Projects:RegistrationLibrary:RegLib C01 - Revision history

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

2017-07-10T17:42:47Z

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

Meier: /* Download */

2012-06-03T20:12:37Z

Download

Meier: /* Discussion: Key Strategies */

2012-06-03T20:00:53Z

Discussion: Key Strategies

Meier: /* Discussion: Key Strategies */

2012-06-03T20:00:26Z

Discussion: Key Strategies

Meier: /* Procedure using the Expert Automated Registration module */

2012-06-03T19:58:44Z

Procedure using the Expert Automated Registration module

Meier at 19:58, 3 June 2012

2012-06-03T19:58:05Z

Meier at 19:41, 3 June 2012

2012-06-03T19:41:23Z

Meier: /* Registration Results */

2012-06-03T19:28:01Z

Registration Results

Meier: /* Download */

2012-06-02T17:00:37Z

Download

Meier at 16:06, 2 June 2012

2012-06-02T16:06:57Z

@@ Line 20: / Line 20: @@
 === 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]
 *[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/AffineRegistration Affine Registration]
 *[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ExpertAutomatedRegistration Expert Automated Registration]

@@ Line 95: / Line 95: @@
 ===Download ===
 *Slicer 3.6.3 packages:
-**'''[[Media:RegLib_C01_Data.zip‎|Image Data + solutions package  <small> (Data, Solution, zip file qqMB) </small>]]'''
+**'''[[Media:RegLib_C01_Data.zip‎|Image Data + solutions package  <small> (NRRD images, SceneFile, Solution Xforms, zip file 11 MB) </small>]]'''
 **'''[[Media:RegLib_C01_BRAINSreg.mov|ScreenCast video: ''General BRAINS registration <small> (Quicktime movie 3min, 20MB) </small>]]'''
 **'''[[Media:RegLib_C01_AffineReg.mov|ScreenCast video: ''Affine registration <small> (Quicktime movie 1.5min, 10MB) </small>]]'''

← Older revision		Revision as of 20:00, 3 June 2012
Line 115:		Line 115:
	*if the pathology change is soo large that it might affect the registration, we should mask it out. The simplest way to do this is to build a box ROI from the ROItool and feed it as input to the registration. Remember that masking does not mean that masked areas aren't matched, they just do not contribute to the cost function driving the registration, but move along passively. Next more involved level would be to outline the tumor. If a segmentation is available, you can use that.		*if the pathology change is soo large that it might affect the registration, we should mask it out. The simplest way to do this is to build a box ROI from the ROItool and feed it as input to the registration. Remember that masking does not mean that masked areas aren't matched, they just do not contribute to the cost function driving the registration, but move along passively. Next more involved level would be to outline the tumor. If a segmentation is available, you can use that.
	*these two images are not too far apart initially, so we reduce the default of expected translational misalignment		*these two images are not too far apart initially, so we reduce the default of expected translational misalignment
−	*because accuracy is more important than speed here, we increase the sampling rate from the default 2% to 15%.
−	*we also expect minimal differences in scale & distortion: so we can either set the expected values to 0 or run a rigid registration
−	*we test the result in areas with good anatomical detail and contrast, far away from the pathology. With rigid body motion a local measure of registration accuracy is representative and can give us a valid limit of detectable change.

@@ Line 113: / Line 113: @@
 *the two images have identical contrast, hence we consider "sharper" cost functions, such as NormCorr or MeanSqrd
 *general practice is to register the follow-up to the baseline. However here the follow-up has slightly higher resolution. From an image quality/data perspective it would be better to use the highest resolution image as your fixed/reference. But here follow the most common convention, i.e. fixed image is the baseline.
 *if the pathology change is soo large that it might affect the registration, we should mask it out. The simplest way to do this is to build a box ROI from the ROItool and feed it as input to the registration. Remember that masking does not mean that masked areas aren't matched, they just do not contribute to the cost function driving the registration, but move along passively.  Next more involved level would be to outline the tumor. If a segmentation is available, you can use that.
 *these two images are not too far apart initially, so we reduce the default of expected translational misalignment

@@ Line 72: / Line 72: @@
 ##Registration Parameters tab:
 ###''Save transform'': create new transform, rename to "Xf1_Affine3"
-###'Initialization''': None (radiobutton)
+###''Initialization'': None (radiobutton)
 ###''Registration'': Affine (radiobutton)
 ##''Advanced Affine Registration Parameters''

@@ Line 49: / Line 49: @@
 #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 movie you can download here shows how to do this.
-== Procedure using ''Affine Registration ==
+== Procedure using the ''Affine Registration'' module ==
 *there is a brief movie in the download section that shows this procedure step by step
-#open the[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/AffineRegistration Affine Registration] module
+#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/AffineRegistration Affine Registration] module (under "All Modules" menu
 ##Registration Parameters tab:  '''Spatial Samples''': 200,000
 ##IO tab:
@@ Line 64: / Line 64: @@
 #use fade slider to shift between fore- and background to view the registration quality.
-== Procedure using ''Expert Automated Registration ==
+== Procedure using the ''Expert Automated Registration'' module ==
 === Registration Results===

@@ Line 21: / Line 21: @@
 === Slicer 4.1 recommended Modules ===
 *[http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BrainsFit]
+*[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/AffineRegistration Affine Registration]
-*[http://www.slicer.org/slicerWiki/index.php/Modules:AffineRegistration-Documentation-3.6 Fast Affine Registration]
+*[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ExpertAutomatedRegistration Expert Automated Registration]
 ===Objective / Background ===
-This is a classic case of change assessment. We want to know if the tumor changed since last exam.
+This is a typical case of change assessment. We want to know if/how the tumor changed since last exam.
 === Keywords ===
 MRI, brain, head, intra-subject, T1, tumor growth, meningioma, change assessment
@@ Line 34: / Line 33: @@
 *moving: T1 SPGR , 0.9375 x 0.9375 x 1.2 mm voxel size, sagittal, RAS orientation.
-== Procedure ==
+== Procedure using ''General (BRAINS) Registration ==
 #open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS) module]
 ##''Fixed Image Volume'': MRMeningioma_1
@@ Line 48: / Line 48: @@
 #this will generate 1) the alignment transform , 2) a resampled volume
 #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 movie you can download here shows how to do this.
 === Registration Results===

@@ Line 51: / Line 51: @@
 === Registration Results===
 {| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C01_AGif_FastAffine.gif|400px|center|Fast Affine registration result]]
+|[[Image:RegLib_C01_unregistered.gif|300px|center|unregistered]]
-|[[Image:RegLib01_GifAnim_reg.gif|200px|center|after orientation]]
+|[[Image:RegLib_C01_AffineBRAINS.gif|300px|center|after affine alignment using the ''General (BRAINS) registration module'']]
 |-
-|''Fast Affine'' registration result
+|unregistered
-|''ExpertAutomatedRegistration'' registration result
+|after affine alignment using the ''General (BRAINS) registration module'']
 |}

@@ Line 63: / Line 63: @@
 *Slicer 3.6.3 packages:
 **'''[[Media:RegLib_C01_Data.zip‎|Image Data + solutions package  <small> (Data, Solution, zip file qqMB) </small>]]'''
-**'''[[Media:RegLib_C01_ScreenCast.mov|ScreenCast video  <small> (Quicktime movie 14MB) </small>]]'''
+**'''[[Media:RegLib_C01_BRAINSreg.mov|ScreenCast video: ''General BRAINS registration <small> (Quicktime movie 3min, 20MB) </small>]]'''
-**[[Media:RegLib_C01_Presets.mrml|download registration & display parameter presets file  <small> (MRML file, use "Import Scene.." to load) </small>]]
+**'''[[Media:RegLib_C01_AffineReg.mov|ScreenCast video: ''Affine registration <small> (Quicktime movie 1.5min, 10MB) </small>]]'''
-:::[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
+**'''[[Media:RegLib_C01_ExpertAutoReg.mov|ScreenCast video: ''Expert Automated registration <small> (Quicktime movie 2min, 13MB) </small>]]'''
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