Projects:RegistrationLibrary:RegLib C02 - Revision history

Meier: /* Slicer 4.1 Modules */

2012-06-11T13:36:37Z

Slicer 4.1 Modules

Meier at 13:36, 11 June 2012

2012-06-11T13:36:07Z

Meier: /* Procedures */

2012-06-11T13:33:53Z

Procedures

Meier: /* Download */

2012-06-11T13:24:47Z

Download

Meier: /* Download */

2012-06-11T13:24:31Z

Download

Meier: /* Registration Results */

2012-06-11T13:22:37Z

Registration Results

Meier at 20:34, 14 April 2011

2011-04-14T20:34:21Z

Meier: /* Download */

2011-04-14T20:32:09Z

Download

Meier: /* Download */

2011-04-14T20:31:29Z

Download

Meier: /* Download */

2011-04-14T20:27:04Z

Download

@@ Line 24: / Line 24: @@
 === Slicer 4.1 Modules ===
-*[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS) module]
+*[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS)]
-*[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSResample ''Resample Image (BRAINS)'' module]
+*[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSResample Resample Image (BRAINS)]
 ===Objective / Background ===

@@ Line 3: / Line 3: @@
 [[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br>
-= <small>v3.6.3</small> [[Image:Slicer363_banner.png‎|150px]]  Slicer Registration Library Case #02: Intra-subject Brain MR FLAIR to MR T1 =
+= <small>updated for '''v4.1'''</small> [[Image:Slicer4_RegLibLogo.png|150px]] <br>Slicer Registration Library Case #02: Intra-subject Brain MR FLAIR to MR T1 =
 === Input ===
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
@@ Line 23: / Line 23: @@
 |}
-=== Modules ===
+=== Slicer 4.1 Modules ===
-*'''Slicer 3.6.3 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution Affine]''', [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated Registration]
+*[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS) module]
 ===Objective / Background ===
@@ Line 54: / Line 55: @@
 ===Key Strategies===
 *we use an affine transform with 12 DOF (rather than a rigid one) to address distortion differences between the two protocols
 *we choose the SPGR as the anatomical reference. Unless there are overriding reasons, always use the highest resolution image as your fixed/reference, to avoid loosing data through the registration.
 === Procedures ===
-*'''Phase I: register FLAIR to T1''
+*'''Phase I: register FLAIR to T1'''
 #open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS) module]
 ##''Fixed Image Volume'': T1
@@ Line 87: / Line 85: @@
 ##click/open the ''Volume Information'' tab
 ##check the ''LabelMap'' checkbox.
-#more details in the ScreenCast movies in the download section above.
+*more details in the ScreenCast movies in the download section above.
 === Registration Results===

@@ Line 61: / Line 61: @@
 === Procedures ===
-'''with  BrainsFit''' (< 1 min):
+*'''Phase I: register FLAIR to T1''
-#download example dataset
+#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS) module]
-#load SlicerScene1.mrml  into 3DSlicer 3.6.3
+##''Fixed Image Volume'': T1
-#open Registration : ''BrainsFit'' module
+##''Moving Image Volume'': FLAIR
-#select Preset_Xf1_BRAINSfit or select as outlined below:
+##Output Settings:
-#Input Parameters: set SPGR as fixed and FLAIR as moving image
+###''Slicer BSpline Transform": none
-#Registration Phases:
+###''Slicer Linear Transform'': create new transform, rename to "Xf1_Affine"
-##select ''none" for ''Initialize Transform Mode''
+###''Output Image Volume'': create new volume,  rename to "FLAIR_Xf1"
-##select ''Initialize with CenterofHeadAlign''
+##''Registration Phases'': check boxes for ''Rigid'' and ''Affine''
-##select ''Include Rigid registration phase''
+##''Main Parameters'':
-##select  "Include Affine registration phase"
+###''Number Of Samples'': 200,000
-#Output Settings: select "New Linear Transform" under ''Slicer Linear Transform''
+##Leave all other settings at default
-#leave all other settings at defaults
+##click: Apply; runtime < 10 sec (MacPro QuadCore 2.4GHz)
-#click apply
+*'''Phase II: Resample labelmap'''
-#program will automatically move FLAIR image  under the result transform; also manually move the labelmap
+#go to [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSResample ''Resample Image (BRAINS)'' module] (in the Registration menu)
-#right click on either image and select ''Harden Transform'' to apply & resample
+##''Image To Warp'': LesionSeg
-#save result images/scene
+##''Reference Image'': T1
-<br>
+##''Output Image'': create new & rename: LesionSeg_Xf1
-'''with  Expert Automated Registration''' (< 2 min):
+##''Pixel Type'': uchar or binary
-#download example dataset
+##''Warp By Transform'':  Xf1_Affine created in Phase I above
-#load SlicerScene1.mrml into 3DSlicer 3.6.3
+##''Interpolation Mode'': '''Nearest Neighbor'''
-#open Registration : ''Expert Automated Registration''' module
+##''Apply''
-#select Preset_Xf2_ExpertAuto or select as outlined below:
+#go to [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Volumes ''Volumes''] module
-##IO Parameters: set SPGR as fixed and FLAIR as moving image, "none" as Resample image
+##''Active Volume'': LesionSeg_Xf1
-##Registration Parameters:
+##click/open the ''Volume Information'' tab
-##''Save Transform": create new, then rename to "Xf2_..."
+##check the ''LabelMap'' checkbox.
-##Initialization: "none", Registration: "Pipeline Affine", Metric: "MI"
+#more details in the ScreenCast movies in the download section above.
 === Registration Results===

@@ Line 36: / Line 36: @@
 **[[Media:RegLib_C02_Data.zip‎|'''Registration Library Case 02: MSBrain intra-subject multi-contrast''' <small> (Data, Presets & Solution Xforms, zip file 19 MB) </small>]]
 *ScreenCast Movies:
-**[[MediaRegLib_C02_Registration.mov|registration via BRAINS<small> (quicktime movie 12 MB </small>]]
+**[[Media:RegLib_C02_Registration.mov|registration via BRAINS<small> (quicktime movie 12 MB </small>]]
-**[[MediaRegLib_C02_Resample.mov|resampling the labelmap with the computed affine transform<small> (quicktime movie 12 MB </small>]]
+**[[Media:RegLib_C02_Resample.mov|resampling the labelmap with the computed affine transform<small> (quicktime movie 12 MB </small>]]
 ===Input Data===

@@ Line 35: / Line 35: @@
 *Data:
 **[[Media:RegLib_C02_Data.zip‎|'''Registration Library Case 02: MSBrain intra-subject multi-contrast''' <small> (Data, Presets & Solution Xforms, zip file 19 MB) </small>]]
-*Presets:
+*ScreenCast Movies:
-**[[Media:RegLib_C02_Presets.mrml|'''Registration Library Case 02: Registration Presets''' <small> (mrml file 12 kB, load via "Import Scene...") </small>]]
+**[[MediaRegLib_C02_Registration.mov|registration via BRAINS<small> (quicktime movie 12 MB </small>]]
-::[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
+**[[MediaRegLib_C02_Resample.mov|resampling the labelmap with the computed affine transform<small> (quicktime movie 12 MB </small>]]
 ===Input Data===

@@ Line 116: / Line 116: @@
 === Registration Results===
 [[Image:RegLib_C02_Unreg_AnimGif.gif|500px|Unregistered Data + segmentation labelmap]] unregistered <br>
-[[Image:RegLib_C02_Result_AnimGif.gif|500px|Robust Multiresolution Registration Result: FLAIR + segmentation aligned with SPGR]] : registered w. Multiresolution affine <br>
+[[Image:RegLib_C02_registered.gif|500px|Robust Multiresolution Registration Result: FLAIR + segmentation aligned with SPGR]] : registered w. Multiresolution affine <br>
 <br>

@@ Line 34: / Line 34: @@
 === Download ===
 *Data:
-**[[Media:RegLib_C02_DATA.zip‎|'''Registration Library Case 02: MSBrain intra-subject multi-contrast''' <small> (Data & Solution Xforms, zip file 18 MB) </small>]]
+**[[Media:RegLib_C02_Data.zip‎|'''Registration Library Case 02: MSBrain intra-subject multi-contrast''' <small> (Data, Presets & Solution Xforms, zip file 19 MB) </small>]]
 *Presets:
-**both recommended modules run with default settings. No presets required.
+**[[Media:RegLib_C02_Presets.mrml|'''Registration Library Case 02: Registration Presets''' <small> (Data, Presets & Solution Xforms, zip file 12 kB) </small>]]
 *Documentation:
 **see outlines below