Projects:RegistrationLibrary:RegLib C38 - Revision history

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

2017-07-10T18:07:36Z

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

Meier: /* Registration Results */

2012-06-06T22:12:52Z

Registration Results

Meier: /* Registration Results */

2012-06-06T22:12:41Z

Registration Results

Meier at 22:11, 6 June 2012

2012-06-06T22:11:52Z

Meier at 22:10, 6 June 2012

2012-06-06T22:10:43Z

Meier at 22:07, 6 June 2012

2012-06-06T22:07:31Z

Meier: /* Procedure */

2012-06-06T22:02:49Z

Procedure

Meier at 21:51, 6 June 2012

2012-06-06T21:51:06Z

Meier: /* Download */

2011-06-23T15:23:33Z

Download

Meier at 23:10, 8 March 2011

2011-03-08T23:10:29Z

@@ Line 31: / Line 31: @@
 === Slicer 4.1 recommended Modules ===
-*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BrainsFit]
+*[https://www.slicer.org/wiki/Documentation/4.1/Modules/BRAINSFit BrainsFit]
 === Download ===

@@ Line 76: / Line 76: @@
 === Registration Results===
-[[Image:RegLib_C38_unregistered.gif|left|300px|unregistered]] unregistered <br>
+[[Image:RegLib_C38_unregistered.gif|300px|unregistered]] unregistered <br>
-[[Image:RegLib_C38_registered.gif|left|300px|registered]] registered
+[[Image:RegLib_C38_registered.gif|300px|registered]] registered

@@ Line 76: / Line 76: @@
 === Registration Results===
-[[Image:RegLib_C38_unregistered.gif|left|300px|unregistered]] unregistered
+[[Image:RegLib_C38_unregistered.gif|left|300px|unregistered]] unregistered <br>
 [[Image:RegLib_C38_registered.gif|left|300px|registered]] registered

@@ Line 36: / Line 36: @@
 *[[Media:RegLib_C38_Data.zip‎|'''TBI case: ''' <small> (Data & Solution Xforms, zip file 40 MB) </small>]]
 *Documentation/Tutorials: short video clips (no sound)
-**register T2-T1: [[Media:RegLib_C38_T2_register.mov]] <small> (quicktime movie, 17 MB)
+**register T2-T1: [[Media:RegLib_C38_T2_register.mov]] <small> (quicktime movie, 17 MB) </small>
-**register T2-SWI: [[Media:RegLib_C38_SWI_register.mov]] <small> (quicktime movie, 14 MB)
+**register T2-SWI: [[Media:RegLib_C38_SWI_register.mov]] <small> (quicktime movie, 14 MB) </small>
-**register T2-GRE: [[Media:RegLib_C38_GRE_register.mov]] <small> (quicktime movie, 14 MB)
+**register T2-GRE: [[Media:RegLib_C38_GRE_register.mov]] <small> (quicktime movie, 14 MB) </small>
-**register T2-FLAIR: [[Media:RegLib_C38_FLAIR_register.mov]] <small> (quicktime movie, 9 MB)
+**register T2-FLAIR: [[Media:RegLib_C38_FLAIR_register.mov]] <small> (quicktime movie, 9 MB) </small>
-**register T2-EP: [[Media:RegLib_C38_EP_register.mov]] <small> (quicktime movie, 9 MB)
+**register T2-EP: [[Media:RegLib_C38_EP_register.mov]] <small> (quicktime movie, 9 MB) </small>
-**apply all Xforms:  [[Media:RegLib_C38_ApplyXform.mov]] <small> (quicktime movie, 6MB)
+**apply all Xforms:  [[Media:RegLib_C38_ApplyXform.mov]] <small> (quicktime movie, 6MB) </small>
 ===Objective / Background ===
@@ Line 76: / Line 76: @@
 === Registration Results===
-[[Image:RegLib_C38_unregistered.gif|unregistered]]
+[[Image:RegLib_C38_unregistered.gif|left|300px|unregistered]] unregistered
-[[Image:RegLib_C38_registered.gif|unregistered]]
+[[Image:RegLib_C38_registered.gif|left|300px|registered]] registered

@@ Line 36: / Line 36: @@
 *[[Media:RegLib_C38_Data.zip‎|'''TBI case: ''' <small> (Data & Solution Xforms, zip file 40 MB) </small>]]
 *Documentation/Tutorials: short video clips (no sound)
-**register T2-T1: [[Media:RegLib_C38_T2_register.mov|register T2]] <small> (quicktime movie, 17MB)
+**register T2-T1: [[Media:RegLib_C38_T2_register.mov]] <small> (quicktime movie, 17 MB)
 ===Objective / Background ===

@@ Line 55: / Line 55: @@
 * we limit registration degree of freedom to 6 DOF (rigid transformation only).
 === Procedure ===
 #Load all datasets via drag&drop or via "AddData / AddVolume" ... do not center the volumes, since they have reasonable alignment at the outset
 #the registration procedure below is identical for all other scans in the sequence, i.e. just replace the ''Moving Volume'' and the ''Slicer Linear Transform", everything else can stay at default

@@ Line 3: / Line 3: @@
 [[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br>
-= <small>v3.6.1</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]]  Slicer Registration Library Case 38: TBI   =
+= <small>updated for '''v4.1'''</small> [[Image:Slicer4_RegLibLogo.png|150px]]    Slicer Registration Library Case 38: TBI   =
 === Input ===
@@ Line 30: / Line 30: @@
 |}
-=== Modules ===
+=== Slicer 4.1 recommended Modules ===
-*'''Slicer 3.6.1 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]'''
+*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BrainsFit]
 === Download ===
 *DATA
 **[[Media:RegLib_C38_Data.zip‎|'''TBI case: ''' <small> (Data & Solution Xforms, zip file 40 MB) </small>]]
 ===Objective / Background ===
@@ Line 55: / Line 52: @@
 ===Key Strategies===
-*we first register the scans within each exam to the T1
+*we register all the scans within each exam to the T1
+* we limit registration degree of freedom to 6 DOF (rigid transformation only).
 === Procedure ===
 *'''Load & Center'''
-#Load T1 MPRAGE datasets via Load Volume...
+#Load all datasets via drag&drop or via "AddData / AddVolume" ... do not center the volumes, since they have reasonable alignment at the outset
-#volumes are note well centered, i.e. their physical origin defined in the image header differs; we therefore first center both images:
+#the registration procedure below is identical for all other scans in the sequence, i.e. just replace the ''Moving Volume'' and the ''Slicer Linear Transform", everything else can stay at default
-##Go to ''Volumes'' module, open ''Info'' tab
+#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS) module]
-##From ''Active Volume'' menu, select each image in turn, then click the ''Center Image'' button
+##''Fixed Image Volume'': T1
-##note how Image origin changes for T1_e1 from 121,-97,-97 to 128,-128,-80 and for T1_e2 from 129,-106,-66 to 128,-128,-80
+##''Moving Image Volume'': T2
-##now that both images have same center their initial misalignment can be seen by placing T1_e1 in the background and T1_e in the foreground and using the toggle-switch
+##Output Settings:
-*'''Align Exam 2 to Exam 1: T1''' 1st pass: unmasked
+###''Slicer BSpline Transform": none
-#Open ''Registration / BRAINSFit'' module
+###''Slicer Linear Transform'': create new transform, rename to "Xf1_T2"
-##Fixed Image: T1_e1, moving image: T1_e2
+###''Output Image Volume'': none
-##Registration Phases: select "Initialize with CenterOfHeadAlign",  ''Include Rigid'', "IncludeScaleVersor3D" and ''Include Affine''
+##''Registration Phases'': check box for ''Rigid'' only
-##Output Settings: under SlicerLinear Transform, select "Create New Linear Transform'', then select ''Rename" and rename it to ''Xf1_e2-e1_Affine''
+##leave all other settings at defaults
-##Registration Parameters: increase the ''Number of Samples'' field to 200,000
+##click: Apply; runtime < 15 sec (MacPro QuadCore 2.4GHz)
-##Leave all other settings at defaults & Click:  ''Apply''. Registration should complete within ~ 30 seconds
+#this will generate the alignment transform. Note that the Slicer4.1 version of BRAINS registration does '''not''' automatically place the moving volume inside the result transform, as it did for Slicer 3.6. In order to see the result, you must either go to the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Data ''Data module''] and drag the moving volume inside the transform node, or select to generate a resampled ''Output Volume'', as done above. The demo movies you can download here show how to do this.
 === Registration Results===

@@ Line 24: / Line 24: @@
 |coronal T2
 |SWI
 |EP50
 |EP75