Documentation:Nightly:Registration:RegistrationLibrary:RegLib C20 - Revision history

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

2013-08-28T21:35:30Z

Download (from NAMIC MIDAS)

Meier: /* Slicer Registration Library Case #20: Align PET/CT pair follow-up to baseline */

2013-08-28T18:55:29Z

Slicer Registration Library Case #20: Align PET/CT pair follow-up to baseline

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

2013-08-28T17:44:58Z

Download (from NAMIC MIDAS)

Meier at 17:37, 28 August 2013

2013-08-28T17:37:03Z

Meier: /* Screencasts / Video */

2013-08-28T17:31:50Z

Screencasts / Video

Meier at 17:28, 28 August 2013

2013-08-28T17:28:19Z

Meier: /* Procedure */

2013-08-28T17:27:39Z

Procedure

Meier at 17:16, 28 August 2013

2013-08-28T17:16:35Z

Meier at 17:13, 28 August 2013

2013-08-28T17:13:36Z

Meier: /* Procedure */

2013-08-28T17:10:55Z

Procedure

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 == 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_C20.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 76 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=116262 '''RegLib_C20.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 76 MB). </small>]
-*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C20_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 171 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=116261 '''RegLib_C20_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 171 MB). </small>]
 == Screencasts / Video ==

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 |moving image<br>follow-up PET/CT
 |}
 == Modules used ==

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 == Download (from NAMIC MIDAS) ==
-*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C20.mrb''':  input data, masks and result transforms <small>(Slicer mrb file. 12 MB). </small>]
+<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>
 == Screencasts / Video ==

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 == Procedure ==
 It is possible to perform both steps of affine and BSpline registration in a single pass within the  [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]], but to better show/judge progress we perform each separately and feed the results of one the the next step. Hence we first run an affine registration, then use that as starting point for a BSpline registration.
-#'''Load & Center Volumes''':
+#'''Load & Center Volumes''': [[Media:RegLib_C20_1_DisplayAndCenter.mov|(screencast for this step)]]
 ##the original unregistered PET/CT pair have very different image origins. When loaded into Slicer there is very little overlap between the two sets. We first re-center all the volumes to correct for this. Alternatively you can select the "Center Volume" option in the File dialog when loading the images.
 ##open to the [[Documentation/Nightly/Modules/Volumes|''Volumes'' module]]
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 ###for "PET_1" and "PET_2" select the "PET" preset (3rd from the left)
 ###since zero in the PET colormap is red, we set a threshold to suppress this: from ''Threshold'' menu, select "Manual" and set the left/lower threshold to ~ 600. You can also drag the pop-up slider until most of the red background turns to black.
-#'''Compute Affine Registration''': open to the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
+#'''Register: Compute Affine Registration''':  [[Media:RegLib_C20_2_RegisterCT.mov|(screencast for this step)]]
 ##''Input Images: Fixed Image Volume'': CT_1
 ##''Input Images: Moving Image Volume'': CT_2
@@ Line 63: / Line 64: @@
 ###switch to the [[Documentation/Nightly/Modules/Data|''Data'' module]], verify that  the "CT_2" node is inside the newly created "Xf1_Affine" node. The registration module should do that automatically for you. You may see a small "+" next to the "Xf1_Affine" node, click on it to reveal the contents.
 ###fade between background and foreground to judge the alignment.
-#'''Compute BSpline Registration''': return to the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
+#'''Compute BSpline Registration''':  [[Media:RegLib_C20_2_RegisterCT.mov|(screencast for this step)]]
 ##''Input Images: Fixed Image Volume'': CT_1
 ##''Input Images: Moving Image Volume'': CT_2
@@ Line 81: / Line 83: @@
 ###Place "CT_1" in the background and "CT_2_Xf2" in the foreground
 ###fade between background and foreground to judge the alignment.
-#'''Apply transform to PET''':
+#'''Apply transform to PET''':  [[Media:RegLib_C20_3_ApplyTransformToPET.mov|(screencast for this step)]]
 ##open the [[Documentation/Nightly/Modules/BRAINSResample|''Registration / Resample Volume (BRAINS)'' module]]
 ##''Image To Warp: PET_2
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 ###''Window/Level editor presets'': click on the "PET" preset (3rd button from the left)
 ###from ''Threshold'' menu, select "Manual" and set the left/lower threshold to ~ 600. You can also drag the pop-up slider until most of the red background turns to black.
-#'''optional: Visualize Deformation''': install and use the '' [[Documentation/Nightly/Extensions/TransformVisualizer| ''TransformVisualizer'']]
+#'''optional: Visualize Deformation''': install the '' [[Documentation/Nightly/Extensions/TransformVisualizer| ''TransformVisualizer'']]:  [[Media:RegLib_C20_4_InstallTransformVisualizer.mov|(screencast for this step)]]
 ##open the [[Documentation/Nightly/SlicerApplication/ExtensionsManager| ''ExtensionsManager'']] [[Image:ExtensionManagerIcon.png|50px]]
 ##locate the ''Transform Visualizer" extension. Click on the "Install" button
 ##you will need to restart Slicer to complete the installation. '''Make sure to save all your work before restarting.'''
 ##upon restart, reload "CT1" and "Xf2_BSpline"
 ##to allow fast interactive use we need to subsample the large CT volumes:

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 == Screencasts / Video ==
+#[[Media:RegLib_C20_1_DisplayAndCenter.mov|Loading volumes, setting colormaps, centering volumes]]
-RegLib_C20_1_DisplayAndCenter.mov
+#[[Media:RegLib_C20_2_RegisterCT.mov|perform affine and BSpline registration of the CT volumes]]
 == Keywords ==

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 == Modules used ==
 *[[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]
-*[[Documentation/Nightly/Modules/BRAINSResample| ''BRAINSResample'']]
+* [[Documentation/Nightly/Modules/BRAINSResample|''Registration / Resample Volume (BRAINS)'' module]]
 *[[Documentation/Nightly/Extensions/TransformVisualizer| ''TransformVisualizer'']]
@@ Line 87: / Line 87: @@
 ###''Window/Level editor presets'': click on the "PET" preset (3rd button from the left)
 ###from ''Threshold'' menu, select "Manual" and set the left/lower threshold to ~ 600. You can also drag the pop-up slider until most of the red background turns to black.
 #'''optional: Visualize Deformation''': install and use the ''
 ==Registration Results==