Projects:RegistrationLibrary:RegLib C06 - Revision history

Meier: /* Methods */

2012-06-06T20:43:54Z

Methods

Meier: /* Methods */

2012-06-06T20:43:17Z

Methods

Meier: /* Download */

2012-06-06T20:42:10Z

Download

Meier: /* Download */

2012-06-06T20:20:11Z

Download

Meier: /* Download */

2012-06-06T20:19:54Z

Download

Meier: /* Discussion: Key Strategies */

2012-06-06T13:30:38Z

Discussion: Key Strategies

Meier at 22:29, 5 June 2012

2012-06-05T22:29:56Z

Meier: /* Registration Results */

2012-06-05T22:26:30Z

Registration Results

Meier: /* Download */

2012-06-05T22:25:12Z

Download

Meier: /* Methods */

2012-06-05T22:21:02Z

Methods

@@ Line 102: / Line 102: @@
 ##Leave all other settings at default
 ##''Apply''
-##this should generate a first alignment. 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''. See demo movie you can download here shows how to do this.
+##this should generate a first alignment. 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''. See demo movie you can download above on how to do this.
 *'''Phase 5: Nonrigid final registration'''
 #open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit ''General Registration (BRAINS)''] module

@@ Line 46: / Line 46: @@
 *'''Phase 1: Extract left breast image of PreRx and PostRx scan'''
 #Open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Crop_Volume ''Crop Volume'' module]
-###''Input volume'':  "PreRx"
+##''Input volume'':  "PreRx"
-###''Input ROI'': "Create new annotation ROI"
+##''Input ROI'': "Create new annotation ROI"
-###''ROI visibilité'': turn on
+##''ROI visibilité'': turn on
-###''Isotropic output voxel'': yes (checkbox)
+##''Isotropic output voxel'': yes (checkbox)
-###''Interpolator'': "WindowedSinc" (radio button)
+##''Interpolator'': "WindowedSinc" (radio button)
-###place/drag the color markers visible in the slice views to enclose the left breast only (right side of image)
+##place/drag the color markers visible in the slice views to enclose the left breast only (right side of image)
 ##click on ''Crop!'' button
 #go to the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Data ''Data module'']

@@ Line 31: / Line 31: @@
 ===Download ===
 *'''[[Media:RegLib_C06_Data.zip|RegLib_C06_BreastCancer_Data.zip  <small> (Data, Solution, zip file 164 MB) </small>]]'''
-*Documentation: short movie clips (no sound)
+*Documentation: short movie clips (no sound), corresponding to phases 1-5 outlined in detail below.
-**'''[[Media:RegLib_C06_1-CropVolume.mov|RegLib_C06_1-CropVolume.mov  <small> (cropping volume, 3min, 12 MB, Quicktime .mov file) </small>]]'''
+**Phase 1: cropping: ''[[Media:RegLib_C06_1-CropVolume.mov|RegLib_C06_1-CropVolume.mov  <small> (3min, 12 MB, Quicktime .mov file) </small>]]''
-**'''[[Media:RegLib_C06_2-BiasCorrection.mov|RegLib_C06_2-BiasCorrection.mov  <small> (bias field inhomogeneity correction 1.5min 3min, Quicktime .mov file) </small>]]'''
+**Phase 2: bias field inhomogeneity correction: ''[[Media:RegLib_C06_2-BiasCorrection.mov|RegLib_C06_2-BiasCorrection.mov  <small> ( 1.5min 3min, Quicktime .mov file) </small>]]''
-**'''[[Media:RegLib_C06_3-Masking.mov|RegLib_C06_3-Masking.mov  <small> (cropping volume, 5min, 21 MB, Quicktime .mov file) </small>]]'''
+**Phase 3: build mask: ''[[Media:RegLib_C06_3-Masking.mov|RegLib_C06_3-Masking.mov  <small> (5min, 21 MB, Quicktime .mov file) </small>]]''
-**'''[[Media:RegLib_C06_4-AffineRegistration.mov|RegLib_C06_4-AffineRegistration.mov <small> (affine linear registration, 2min, 10 MB, Quicktime .mov file) </small>]]'''
+**Phase 4: affine registration: ''[[Media:RegLib_C06_4-AffineRegistration.mov|RegLib_C06_4-AffineRegistration.mov <small> (2min, 10 MB, Quicktime .mov file) </small>]]''
-**'''[[Media:RegLib_C06_5-BSplineRegistration.mov|RegLib_C06_5-BSplineRegistration.mov<small> (nonrigid registration 3min, 17 MB, Quicktime .mov file) </small>]]'''
+**Phase 5: nonrigid registration: ''[[Media:RegLib_C06_5-BSplineRegistration.mov|RegLib_C06_5-BSplineRegistration.mov<small> (3min, 17 MB, Quicktime .mov file) </small>]]''
 ===Input Data===

@@ Line 34: / Line 34: @@
 **'''[[Media:RegLib_C06_1-CropVolume.mov|RegLib_C06_1-CropVolume.mov  <small> (cropping volume, 3min, 12 MB, Quicktime .mov file) </small>]]'''
 **'''[[Media:RegLib_C06_2-BiasCorrection.mov|RegLib_C06_2-BiasCorrection.mov  <small> (bias field inhomogeneity correction 1.5min 3min, Quicktime .mov file) </small>]]'''
-**'''[[Media:RegLib_C06_3-Masking.mov|RegLib_C06_1-Masking.mov  <small> (cropping volume, 5min, 21 MB, Quicktime .mov file) </small>]]'''
+**'''[[Media:RegLib_C06_3-Masking.mov|RegLib_C06_3-Masking.mov  <small> (cropping volume, 5min, 21 MB, Quicktime .mov file) </small>]]'''
 **'''[[Media:RegLib_C06_4-AffineRegistration.mov|RegLib_C06_4-AffineRegistration.mov <small> (affine linear registration, 2min, 10 MB, Quicktime .mov file) </small>]]'''
 **'''[[Media:RegLib_C06_5-BSplineRegistration.mov|RegLib_C06_5-BSplineRegistration.mov<small> (nonrigid registration 3min, 17 MB, Quicktime .mov file) </small>]]'''

@@ Line 31: / Line 31: @@
 ===Download ===
 *'''[[Media:RegLib_C06_Data.zip|RegLib_C06_BreastCancer_Data.zip  <small> (Data, Solution, zip file 164 MB) </small>]]'''
 ===Input Data===

@@ Line 135: / Line 135: @@
 === Discussion: Key Strategies ===
 *because of the strong changes in shape and position, we break the problem down and register each breast separately.
-*we perform a bias-field correction on both images before registration
+*a bias-field correction on both images is necessary before registration
-*we use the Multires version of RegisterImages for an initial affine alignment
+*to get better control over the process, we separate affine prior from final nonrigid alignment. The result of the affine registration is used as initialization for the nonrigid portion
-*the nonlinear portion is then addressed with a BSpline or DiffeomorphicDemons algorithm
+*masking the tumor area is critical for a feasible solution, i.e. the tumor area in both scans should '''not''' participate actively in the registration, i.e. we create a mask that includes everything except the tumor area

@@ Line 17: / Line 17: @@
 <big>[[Projects:RegistrationLibrary:RegLib_C06B|'''For the Slicer 3.6 version of this tutorial see here''']]</big>
-=== Modules  ===
+=== Slicer 4.1 Modules used ===
-*'''Slicer 3.6.1 recommended modules:
+*[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/N4ITKBiasFieldCorrection ''N4ITKBiasFieldCorrection'']
-** [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution Affine]'''
+*[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Crop_Volume ''Crop Volume'']
-** [http://www.slicer.org/slicerWiki/index.php/Modules:DeformableB-SplineRegistration-Documentation-3.6 Fast Nonrigid BSpline]'''
+*[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ForegroundMasking ''Foregroud masking (BRAINS)'']
+*[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Editor ''Editor'']
 ===Objective / Background ===
 We seek to align the post-treatment (PostRx) scan with the pre-treatment scan to compare local effects (left side only).

@@ Line 115: / Line 115: @@
 === Registration Results===
-[[Image:RegLib_C06_LeftUnreg_AnimGif.gif||300px|unregistered]]
+[[Image:RegLib_C06_unregistered.gif||300px|unregistered]] unregistered
-[[Image:RegLib_C06_LeftAffreg_AnimGif.gif|300px|affine registered]]
+[[Image:RegLib_C06_Affine.gif|300px|affine registered]] after affine registration
-[[Image:RegLib_C06_LeftBSplreg_AnimGif.gif|300px|Bspline registered]]
+[[Image:RegLib_C06_BSpline.gif|300px|Bspline registered]] after nonrigid (BSpline) registration

@@ Line 76: / Line 76: @@
 ##''Apply''
 #repeat for Post_Rx_left_n4
 #save intermediate results
 *'''Phase 4: Affine pre-Registration'''
@@ Line 90: / Line 102: @@
 ##Leave all other settings at default
 ##''Apply''
-##this should generate a first alignment. To see it you need to:
+##this should generate a first alignment. 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''. See demo movie you can download here shows how to do this.
+*'''Phase 5: Nonrigid final registration'''
-t and also 2 masks. We already have a DWI mask, so we care not  about "DWI_mask_ROIauto", but we will use the T1_mask_ROIauto" output to edit/cleanup and use as mask in the subsequent nonrigid registration
+#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit ''General Registration (BRAINS)''] module
-*'''Phase IV: T1 mask'''
+##''Fixed Image Volume'': PreRx_left_n4
-#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Editor Editor module]
+##''Moving Image Volume'': PostRx_left_n4
 ##Output Settings:
-###''Slicer BSpline Transform": create new transform, rename to "Xf2_DWI-T1_BSpline"
+###''Slicer BSpline Transform": create & rename new transform, rename to "Xf2_BSpline"
 ###''Slicer Linear Transform'': none
-###''Output Image Volume'': create new volume,  rename to "DWI_baseline_Xf2"
+###''Output Image Volume'': create & rename new transform, rename to "PostRx_left_Xf2"
-##''Registration Phases'': check boxes for ''BSpline'' only
+##''Registration Phases'': uncheck rigid & affine boxes, check box for ''BSpline'' only
 ##''Main Parameters'':
-###''Number Of Samples'': 200,000
+###''Number Of Samples'': 300,000
-###''B-Spline Grid Size'': 5,5,5
+###''B-Spline Grid Size'': 7,7,5
 ##''Mask Option'': select ''ROI'' button
-###''ROI Masking input fixed'': select  " "T1_mask_ROIauto" or "T1_mask_edit" edited in phase III above
+###''ROI Masking input fixed'': select  "PreRx_mask" generated in Phase 3 above
-###''ROI Masking input moving'':  select  "DWI_mask" created in phase I above
+###''ROI Masking input moving'':  select  "PostRx_mask" generated in Phase 3 above
 ##Leave all other settings at default
 ##click: Apply