Projects:RegistrationLibrary:RegLib C03 - Revision history

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

2017-07-10T17:29:10Z

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

Meier at 15:35, 2 June 2012

2012-06-02T15:35:15Z

Meier at 19:53, 4 May 2012

2012-05-04T19:53:00Z

Meier at 15:39, 27 April 2012

2012-04-27T15:39:02Z

Meier: /* Procedure */

2012-04-27T15:05:54Z

Procedure

Meier: /* Procedure */

2012-04-27T15:05:18Z

Procedure

Meier: /* Procedure */

2012-04-27T15:04:37Z

Procedure

Meier: /* Procedure */

2012-04-27T15:02:31Z

Procedure

Meier: /* Download */

2012-04-27T15:00:13Z

Download

Meier: /* Download */

2012-04-27T14:59:38Z

Download

@@ Line 21: / Line 21: @@
 === Slicer 4.1 Modules Used ===
-*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BrainsFit]
+*[https://www.slicer.org/wiki/Documentation/4.1/Modules/BRAINSFit BrainsFit]
-*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume]
+*[https://www.slicer.org/wiki/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume]
-*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation]
+*[https://www.slicer.org/wiki/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation]
 === Alternate Versions ===
@@ Line 34: / Line 34: @@
 === Procedure ===
-This assumes you have the following: 1) a T2 reference image, 2) a DTI baseline image and  3) the DTI volume (both obtained from the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation module]).
+This assumes you have the following: 1) a T2 reference image, 2) a DTI baseline image and  3) the DTI volume (both obtained from the  [https://www.slicer.org/wiki/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation module]).
 *Image Data:
 *'''Overview''':
-::#Using  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]''', register DTI_baseline to T2 (affine+nonrigid) w/o masking
+::#Using  [https://www.slicer.org/wiki/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]''', register DTI_baseline to T2 (affine+nonrigid) w/o masking
-:#Resample the DTI with above transform with the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume] module
+:#Resample the DTI with above transform with the  [https://www.slicer.org/wiki/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume] module
-#open  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit Registration : ''General Registration (BRAINS)'']  module
+#open  [https://www.slicer.org/wiki/Modules:BRAINSFit Registration : ''General Registration (BRAINS)'']  module
 ##''Input Images'': fixed = T2 , moving = DTI_base
 ##''Output Settings'':
@@ Line 52: / Line 52: @@
 ##click: ''Apply''; runtime < 1 min.
 #Resample DTI
-#Open the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume] module (found under: All Modules)
+#Open the  [https://www.slicer.org/wiki/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume] module (found under: All Modules)
 ##Input Volume: select DTI
 ##Output Volume: select ''create new Diffusion Tensor Volume'',and rename it to ''DTI_Xf1''

@@ Line 20: / Line 20: @@
 Goal is to align the DTI image with the structural reference T2 scan that provides accuracte anatomical reference.
-=== Modules Used ===
+=== Slicer 4.1 Modules Used ===
-*'''Slicer 4.1 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BrainsFit]''', [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume], [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation]
+*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BrainsFit]
 === Alternate Versions ===

@@ Line 3: / Line 3: @@
 [[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br>
-== <small>updated for '''v4.1'''</small> [[Image:Slicer4_RegLibLogo.png|150px]] Slicer Registration Library Case #3: Diffusion Weighted Image Volume: align with structural reference MRI==
+== <small>updated for '''v4.1'''</small> [[Image:Slicer4_RegLibLogo.png|150px]] <br>Slicer Registration Library Case #3: Diffusion Weighted Image Volume: align with structural reference MRI==
 === Input ===
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"

@@ Line 17: / Line 17: @@
 |}
-=== Modules ===
+===Objective / Background ===
 *'''Slicer 4.1 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BrainsFit]''', [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume], [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation]
-===Objective / Background ===
+=== Alternate Versions ===
-Goal is to align the DTI image with the structural reference T2 scan that provides accuracte anatomical reference.
+*this example covers the most basic form of directly registering a DTI + baseline to a T2. There is another (more advanced) version that show how to address additional issues of a strong initial rotation and strong voxel-anisotropy for the raw DWI image acquired.  [[Projects:RegistrationLibrary:RegLib_C03B|You will find the advanced version here]].
-*'''Alternate Versions:''' this example covers the most basic form of directly registering a DTI + baseline to a T2. There is another (more advanced) version that show how to address additional issues of a strong initial rotation and strong voxel-anisotropy for the raw DWI image acquired.  [[Projects:RegistrationLibrary:RegLib_C03_2|You will find the advanced version here]].
+*[[Projects:RegistrationLibrary:RegLib_C03_v3|for the Slicer 3.6.3 version of this case see here]]
 ===Download ===

@@ Line 52: / Line 52: @@
 ##Output Volume: select ''create new Diffusion Tensor Volume'',and rename it to ''DTI_Xf1''
 ##Reference Volume: select ''T2''
-##Transform Parameters: select transform node "Xf2_DTI-T2_BSpline", for  ''Deformation Field'': none ; '''check the ''displacement'' checkbox'''
+##Transform Parameters: select transform node "Xf1_DTI-T2_BSpline", for  ''Deformation Field'': none ; '''check the ''displacement'' checkbox'''
 ##Leave all other settings at defaults
 ##Click Apply; runtime ~ 2 min.
-#set ''T2'' as background and new  ''DTI_Xf2'' volume as foreground
+#set ''T2'' as background and new  ''DTI_Xf1'' volume as foreground
-#fade between back- and foreground to see DTI overlay onto the T2 image. Note that you can also fade via holding the OPTION+CMD keys (mac) + left mouse.
+#fade between back- and foreground to see DTI overlay onto the T2 image. Note that you can also fade via holding the OPTION+CMD keys (mac) + dragging left mouse.
 === Registration Results  (click to enlarge) ===