Projects:RegistrationLibrary:RegLib C12 - Revision history

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

2017-07-10T18:04:31Z

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

Meier at 17:03, 10 May 2012

2012-05-10T17:03:52Z

Meier at 17:00, 10 May 2012

2012-05-10T17:00:21Z

Meier: /* Download */

2012-05-10T16:59:36Z

Download

Meier at 16:53, 10 May 2012

2012-05-10T16:53:59Z

Meier: /* Procedures */

2012-05-10T16:49:13Z

Procedures

Meier: /* Procedures */

2012-05-10T16:47:46Z

Procedures

Meier: /* Registration Results */

2011-08-18T20:05:18Z

Registration Results

Meier: /* Procedures */

2011-08-18T20:00:38Z

Procedures

Meier: /* Procedures */

2011-08-18T19:59:30Z

Procedures

@@ Line 59: / Line 59: @@
 #select the ''Dilate'' tool and click ''Apply'' 3-4 times to extend the mask area
 #repeat for both masks
-#In the  [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 ''Editor'' module], use the ''Dilate'' function to expand the outline by 2-3 pixels (click on ''Apply'' button 2-3 times)
+#In the  [https://www.slicer.org/wiki/Modules:Editor-Documentation-3.6 ''Editor'' module], use the ''Dilate'' function to expand the outline by 2-3 pixels (click on ''Apply'' button 2-3 times)
 #save dilated labelmasks under new name (e.g. CT_mask.nrrd)
 *'''Phase II: MR-CTpre registration''' (Affine)

@@ Line 103: / Line 103: @@
 |unregistered MRI & CT
 |-
-|[[Image:RegLib_C12_masks.png|300px|left|registration masks]]
+|[[Image:RegLib_C12_Masks.png|300px|left|registration masks]]
 |registration masks
 |-
 |[[Image:RegLib_C12_Affine.gif|300px|left|affine registered MRI & CT]]
 |affine registered MRI & CT
 |-
-|[[Image:RegLib_C12_Nonrigid.gif|300px|left|nonrigid registered MRI & CT]]
+|[[Image:RegLib_C12_BSpline.gif|300px|left|nonrigid registered MRI & CT]]
 |nonrigid registered MRI & CT
 |-
-|[[Image:RegLib C12 CT-CT registered.gif|300px|left|nonrigid registered CTpre to CTintra]]
+|[[Image:RegLib_C12_ConstrainFailure.gif|300px|left|insufficient mask: nonrigid registered with liver mask only, note the misalignment in the remaining abdomen]]
-|nonrigid registered CTpre to CTintra
+|insufficient mask: nonrigid registered with liver mask only, note the misalignment in the remaining abdomen
 |}

@@ Line 20: / Line 20: @@
 ===Download ===
-*[[Media:RegLib_C12_Data.zip|'''download input image data'''  <small> (Input Data, NRRD images,  zip file 65 MB) </small>]]
+*[[Media:RegLib_C12_Data.zip|'''download input image data'''  <small> (Input Data, Masks, Solution Transforms, Resampled results (NRRD images,  zip file 65 MB) </small>]]
 ===Objective / Background ===

@@ Line 20: / Line 20: @@
 ===Download ===
-*[[Media:RegLib_C12_Data.zip|'''download input image data'''  <small> (Input Data, NRRD images,  zip file 42 MB) </small>]]
+*[[Media:RegLib_C12_Data.zip|'''download input image data'''  <small> (Input Data, NRRD images,  zip file 65 MB) </small>]]
 ===Objective / Background ===

@@ Line 3: / Line 3: @@
 [[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br>
-==<small>v3.6.3</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case #12:  Liver Tumor Cryoablation ==
+==<small>updated for '''v4.1'''</small> [[Image:Slicer4_RegLibLogo.png|150px]] <br>  Slicer Registration Library Case #12:  Liver Tumor Cryoablation ==
 === Input ===
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C12_Thumb1.png|150px|lleft|this is the intra-op CT reference image. All images are aligned into this space]]
+|[[Image:RegLib_C12_Thumb1.png|150px|lleft|this is a pre-op CT + contrast reference image. All images are aligned into this space]]
 |[[Image:RegArrow_NonRigid.png|100px|lleft]]
-|[[Image:RegLib_C12_Thumb2.png|150px|lleft|this is an intermediate pre-op CT, used as reference to match the MRI]]
+|[[Image:RegLib_C12_Thumb2.png|150px|lleft|this is the pre-op MRI we seek to align with the CT]]
 |-
 |fixed image/target
+|
 |moving image
 |}
-=== Modules ===
+=== Slicer4 Modules used ===
-*'''Slicer 3.6.3 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]'''
+* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS) module]
 ===Objective / Background ===
-We seek to align a pre-operative MRI with the intra-operative CT for surgical guidance.
+We seek to align a pre-operative MRI with a contrast enhanced CT for surgical guidance.
 === Keywords ===
@@ Line 40: / Line 39: @@
 === Notes / Overall Strategy ===
 *masking is required to focus the registration algorithm on the structure of interest
 *Overall strategy:
@@ Line 121: / Line 119: @@
 |}
 === Acknowledgments ===
 Thanks to Dr.Stuart Silverman and Dr. Nobuhiko Hata for sharing this case.

@@ Line 74: / Line 74: @@
 ##''Registration Phases'': check boxes for ''Rigid'' , ''Rigid+Scale'' and ''Affine''
 ##''Mask Option'': select ''ROI'' button
-###''(ROIAUTO) Input fixed mask'': CT_mask
+###''(ROI)Masking input fixed'': CT_mask
-###''(ROIAUTO) Input moving mask'': MRI_mask
+###''(ROI)Masking input moving'': MRI_mask
 ##Leave all other settings at default
 ##click: Apply; runtime < 1 min (MacPro QuadCore 2.4GHz)
@@ Line 95: / Line 95: @@
 ###''B-Spline Grid Size'': 7,7,3
 ##''Mask Option'': select ''ROI'' button
-###''(ROIAUTO) Input fixed mask'': CT_mask
+###''(ROI)Masking input fixed'': CT_mask
-###''(ROIAUTO) Input moving mask'': MRI_mask
+###''(ROI)Masking input moving'': MRI_mask
 ##Leave all other settings at default
 ##click: Apply

@@ Line 51: / Line 51: @@
 === Procedures ===
 *'''Phase I: Build Masks'''
-#load RegLib_C12 Dataset (e.g. via "RegLib_C12_SlicerScene.mrml"
+: Note: for illustration the example set contains 2 masks: one with only the liver and one also including spleen and kidney (Mask2).  As shown in the results below, the liver-only mask is insufficiently constraining the registration, yielding a result that at first glance looks ok for the liver, but has significant misalignment in the remaining abdominal area. Hence it is advisable to stabilize the registration further by including more structures with good contrast in both images (Spleen, Kidney).
-#go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 ''Editor'' module]
+#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Editor Editor module]
-##Select "CT_preop_contrast" as master volume
+#select  "MRI" as the master volume ; a new "MRI_label" is created
-##create new labelmap "CT_preop_contrast"
+#using the Brush tool, trace the liver contour from axial slices. Also include kidneys and spleen.
-##trace the liver contour from axial slices, or use one of the Segmentation modules (e.g. FastMarching) as starting point
+#repeat the same for the CT.
-##Save result labelmap
+#you should end up with 2 label maps similar to those included in the example dataset. See snapshots in Result section below.
-#repeat outlining on the MR image
+#save the label maps as "MRI-label.nrrd" or similar
 #In the  [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 ''Editor'' module], use the ''Dilate'' function to expand the outline by 2-3 pixels (click on ''Apply'' button 2-3 times)
 #save dilated labelmasks under new name (e.g. CT_mask.nrrd)
-*'''Phase II: MR-CTpre registration'''
+*'''Phase II: MR-CTpre registration''' (Affine)
-#Following the concept of manual registration, create an initial transform that roughly aligns the MR to the pre-op CT. Details and links [http://www.slicer.org/slicerWiki/index.php/Slicer-3-6-FAQ#Can_I_manually_adjust_or_correct_a_registration.3F in the Slicer Registration FAQ]
+#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS) module]
-##In the ''Data'' module, create a new transform node (right click on Scene node), rename to "Xf1_ManualInit", then drag the image volume inside the registration transform node
+##''Fixed Image Volume'': CT
-##Select the views so that the volume is displayed in the slice views
+##''Moving Image Volume'': MRI
-##Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module] and adjust the translation and rotation sliders to adjust the current position. To get a finer degree of control, enter smaller numbers for the translation limits and enter rotation angles numerically in increments of a few degrees at a time
+##Output Settings:
-#Affine Registration
+###''Slicer BSpline Transform": none
-##go to [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit module]
+###''Slicer Linear Transform'': create new transform, rename to "Xf1_MRI-CT_Affine"
-###fixed: "CT_preop", moving: "MRI_preop"
+###''Output Image Volume'': create new volume,  rename to "MRI_Xf1" (we use this for ease of validation only)
-###Initialize with transform, select "Xf1_ManualInit"
+##''Initialization'': select the ''useCenterOfROIAlign''
-###select/check the following boxes: ''Include Rigid...", ''Include Scale", "Include Affine registration phase''
+##''Registration Phases'': check boxes for ''Rigid'' , ''Rigid+Scale'' and ''Affine''
-##Output Settings: select a new transform "Slicer Transform", rename to "Xf2_Affine"
+##''Mask Option'': select ''ROI'' button
-###Registration Parameters: increase ''Number Of Samples'' to 200,000
+###''(ROIAUTO) Input fixed mask'': CT_mask
-###Masking: check "ROI" box
+###''(ROIAUTO) Input moving mask'': MRI_mask
-####''Input Fixed Mask'': select the "CT_preop_mask" generated above
+##Leave all other settings at default
-####''Input Moving Mask'': select the "MR_preop_mask" generated above
+##click: Apply; runtime < 1 min (MacPro QuadCore 2.4GHz)
-###click ''Apply''
+##this should generate a first alignment.
-#NonRigid Registration
+*'''Phase III: Nonrigid Registration'''
-##go to [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit module]
+#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS) module]
-###fixed: "CT_preop", moving: "MRI_preop"
+##''Fixed Image Volume'': CT
-###Initialize with transform, select "Xf2_Affine"
+##''Moving Image Volume'': MRI
-###Output Settings: select a new transform "Slicer BSpline Transform", rename to "Xf3_BSpline"
+##Output Settings:
-###select a new volume "Output Image Volume'', rename to "MR_preop_Xf3"
+###''Slicer BSpline Transform": create new transform, rename to "Xf2_MRI-CT_BSpline"
-##Registration Parameters: increase ''Number Of Samples'' to 200,000
+###''Slicer Linear Transform'': none
-##Registration Parameters: set  ''Number Of Grid Subdivisions'' to 7,7,5
+###''Output Image Volume'': create new volume,  rename to "MRI_Xf2"
-###Masking: check "ROI" box
+##''Initialization'':
-####''Input Fixed Mask'': select the "CT_preop_mask" generated above
+###''Initialization Transform'': select  "Xf1_MRI-CT_Affine" created in Phase II above
-####''Input Moving Mask'': select the "MR_preop_mask" generated above
+###''Initialization Transform Mode'': Off
 ##Leave all other settings at default
 ##click: Apply
 === Registration Results===