Projects:RegistrationLibrary:RegLib C17 - Revision history

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

2017-07-10T17:36:33Z

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

Meier at 15:51, 5 September 2011

2011-09-05T15:51:05Z

Meier at 15:50, 5 September 2011

2011-09-05T15:50:53Z

Meier at 15:48, 5 September 2011

2011-09-05T15:48:33Z

Meier: /* Registration Results */

2011-09-05T15:47:43Z

Registration Results

Meier: /* Procedures */

2011-09-05T15:45:19Z

Procedures

Meier at 15:44, 5 September 2011

2011-09-05T15:44:57Z

Meier: Created page with 'Back to ARRA main page
Back to Registration main page
[[Projects:RegistrationDocumentation:UseCaseInv…'

2011-09-05T15:28:17Z

Created page with 'Back to ARRA main page Back to Registration main page [[Projects:RegistrationDocumentation:UseCaseInv…'

New page

[[Projects:ARRASuplements|Back to ARRA main page]] 
[[Projects:RegistrationDocumentation|Back to Registration main page]] 
[[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] 

==v3.6.3 [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case #17: Kidney pre-op MR to intra-op CT==
=== Input ===
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C17_Thumb1.png|150px|lleft|this is the fixed reference image. All images are aligned into this space]]
|[[Image:RegArrow_Rigid.png|100px|lleft]]
|[[Image:RegLib_C17_Thumb2.png‎|150px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]]
|-
|fixed image/target: intra-operative CT
|
|moving image: per-operative MRI
|}

=== Modules ===
*[http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit '''BRAINSfit''']
*for mask generation: ''Draw'' tool in the [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor] and/or [http://www.slicer.org/slicerWiki/index.php/Modules:FastMarchingSegmentation-Documentation-3.6 Fast-Marching Segmentation],

=== Keywords ===
CT, MRI, abdominal, image-guided therapy, IGT, tumor ablation

===Input Data===
*fixed: intra-operative CT, oblique, 0.58 x 0.58 x 3 mm voxel size, dimensions 512 x 512 x 20
*moving: opre-operative MRI lique, 1.2 x 1.2 x 4 mm voxel size, dimensions 320 x 240 x 64

===Registration Challenges===
* intra-operative CT is acquired with limited FOV and very oblique position
* intra-operative CT contains artifacts from surgical needles
* both datasets have strong voxel anisotropy
* the region of interest (kidney) is small compared to the FOV, i.e. there is substantial "distracting" image content

===Key Strategies===
*manual alignment to obtain initial pose
*rough segmentation of both kidneys to mask "distracting" image content
*gradual increase in registration DOF.

=== Procedures===
*''Phase 1'': obtain masks for kidney ROI
#Use the ''Draw'' tool in the
=== Registration Results===
[[Image:RegLib_C17_unregistered.gif||400px|original unregistered]]
[[Image:RegLib_C17_manualInit.gif||400px|after manual initial alignment]]
[[Image:RegLib_C17_Rigid.gif||400px|after rigid registration]]
[[Image:RegLib_C17_Affine.gif||400px|after affine registration]]

=== Download ===
*Data
**[[Media:RegLib_C17_Data.zip‎|'''Registration Library Case 17: Kidney MR-CT''' (Data,Presets, Solution, zip file 11 MB) ]]
*Presets
**[[Media:RegLib_C17_Presets.mrml‎|'''Registration Library Case 17: Parameter Presets (Slicer 3.6.3)''' (.mrml file 16 kB) ]]
**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]

@@ Line 17: / Line 17: @@
 === Modules ===
-*[http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit '''BRAINSfit''']
+*[https://www.slicer.org/wiki/Modules:BRAINSFit '''BRAINSfit''']
-*for mask generation: ''Draw'' tool in the [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor]  and/or [http://www.slicer.org/slicerWiki/index.php/Modules:FastMarchingSegmentation-Documentation-3.6 Fast-Marching Segmentation],
+*for mask generation: ''Draw'' tool in the [https://www.slicer.org/wiki/Modules:Editor-Documentation-3.6 Editor]  and/or [https://www.slicer.org/wiki/Modules:FastMarchingSegmentation-Documentation-3.6 Fast-Marching Segmentation],
 === Keywords ===
@@ Line 47: / Line 47: @@
 === Procedures===
 *'''Phase 1''': obtain masks for kidney ROI
-#Use the ''Draw'' tool in the [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor]  and/or use the [http://www.slicer.org/slicerWiki/index.php/Modules:FastMarchingSegmentation-Documentation-3.6 Fast-Marching Segmentation] module to obtain segmentations of the kidney in both CT and MR image. In the example dataset, you can find those segementations as files "Probe1CT_seg.nrrd" and "MRl_seg.nrrd"
+#Use the ''Draw'' tool in the [https://www.slicer.org/wiki/Modules:Editor-Documentation-3.6 Editor]  and/or use the [https://www.slicer.org/wiki/Modules:FastMarchingSegmentation-Documentation-3.6 Fast-Marching Segmentation] module to obtain segmentations of the kidney in both CT and MR image. In the example dataset, you can find those segementations as files "Probe1CT_seg.nrrd" and "MRl_seg.nrrd"
-#See the  [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training tutorials]  for the Editor and and segmentation methods for details on how to obtain an efficient segmentation.
+#See the  [https://www.slicer.org/wiki/Slicer_3.6:Training tutorials]  for the Editor and and segmentation methods for details on how to obtain an efficient segmentation.
 *'''Phase 2''': obtain initial manual alignment
-**Details in the [http://www.slicer.org/slicerWiki/index.php/Slicer3.6:Training  manual registration tutorial] and also in the [http://www.slicer.org/slicerWiki/index.php/Slicer-3-6-FAQ#How_do_I_initialize.2Falign_images_with_very_different_orientations_and_no_overlap.3F Slicer FAQ]
+**Details in the [https://www.slicer.org/wiki/Slicer3.6:Training  manual registration tutorial] and also in the [https://www.slicer.org/wiki/Slicer-3-6-FAQ#How_do_I_initialize.2Falign_images_with_very_different_orientations_and_no_overlap.3F Slicer FAQ]
-#go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 Data module]
+#go to the [https://www.slicer.org/wiki/Modules:Data-Documentation-3.6 Data module]
 #right click on the "Scene" mode and select ''Insert New Transform''. In the MRML edit field below, rename it to "Xf0_manual" or similar
 #In the ''Data'' module, drag the "MRI" image volume inside the"Xf0_manual" node
 #Select the views so that the MR and CT volumes are displayed in the slice views
-#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
+#Go to the [https://www.slicer.org/wiki/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
 *'''Phase 3''': automated rigid/affine alignment
-#Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit '''BRAINSfit'''] module
+#Go to the [https://www.slicer.org/wiki/Modules:BRAINSFit '''BRAINSfit'''] module
 ##select Presets "Xf1_Rigid" or "Xf2_Affine" or set the parameters as given below:
 ##fixed image: "Probe1CT", moving image: "MRI"
@@ Line 67: / Line 67: @@
 ##Mask Processing: check ''ROI'' box, ''Input Fixed Mask'' select CT segmentation created in Phase 1 above. For  ''Input Moving Mask'' select MRI segmentation created in Phase 1 above.
 ##Click Apply
-#return to the  [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 Data module] and drag the MRI inside/outside the different registration transforms to compare the alignment
+#return to the  [https://www.slicer.org/wiki/Modules:Data-Documentation-3.6 Data module] and drag the MRI inside/outside the different registration transforms to compare the alignment
 #to obtain a resampled volume: move MRI inside Xform of choice and then right-click on the volume and select ''Harden Transforms''. Save MRI under new name.

@@ Line 4: / Line 4: @@
-==<small>v3.6.3</small> [[Image:Slicer_cvers_banner.png|70px|This case is complete and up to date for version 3.6.3]] Slicer Registration Library Case #17: <br>Kidney pre-op MR to intra-op CT==
+==<small>v3.6.3</small> [[Image:Slicer_cvers_banner.png|70px|This case is complete and up to date for version 3.6.3]] Slicer Registration Library Case #17:  Kidney pre-op MR to intra-op CT==
 === Input ===
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"

@@ Line 4: / Line 4: @@
-==<small>v3.6.3</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case #17: <br>Kidney pre-op MR to intra-op CT==
+==<small>v3.6.3</small> [[Image:Slicer_cvers_banner.png|70px|This case is complete and up to date for version 3.6.3]] Slicer Registration Library Case #17: <br>Kidney pre-op MR to intra-op CT==
 === Input ===
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"

@@ Line 26: / Line 26: @@
 *fixed: intra-operative CT, oblique,  0.58 x 0.58 x 3  mm voxel size, dimensions 512 x 512 x 20
 *moving: opre-operative MRI lique,  1.2 x 1.2 x 4  mm voxel size, dimensions 320 x 240 x 64
 ===Registration Challenges===
@@ Line 68: / Line 75: @@
 [[Image:RegLib_C17_Rigid.gif||400px|after rigid registration]] after rigid registration  <br>
 [[Image:RegLib_C17_Affine.gif||400px|after affine registration]] after affine registration  <br>

@@ Line 39: / Line 39: @@
 === Procedures===
-*''Phase 1'': obtain masks for kidney ROI
+*'''Phase 1''': obtain masks for kidney ROI
 #Use the ''Draw'' tool in the [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor]  and/or use the [http://www.slicer.org/slicerWiki/index.php/Modules:FastMarchingSegmentation-Documentation-3.6 Fast-Marching Segmentation] module to obtain segmentations of the kidney in both CT and MR image. In the example dataset, you can find those segementations as files "Probe1CT_seg.nrrd" and "MRl_seg.nrrd"
 #See the  [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training tutorials]  for the Editor and and segmentation methods for details on how to obtain an efficient segmentation.
-*''Phase 2'': obtain initial manual alignment
+*'''Phase 2''': obtain initial manual alignment
 **Details in the [http://www.slicer.org/slicerWiki/index.php/Slicer3.6:Training  manual registration tutorial] and also in the [http://www.slicer.org/slicerWiki/index.php/Slicer-3-6-FAQ#How_do_I_initialize.2Falign_images_with_very_different_orientations_and_no_overlap.3F Slicer FAQ]
 #go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 Data module]
@@ Line 49: / Line 49: @@
 #Select the views so that the MR and CT volumes are displayed in the slice views
 #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
-*''Phase 3'': automated rigid/affine alignment
+*'''Phase 3''': automated rigid/affine alignment
 #Go to the [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit '''BRAINSfit'''] module
 ##select Presets "Xf1_Rigid" or "Xf2_Affine" or set the parameters as given below:

@@ Line 64: / Line 64: @@
 === Registration Results===
-[[Image:RegLib_C17_unregistered.gif||400px|original  unregistered]]
+[[Image:RegLib_C17_unregistered.gif||400px|original  unregistered]] original  unregistered <br>
-[[Image:RegLib_C17_manualInit.gif||400px|after manual initial alignment]]
+[[Image:RegLib_C17_manualInit.gif||400px|after manual initial alignment]]  after manual initial alignment<br>
-[[Image:RegLib_C17_Rigid.gif||400px|after rigid registration]]
+[[Image:RegLib_C17_Rigid.gif||400px|after rigid registration]] after rigid registration  <br>
-[[Image:RegLib_C17_Affine.gif||400px|after affine registration]]
+[[Image:RegLib_C17_Affine.gif||400px|after affine registration]] after affine registration  <br>
 === Download ===