Projects:RegistrationLibrary:RegLib C10 - Revision history

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

2017-07-10T17:25:18Z

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

Meier at 15:59, 12 October 2010

2010-10-12T15:59:44Z

Meier: /* Registration Results */

2010-10-12T15:57:50Z

Registration Results

Meier: /* Methods */

2010-10-12T15:54:22Z

Methods

Meier: /* Methods */

2010-10-12T15:54:06Z

Methods

Meier: /* Methods */

2010-10-12T15:53:56Z

Methods

Meier: /* Download */

2010-10-12T15:49:45Z

Download

Meier: /* Download */

2010-10-12T15:49:15Z

Download

Meier: /* Download */

2010-10-12T15:49:03Z

Download

Meier: /* Methods */

2010-10-12T14:59:34Z

Methods

@@ Line 16: / Line 16: @@
 === Modules ===
-*'''Slicer 3.6.1 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]'''
+*'''Slicer 3.6.1 recommended modules:  [https://www.slicer.org/wiki/Modules:BRAINSFit BrainsFit]'''
 ==Slicer Registration Library Exampe #10: Co-registration of probabilistic tissue atlas for subsequent EM segmentation ==

@@ Line 83: / Line 83: @@
 === Discussion: Registration Challenges ===
 *Because the atlas represents a probabilistic image (i.e. contains blurring from combining multiple subjects), its contrast differs significantly from the target image.
-*The atlas has strong rotational misalignment that can cause difficulty for automated affine registration.
+*The atlas has rotational misalignment that can cause difficulty for automated affine registration.
 *The two images represent different anatomies, a non-rigid registration is required
 === Discussion: Key Strategies ===
 *Because of the strong differences in image contrast, Mutual Information is recommended as the most robust metric.
-*masking (skull stripping) is highly recommended to obtain good results for the initial affine alignment. For the 2nd stage BSpline use the full image (i.e. do NOT use the masked version) unless high-quality masks are available for '''both''' fixed & moving image. Using the crude mask created for the initial alignment for the BSpline will likely destabilize.
+*masking (skull stripping) is recommended to obtain good results for the initial affine alignment. For the 2nd stage BSpline use the full image (i.e. do NOT use the masked version) unless high-quality masks are available for '''both''' fixed & moving image. Using the crude mask created for the initial alignment for the BSpline will likely destabilize.
-*because speed is not that critical, we increase the sampling rate for both affine and BSpline registration
+*because speed is not that critical, increase the default sampling rate for both affine and BSpline registration
 *we also expect larger differences in scale & distortion than with regular structural scans: so we significantly  (2x-3x) increase the expected values for scale and skew from the defaults.
 *a good affine alignment is important before proceeding to non-rigid alignment to further correct for distortions.

@@ Line 66: / Line 66: @@
 === Registration Results===
-{| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
+[[Image:RegLib_C10_unreg_AnimGif.gif|300px|unregistered]] unregistered
-|[[Image:RegLib_C10_unreg_AnimGif.gif|200px|left|unregistered]] [[Image:RegLib_C10_BSpline_AnimGif.gif|200px|left|after BSpline non-rigid registration]]
+[[Image:RegLib_C10_BSpline_AnimGif.gif|300px|after BSpline non-rigid registration]] afterAffine+ fast BSpline non-rigid registration<br><br>
-|}
+[[Image:RegLib_C10_BFit_AGif.gif‎|400px|after BRAINSfit affine+ non-rigid registration]] after BRAINSfit affine+ non-rigid registration<br>
 ===Download ===

@@ Line 48: / Line 48: @@
 ##Click: ''Apply''
 ##manually edit brain mask with '''Editor''' module. required manual fix at frontal and occipital lobe
-#open '''Expert Automated Registration'' module
+#open ''Expert Automated Registration'' module
 ##Settings: Fixed Image: fixed, moving image: moving
 ##Save Transform: ''Xf1_Affine_wmsk''

@@ Line 30: / Line 30: @@
 === Methods ===
-*'''Version 1: BRAINSfit w/o masking''
+*'''Version 1: BRAINSfit w/o masking'''
 #open BRAINSfit module
 ##fixed image: fixed;  moving image: moving

@@ Line 64: / Line 64: @@
 ===Download ===
 *Data
-**'''[[Media:RegLib_C10_MRI-AtlasSegmentation.zip‎‎|RegLib C10 Example Dataset  <small> (Data,Presets, Solutions, zip file 17 MB) </small>]]'''
+**'''[[Media:RegLib_C10_Data.zip‎‎|RegLig_C10_Data  <small> (Data,Presets, Solutions, zip file 17 MB) </small>]]'''
 *Presets
 **'''[[Media:RegLib_C10_Presets_BFit.mrml|download registration parameter presets only<small> (Slicer MRML file, 4 kB) </small>]]'''

@@ Line 70: / Line 70: @@
 **[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
 *Documentation
-*'''[[Media:RegLib_C10_Tutorial.ppt‎‎|download step-by-step tutorial <small> (PowerPoint, 3 MB) </small>]]'''
+**'''[[Media:RegLib_C10_Tutorial.ppt‎‎|download step-by-step tutorial <small> (PowerPoint, 3 MB) </small>]]'''
-*'''[[Media:RegLib_C10_Tutorial.pdf|download step-by-step tutorial <small> (PDF, 5 MB) </small>]]'''
+**'''[[Media:RegLib_C10_Tutorial.pdf|download step-by-step tutorial <small> (PDF, 5 MB) </small>]]'''
 === Discussion: Registration Challenges ===

@@ Line 30: / Line 30: @@
 === Methods ===
-*'''Version 1: Expert Automated + Fast BSpline Modules incl. masking'''
+*'''Version 1: BRAINSfit w/o masking''
 #build brain mask for the fixed image only:
 ##open '''Skull Stripping''' module.
@@ Line 52: / Line 55: @@
 ## initial transform:  "Xf1_Affine_wmsk"
 ##Output Transform: Xf2_BSpline1
 === Registration Results===