Documentation:Nightly:Registration:RegistrationLibrary:RegLib C06 - Revision history

Grundlett: Text replacement - "\[http:\/\/wiki\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:15:40Z

Text replacement - "\[http:\/\/wiki\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Meier: /* Download (from NAMIC MIDAS) */

2013-09-02T20:46:55Z

Download (from NAMIC MIDAS)

Meier: /* Description */

2013-09-02T20:42:50Z

Description

Meier: /* Download (from NAMIC MIDAS) */

2013-09-02T20:40:39Z

Download (from NAMIC MIDAS)

Meier at 20:38, 2 September 2013

2013-09-02T20:38:35Z

Meier at 20:34, 2 September 2013

2013-09-02T20:34:51Z

Meier: /* Input */

2013-09-02T20:33:08Z

Input

Meier: /* Input */

2013-09-02T20:32:57Z

Input

Meier: /* Input */

2013-09-02T20:31:20Z

Input

Meier: /* Procedure */

2013-09-02T20:30:00Z

Procedure

@@ Line 72: / Line 72: @@
 ##(alternatively you can also use the threshold tool in the Editor to obtain a quick mask)
 ##we need to exclude the tumor from the mask, to prevent the registration from trying to match that region. Much should already be excluded from the above segmentation, but we also need to dilate the mask a bit to extend beyon the edge and include some of the background, which will fill in the tumor space again. Hence we make some manual edits to delete the tumor area from the mask:
-##Go to the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Editor ''Editor''] module
+##Go to the [[Documentation/4.1/Modules/Editor|''Editor'']] module
 ###Click ''Apply'' on the popup do confirm colormap selection (choice does not matter)
 ###Master Volume: PreRx_left

@@ Line 27: / Line 27: @@
 == Download (from NAMIC MIDAS) ==
 <small>''Why 2 sets of files?  The "input data" mrb includes only the unregistered data to try the method yourself from start to finish. The full dataset includes intermediate files and results (transforms, resampled images etc.). If you use the full dataset we recommend to choose different names for the images/results you create yourself to distinguish the old data from the new one you generated yourself. ''</small>
-*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C06.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 40 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=116852 '''RegLib_C06.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 40 MB). </small>]
-*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C06_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 65 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=116851 '''RegLib_C06_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 65 MB). </small>]
 == Keywords ==

@@ Line 14: / Line 14: @@
 ==Description ==
 This is an example of serial/logitudinal imaging for change assessment. We have a pre- and post-treatment MRI. To assess the treatment effect we seek to register the postRx scan to the baseline. Because of the strong changes in image content and contrast between the two exams, some additional work is necessary to obtain a good registration: 1) we will register only the left breast containing the tumor, i.e. we will crop the image to a much smaller FOV, while also obtaining a more isotropic resolution; 2) we have strong intensity bias in the images (originating from MR receiver coil sensitivity) that needs to be corrected first, otherwise it will negatively bias the registration; and 3) we will generate masks that include the breast but not the tumor, to ensure the nonrigid portion of the registration will not try to compensate for the tumor change.
 == Modules used ==

@@ Line 25: / Line 25: @@
 == Download (from NAMIC MIDAS) ==
 <small>''Why 2 sets of files?  The "input data" mrb includes only the unregistered data to try the method yourself from start to finish. The full dataset includes intermediate files and results (transforms, resampled images etc.). If you use the full dataset we recommend to choose different names for the images/results you create yourself to distinguish the old data from the new one you generated yourself. ''</small>
-*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C06.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 19 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C06.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 40 MB). </small>]
-*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C06_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 19 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C06_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 65 MB). </small>]
 == Keywords ==

@@ Line 38: / Line 38: @@
 == Procedure ==
-#'''Crop''':Extract left breast image of PreRx and PostRx scan
+#'''Crop''':Extract left breast image of PreRx and PostRx scan [[Media:RegLib_C06_1_Import&Crop.mov|(screencast for this step)]]
 ##Open the  [[Documentation/Nightly/Modules/Crop_Volume| ''Crop Volume'']]  module (under ''Converters'' menu)
 ##''Input volume'':  "PreRx"
@@ Line 52: / Line 52: @@
 ##repeat the same for the "PostRx" image. Since this image is smaller, choose '''2''' for the ''Input spacing scaling constant'' (vs. 3 above).
 ##Save intermediate results. You should have now 2 new volumes at ~ 1.3 mm isotropic resolution.
-#'''Bias Correction''': Correct for local intensity inhomogeneities
+#'''Bias Correction''': Correct for local intensity inhomogeneities [[Media: RegLib_C06_2_BiasCorrection.mov|(screencast for this step)]]
 ##Open the [[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection| ''N4ITK MRI Bias Correction'']] module  (under ''Filters'' menu)
 ###Input Image: "PreRx_left"
@@ Line 63: / Line 63: @@
 ##repeat for the Post_Rx image. Same settings
 ##save intermediate results
-#'''Build Masks''':
+#'''Build Masks''': [[Media: RegLib_C06_3_BuildMask.mov|(screencast for this step)]]
 ##open the  [[Documentation/Nightly/Modules/ForegroundMasking| ''Foregroud masking (BRAINS)'']] module (under Segmentation:Specialized)
 ###''Input Image Volume'': PreRx_left_n4
@@ Line 81: / Line 81: @@
 ##repeat for the Post_Rx_mask
 ##save intermediate results
-#'''Affine pre-Registration''':
+#'''Affine pre-Registration''': [[Media: RegLib_C06_4_Registration.mov|(screencast for this step)]]
 ##open the *[[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']] module
 ###''Fixed Image Volume'': PreRx_left_n4
@@ Line 96: / Line 96: @@
 ###this should generate a first alignment. note that we need not generate an output volume, because this is an intermediate result, and the BRAINS registration tool will automatically place the moving volume inside the result transform.
 ###Place "PreRx_left_n4" in the background and "PostRx_left_n4" in the foreground. Use fade slider to evaluate the result.
-#'''Nonrigid final Registration''':
+#'''Nonrigid final Registration''':  [[Media: RegLib_C06_4_Registration.mov|(screencast for this step)]]
 ##open the [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']] module
 ###''Fixed Image Volume'': PreRx_left_n4
@@ Line 127: / Line 127: @@
 -->
-=== Discussion: Registration Challenges ===
+== Discussion: Registration Challenges ==
 *soft tissue deformations during  image acquisition cause large differences in appearance
 *the large tumor recession represents a significant pre/post difference in image content that will influence unmasked intensity-driven registration, which becomes a problem for the non-rigid portion of registration, particularly at higher DOF, because the registration will try to "recreate" the tumor area from the postRx image in order to match the content.
@@ Line 135: / Line 135: @@
 *resolution and FOV change between the two scans
-=== Discussion: Key Strategies ===
+== Discussion: Key Strategies ==
 *because of the strong changes in shape and position, we break the problem down and register each breast separately.
 *a bias-field correction on both images is necessary before registration
 *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
 *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 116: / Line 116: @@
 ###click: Apply
 ==Registration Results==
-=== Acknowledgments ===
+<!--

@@ Line 5: / Line 5: @@
 |[[Image:RegLib_C06_Thumb1.png|100px|lleft|this is the main fixed reference image. All images are ev. aligned into this space]]
 |[[Image:RegArrow_NonRigid.png|100px|left]]
-|[[Image:RegLib_C06_Thumb_T2.png|100px|lleft|this is the moving image.]]
+|[[Image:RegLib_C06_Thumb2.png|100px|lleft|this is the moving image.]]
 |-
 |exam 1: baseline Pre Rx

@@ Line 3: / Line 3: @@
 == Input ==
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
-|[[Image:Reglib_C06_Thumb1.png|100px|lleft|this is the main fixed reference image. All images are ev. aligned into this space]]
+|[[Image:RegLib_C06_Thumb1.png|100px|lleft|this is the main fixed reference image. All images are ev. aligned into this space]]
 |[[Image:RegArrow_NonRigid.png|100px|left]]
-|[[Image:Reglib_C06_Thumb_T2.png|100px|lleft|this is the moving image.]]
+|[[Image:RegLib_C06_Thumb_T2.png|100px|lleft|this is the moving image.]]
 |-
 |exam 1: baseline Pre Rx

@@ Line 97: / Line 97: @@
 ###Place "PreRx_left_n4" in the background and "PostRx_left_n4" in the foreground. Use fade slider to evaluate the result.
 #'''Nonrigid final Registration''':
-##open the [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]
+##open the [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']] module
 ###''Fixed Image Volume'': PreRx_left_n4
 ###''Moving Image Volume'': PostRx_left_n4
@@ Line 109: / Line 108: @@
 ###''Registration Phases'': uncheck rigid & affine boxes, check box for ''BSpline'' only
 ###''Main Parameters'':
-####''Number Of Samples'': 300,000
+###''Number Of Samples'': 300,000
-####''B-Spline Grid Size'': 7,7,5
+###''B-Spline Grid Size'': 7,7,5
 ###''Mask Option'': select ''ROI'' button
 ####''ROI Masking input fixed'': select  "PreRx_mask" generated in Phase 3 above
-####''ROI Masking input moving'':  select  "PostRx_mask" generated in Phase 3 above
+###''ROI Masking input moving'':  select  "PostRx_mask" generated in Phase 3 above
-##Leave all other settings at default
+###Leave all other settings at default
-##click: Apply
+###click: Apply
 ==Registration Results==