Projects:RegistrationLibrary:RegLib C46 - Revision history

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

2017-07-10T18:07:28Z

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

Meier: moved Projects:RegistrationDocumentation:RegLib C46 to Projects:RegistrationLibrary:RegLib C46

2011-08-05T13:51:14Z

moved Projects:RegistrationDocumentation:RegLib C46 to Projects:RegistrationLibrary:RegLib C46

Meier: /* Acknowledgments */

2011-06-29T17:02:53Z

Acknowledgments

Meier: /* Acknowledgments */

2011-06-29T17:02:37Z

Acknowledgments

Meier: /* Download */

2011-06-29T13:43:48Z

Download

Meier: /* Notes / Overall Strategy */

2011-06-29T13:37:28Z

Notes / Overall Strategy

Meier: /* Download */

2011-06-29T13:32:09Z

Download

Meier: /* Download */

2011-06-29T13:31:48Z

Download

Meier: /* Notes / Overall Strategy */

2011-06-29T13:29:12Z

Notes / Overall Strategy

Meier at 13:27, 29 June 2011

2011-06-29T13:27:06Z

@@ 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:  [https://www.slicer.org/wiki/Modules:BRAINSFit BrainsFit]'''
 ===Objective / Background ===
@@ Line 68: / Line 68: @@
 ##upon completion, read the transform files with an editor and extract the displacements of interest
 ##The ITK transform files describe displacements at the grid nodes, many of which are outside the region of interest. Because BRAINSfit pads the grid with 1 voxel, the grid returned is actually 8x8x8. We use only the plane (*,*,4) for analysis and discard the y-direction displacements, which as expected are all zero.
-##for details on the ITK transform format see the [http://www.slicer.org/slicerWiki/index.php/Slicer-3-6-FAQ#What_is_the_Meaning_of_.27Fixed_Parameters.27_in_the_transform_file_.28.tfm.29_of_a_BSpline_registration_.3F '''FAQ''' here]
+##for details on the ITK transform format see the [https://www.slicer.org/wiki/Slicer-3-6-FAQ#What_is_the_Meaning_of_.27Fixed_Parameters.27_in_the_transform_file_.28.tfm.29_of_a_BSpline_registration_.3F '''FAQ''' here]
-##To obtain displacements at arbitrary coordinates, interpolate the transform into a deformation field, e.g. using this module (details  [http://www.slicer.org/slicerWiki/index.php/Slicer-3-6-FAQ#How_can_I_convert_a_BSpline_transform_into_a_deformation_field.3F FAQ here]):
+##To obtain displacements at arbitrary coordinates, interpolate the transform into a deformation field, e.g. using this module (details  [https://www.slicer.org/wiki/Slicer-3-6-FAQ#How_can_I_convert_a_BSpline_transform_into_a_deformation_field.3F FAQ here]):
   /Applications/Slicer3.6.3/lib/Slicer3/Plugins/BSplineToDeformationField

← Older revision		Revision as of 17:02, 29 June 2011
Line 93:		Line 93:

	=== Acknowledgments ===		=== Acknowledgments ===
−	Thanks to Amir Owrangi and [www.imaging.robarts.ca/~gep Dr.Grace Parraga] from the [http://www.robarts.ca Robarts Institute] for sharing the registration problem and data.	+	Thanks to Amir Owrangi and [http://www.imaging.robarts.ca/~gep Dr.Grace Parraga] from the [http://www.robarts.ca Robarts Institute] for sharing the registration problem and data.

← Older revision		Revision as of 17:02, 29 June 2011
Line 93:		Line 93:

	=== Acknowledgments ===		=== Acknowledgments ===
−	Thanks to Amir Owrangi and the [http://www.robarts.ca Robarts Institute] for sharing the registration problem and data.	+	Thanks to Amir Owrangi and [www.imaging.robarts.ca/~gep Dr.Grace Parraga] from the [http://www.robarts.ca Robarts Institute] for sharing the registration problem and data.

@@ Line 90: / Line 90: @@
 *Results
 **[[Media:RegLib_C46_RegistrationTransforms.zip‎ ‎|'''RegLib_C46_RegistrationTransforms.zip''' : the 200 BSpline registration transforms <small> (ITK transform (text) files, zip file 274 kB) </small>]]'''
 === Acknowledgments ===
 Thanks to Amir Owrangi and the [http://www.robarts.ca Robarts Institute] for sharing the registration problem and data.

@@ Line 32: / Line 32: @@
 *Because the implementation of the BRAINSfit module used here expects a 3D volume, we choose a slightly larger grid and make it isotropic, although the 3rd dimension of the grid is not used. We expect the optimizer in the registration to not move outside the slice plane and simply return 0 deformations there.
 *An alternative strategy would be to register each image to its immediate previous timepoint, and then integrating the displacements. This has the advantage that nonrigid registration tends to be better for smaller differences, but it bears the risk of accumulating error and hence a lower robustness.
 *Overall strategy:
 :#select one frame within the breathing cycle as reference frame

← Older revision	Revision as of 13:51, 5 August 2011
(No difference)

@@ Line 85: / Line 85: @@
 ===Download ===
 *Data
-**[[Media:RegLib_C46_Data.zip‎ ‎|'''RegLib_C46_Data'''  DICOM 2D series  <small> (DICOM files, zip file 18 MB) </small>]]'''
+**[[Media:RegLib_C46_Data.zip‎ ‎|'''RegLib_C46_Data''' : DICOM 2D series  <small> (DICOM files, zip file 18 MB) </small>]]'''
 *Results
-**[[Media:RegLib_C46_RegistrationTransforms.zip‎ ‎|'''RegLib_C46_RegistrationTransforms.zip'''  The 200 BSpline registration transforms <small> (ITK transform (text) files, zip file 274 kB) </small>]]'''
+**[[Media:RegLib_C46_RegistrationTransforms.zip‎ ‎|'''RegLib_C46_RegistrationTransforms.zip''' : the 200 BSpline registration transforms <small> (ITK transform (text) files, zip file 274 kB) </small>]]'''
 === Acknowledgments ===
 Thanks to Amir Owrangi and the [http://www.robarts.ca Robarts Institute] for sharing the registration problem and data.

← Older revision		Revision as of 13:27, 29 June 2011
Line 70:		Line 70:

	=== Registration Results===		=== Registration Results===
		+	{\| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
		+	\|[[Image:RegLib_C46_Thumb2.gif\|300px\|lleft\|moving input]]
		+	\|[[Image:RegLib_C46_Moving_animReg.gif\|300px\|lleft\|moving input after registration (only frames 1-27 shown)]]
		+	\|[[Image:RegLib_C46_Displacements.png\|300px\|lleft\|displacements]]
		+	\|-
		+	\|unregistered moving series
		+	\|moving input after registration (only frames 1-27 shown)
		+	\|[[Media:RegLib_C46_Displacements.pdf\|displacements (PDF)]]
		+	\|}
		+

−	~~[[Image:RegLib_C46_Thumb2.gif\|300px\|lleft\|moving input]] unregistered moving series~~
−	~~[[Image:RegLib_C46_Moving_animReg.gif\|300px\|lleft\|moving input after registration (only frames 1-27 shown)]] moving input after registration (only frames 1-27 shown)~~
−	~~[[Image:RegLib_C46_Displacements.png\|300px\|lleft\|displacements]]~~
−	~~[[Media:RegLib_C46_Displacements.pdf\|displacements (PDF)]]~~

	===Download ===		===Download ===