950655 0.024335 0.0259082 0.857786
0.0086567 0.8889 -0.379321 -6.77365
-0.0395529 0.39257 0.835359 14.664
0 0 0 1

* Software
** Slicer3 svn trunk 2008-04-10

* Parameters
** Defaults

* Method
** Use T1 as fixed, Gradient as moving

* Results 2008-04-10
** Cannot run due to sampling issue

<pre>
itk::ExceptionObject (0x1990140)
Location: "void itk::MattesMutualInformationImageToImageMetric<TFixedImage, TMovingImage>::GetValueAndDerivative(const typename itk::ImageToImageMetric<TFixedImage, TMovingImage>::ParametersType&, typename itk::ImageToImageMetric<TFixedImage, TMovingImage>::MeasureType&, typename itk::ImageToImageMetric<TFixedImage, TMovingImage>::DerivativeType&) const [with TFixedImage = itk::OrientedImage<short int, 3u>, TMovingImage = itk::OrientedImage<short int, 3u>]"
File: /Users/pieper/slicer3/latest/Slicer3-lib/Insight/Code/Algorithms/itkMattesMutualInformationImageToImageMetric.txx
Line: 1036
Description: itk::ERROR: MattesMutualInformationImageToImageMetric(0x198d470): Too many samples map outside moving image buffer: 2481 / 10000

ERROR: In /Users/pieper/slicer3/latest/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1326
vtkCommandLineModuleLogic (0x1d265ac0): Affine registration completed with errors
</pre>

@@ Line 122: / Line 122: @@
 ** Using RegisterImages module
 ** DO NOT USE DEFAULT PARAMETERS
-*** The difficulty is that fixed image is much larger than the moving image.   As a result, too many random samples chosen from the fixed image will fall outside of the moving image, even when they are registered.   The RegisterImages module has the option to limit the fixed image samples to the volume of overlap between the fixed and moving image.   This volume of overlap is computed only once, after the initial (center of mass, image centers, landmarks, or none) registration.
+*** One additional option must be set
-*** In the tab, "Advanced registration options" select "Use Overlap as ROI"
+*** The difficulty is that fixed image is much larger than the moving image.   As a result, too many random samples chosen from the fixed image will fall outside of the moving image, even when they are registered.   ITK (correctly or incorrectly, its arguable) throw an exception when this happens.
 ** Output volume looks correct, see below (right)
 ** Output transform looks correct
-.0094 -0.0573823 -0.000750058
+.984504 0.00242558 0.0181733
-.0351927 1.06887 0.0810613
+.00837315 0.921599 -0.432808
-.00242838 -0.0205891 0.991571
+  -0.0215383 0.400563 0.942328
-.20002 -15.8546 -16.3295
+  -0.727524 -0.771725 -14.9462
 {|
 |-
-| [[Image:RegisterImages-T2-fa-registration-setup-2008-07-30.png|thumb|250px|Setup using RegisterImages as of 2008-07-30]]
+| [[Image:RegisterImages-Debrecen-affine-setup-2008-07-30.png|thumb|250px|Setup using RegisterImages as of 2008-07-30]]
-| [[Image:RegisterImages-T2-fa-registration-results-2008-07-30.png|thumb|250px|Results using RegisterImages as of 2008-07-30]]
+| [[Image:RegisterImages-Debrecen-affine-results-2008-07-30.png|thumb|250px|Results using RegisterImages as of 2008-07-30]]
 |-
 |}

@@ Line 51: / Line 51: @@
   -0 0 -0 1
-[[Image:RegisterImages-T2-fa-registration-setup-2008-07-30.png|thumb|right|250px|Setup using RegisterImages as of 2008-07-30]]
 * Results 2008-07-30
 ** Using RegisterImages module
-** Using Default parameters
+** Using Default parameters, see below (left)
-** Output volume looks correct
+** Output volume looks correct, see below (right)
 ** Output transform looks correct
 .0094 -0.0573823 -0.000750058
@@ Line 64: / Line 63: @@
 .20002 -15.8546 -16.3295
 ----

← Older revision		Revision as of 11:02, 30 July 2008
Line 51:		Line 51:
	-0 0 -0 1		-0 0 -0 1

		+	[[Image:RegisterImages-T2-fa-registration-setup-2008-07-30.png\|thumb\|right\|250px\|Setup using RegisterImages as of 2008-07-30]]
		+	[[Image:RegisterImages-T2-fa-registration-results-2008-07-30.png\|thumb\|right\|250px\|Results using RegisterImages as of 2008-07-30]]
		+
		+	* Results 2008-07-30
		+	** Using RegisterImages module
		+	** Using Default parameters
		+	** Output volume looks correct
		+	** Output transform looks correct
		+	1.0094 -0.0573823 -0.000750058
		+	0.0351927 1.06887 0.0810613
		+	0.00242838 -0.0205891 0.991571
		+	3.20002 -15.8546 -16.3295

@@ Line 114: / Line 114: @@
 Line: 1036
 Description: itk::ERROR: MattesMutualInformationImageToImageMetric(0x198d470): Too many samples map outside moving image buffer: 2481 / 10000
 ERROR: In /Users/pieper/slicer3/latest/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1326
 vtkCommandLineModuleLogic (0x1d265ac0): Affine registration completed with errors
 </pre>

@@ Line 2: / Line 2: @@
-See also [[ITK_Registration_Optimization#Algorithmic_Requirements_and_Use_Cases | additional use cases collected for nonlinear registration optimization]].
+See also [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization#Algorithmic_Requirements_and_Use_Cases additional use cases collected for nonlinear registration optimization].
 __TOC__
@@ Line 18: / Line 18: @@
 * Input Volumes
-** [[media:T2 Aligned.nrrd]] (Sagittal)
+** [[media:T2 Aligned.nrrd|T2 Aligned Sagittal]]
-** [[media:FA-slicer3-2008-04-08.nrrd]] (Rotated Axial)
+** [[media:FA-slicer3-2008-04-08.nrrd| Rotated Axial]]
 * Reference 'Gold Standard'
@@ Line 66: / Line 66: @@
 * Input Volumes
 ** Provided by András Jakab, University of Debrecen Medical School and Health Science Center
-** [http://cooler.underground.hu/docs/imaging/send/extract_brain_3dt1_manual_volume.nrrd]
+**[http://cooler.underground.hu/docs/imaging/send/extract_brain_3dt1_manual_volume.nrrd Manual Volume]
-** [http://cooler.underground.hu/docs/imaging/send/AVGgradient.nrrd]
+**[http://cooler.underground.hu/docs/imaging/send/AVGgradient.nrrd AVG gradient]
 * Reference 'Gold Standard'

← Older revision	Revision as of 17:56, 15 May 2008
(No difference)