Documentation:Nightly:Registration:RegistrationLibrary:RegLib C15 - Revision history

Meier: /* Slicer Registration Library Case #15: Align brain MRI along anatomical AC-PC line */

2013-08-28T18:48:21Z

Slicer Registration Library Case #15: Align brain MRI along anatomical AC-PC line

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

2013-07-01T19:54:53Z

Download (from NAMIC MIDAS)

Meier at 19:53, 1 July 2013

2013-07-01T19:53:40Z

Meier at 19:52, 1 July 2013

2013-07-01T19:52:37Z

Meier: /* Procedure */

2013-07-01T19:51:18Z

Procedure

Meier: /* Procedure */

2013-07-01T19:50:54Z

Procedure

Meier: /* Procedure */

2013-07-01T19:50:21Z

Procedure

Meier: /* Procedure */

2013-07-01T19:50:00Z

Procedure

Meier: /* Procedure */

2013-07-01T19:40:03Z

Procedure

Meier: Created page with 'Back to Registration Library
= Slicer Registration Library Case #15: Align brain MRI along anatomical AC-PC line …'

2013-07-01T19:20:45Z

Created page with 'Back to Registration Library = Slicer Registration Library Case #15: Align brain MRI along anatomical AC-PC line …'

New page

[[Documentation/Nightly/Registration/RegistrationLibrary|Back to Registration Library]] 
= Slicer Registration Library Case #15: Align brain MRI along anatomical AC-PC line =
== Input ==
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C15_Thumb1.png|150px|lleft|this is the target orientation in which is AC-PC line is horizontal and the inter-hemispheral midline is vertical]]
|[[Image:RegArrow_Rigid.png|100px|lleft]]
|[[Image:RegLib_C15_Thumb2.png|150px|lleft|this is the PET scan, to be aligned with the MRI]]
|-
|target POS MRI
|
|moving image MRI
|}

== Modules used ==
*[[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]

== Download (from NAMIC MIDAS) ==
''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. ''
*[http://slicer.kitware.com/midas3/download/?items=103751 '''RegLib_C15.mrb''': input data only (incl. fiducials), use this to run the tutorial from the start (Slicer mrb file. 22 MB). ]
*[http://slicer.kitware.com/midas3/download/?items=103750 '''RegLib_C15_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify (Slicer mrb file. 22 MB). ]

== Keywords ==
MRI, brain, head, AC-PC, landmark, registration

== Video Screencasts ==
#[[Media:RegLib_C15.mov|Movie/screencast showing registration for Case #15, incl. selection of fiducial landmarks]]

== Procedure ==
#'''Create Fiducial Landmarks''': open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
##''Input Images: Fixed Image Volume'': MRI
##'''Input Images: Moving Image Volume'': PET
##''Output Settings'':
###''Slicer Linear Transform'' (create new transform, rename to: "Xf1_Affine")
###''Output Image Volume'' (create new volume, rename to: "PET_Xf1" or similar. We need this for visualization only. You may leave this at None and just use the transform result.
##''Registration Phases'': select/check ''Rigid'' , ''Rigid+Scale'', ''Affine''
##''Main Parameters'':
###increase ''Number Of Samples'' to 200,000
##Leave all other settings at default
##click: ''Apply''; runtime < 1 min.
#'''Apply transform to PET:''' We have now computed the registration transform, but we still need to apply this transform to the PET image. The preferred way to do this is without resampling the image, i.e. by applying the linear transform to the spatieal orientation information in the image header. You can of course also create a resampled version, like the MRI_Xf1 output volume produced above.
##Go to the [[Documentation/Nightly/Modules/Data|''Data'']] module
###Find the original PET image, labeled as "PET"
###drag the "PET" node '''onto''' the transform node, labeled "Xf1_Affine". You should see a small + appear next to the transform node. When you click it you should see the "PET" image now residing inside the transform. If you have the PET image in one of the Slice views, it should show you now the aligned position of the PET image.
###apply the transform: right click on the "PET" image and from the pop-up menu, select ''Harden Transform''. This will apply the transform '''without resampling''' and move it back to the main hierarchy level.
###double click on the PET node and rename it to something like "PET_registered" or "PET_XF1applied" 3etc. to document that this image has now a transform applied to it.
##Click on the Save icon and save the new "PET" image under a new name.

==Registration Results==

{|cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C14_unregistered.png|300px]] ||MRI and PET before registration (click to enlarge)
|-
|[[Image:RegLib_C14_registered.gif|300px]]||MRI and PET after registration (click to enlarge)
|}

=== Acknowledgments ===

@@ Line 12: / Line 12: @@
 |}
 == Modules used ==
 *[[Documentation/Nightly/Modules/ACPCTransform|''ACPC Transform'' module]]

@@ Line 18: / Line 18: @@
 == 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=103751 '''RegLib_C15.mrb''': input data only (incl. fiducials), use this to run the tutorial from the start <small>(Slicer mrb file. 22 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=103755 '''RegLib_C15.mrb''': input data only (incl. fiducials), use this to run the tutorial from the start <small>(Slicer mrb file. 22 MB). </small>]
-*[http://slicer.kitware.com/midas3/download/?items=103750 '''RegLib_C15_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 22 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=103754 '''RegLib_C15_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 22 MB). </small>]
 == Keywords ==

@@ Line 5: / Line 5: @@
 |[[Image:RegLib_C15_Thumb1.png|150px|lleft|this is the target orientation in which is AC-PC line is horizontal and the inter-hemispheral midline is vertical]]
 |[[Image:RegArrow_Rigid.png|100px|lleft]]
-|[[Image:RegLib_C15_Thumb2.png|150px|lleft|this is the PET scan, to be aligned with the MRI]]
+|[[Image:RegLib_C15_Thumb2.png|150px|lleft|this is the MRI image in the original position.]]
 |-
 |target POS<br>MRI
@@ Line 48: / Line 48: @@
 ###drag the "MRI" node '''onto''' the transform node, labeled "Xf1_ACPC". You should see a small + appear next to the transform node. When you click it you should see the image now residing inside the transform. If you have the Slice views, it should show you now the aligned position of the MRI image.
 ###apply the transform: right click on the "MRI" image and from the pop-up menu, select ''Harden Transform''. This will apply the transform '''without resampling''' and move it back to the main hierarchy level.
-###double click on the PET node and rename it to something like "MRI_ACPCAligned" or similar, to document that this image has now a transform applied to it.
+###double click on the MRI node and rename it to something like "MRI_ACPCAligned" or similar, to document that this image has now a transform applied to it.
 ##Click on the Save icon and save the new image under a new name.
@@ Line 54: / Line 54: @@
 {|cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C14_unregistered.png|300px]] ||MRI and PET before registration (click to enlarge)
+|[[Image:RegLib_C15_registered.gif|300px]]||MRI and PET after registration (click to enlarge)
 |}
 === Acknowledgments ===

@@ Line 38: / Line 38: @@
 ##The "AC-PC" hierarchy should only contain 2 landmarks for AC and PC, respectively
 ##The "Midline'' hierarchy should only contain 4 or more landmarks defining the interhemispheral midline
-#'''Calculate the Transform''': Open the  [[Documentation/Nightly/Modules/ACPCTransform|''ACPC Transform'' module]]
+#'''Calculate the transform''': Open the  [[Documentation/Nightly/Modules/ACPCTransform|''ACPC Transform'' module]]
 ##''ACPC Line'': select the fiducial list created above, named "AC-PC"
 ##''Midline:''  select the fiducial list created above, named "Midline"
 ##''Output transform'':  create new & rename: rename to "Xf1_ACPC" or similar
 ##click: ''Apply''; runtime ~ 1 second.
-#'''Apply transform:''' We have now computed the registration transform, but we still need to apply this transform to the MRI image. The preferred way to do this is without resampling the image, i.e. by applying the linear transform to the spatial orientation information in the image header.
+#'''Apply the transform:''' We have now computed the registration transform, but we still need to apply this transform to the MRI image. The preferred way to do this is without resampling the image, i.e. by applying the linear transform to the spatial orientation information in the image header.
 ##Go to the [[Documentation/Nightly/Modules/Data|''Data'']] module
 ###Find the original image, labeled as "MRI"

@@ Line 40: / Line 40: @@
 #'''Calculate the Transform''': Open the  [[Documentation/Nightly/Modules/ACPCTransform|''ACPC Transform'' module]]
 ##''ACPC Line'': select the fiducial list created above, named "AC-PC"
-##''Midline:"  select the fiducial list created above, named "Midline"
+##''Midline:''  select the fiducial list created above, named "Midline"
 ##''Output transform'':  create new & rename: rename to "Xf1_ACPC" or similar
 ##click: ''Apply''; runtime ~ 1 second.

@@ Line 27: / Line 27: @@
 == Procedure ==
-#'''Create Fiducial Landmarks''': open the [[Documentation/Nightly/Modules/Annotations|''Annotations'' module]]
+#'''Create Fiducial Landmarks''': open the [[Documentation/Nightly/Modules/Annotations|''Annotations'' module]]. We will create 2 annotation lists, one containing the anterior and posterior commissure, and one containing midline points.
 ##in a slice view, locate the anterior commissure (sagittal view recommended).
 ##Click on the Fiducial placement button in the toolbar. This declares the next left mouseclick to be a fiducial selection.
@@ Line 38: / Line 38: @@
 ##The "AC-PC" hierarchy should only contain 2 landmarks for AC and PC, respectively
 ##The "Midline" hierarchy should only contain 4 or more landmarks defining the interhemispheral midline
-#Open the  [[Documentation/Nightly/Modules/ACPCTransform|''ACPC Transform'' module]]
+#'''Calculate the Transform''': Open the  [[Documentation/Nightly/Modules/ACPCTransform|''ACPC Transform'' module]]
 ##''ACPC Line'': select the fiducial list created above, named "AC-PC"
 ##''Midline:"  select the fiducial list created above, named "Midline"

@@ Line 27: / Line 27: @@
 == Procedure ==
-#'''Create Fiducial Landmarks''': open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
+#'''Create Fiducial Landmarks''': open the [[Documentation/Nightly/Modules/Annotations|''Annotations'' module]]
-##''Input Images: Fixed Image Volume'': MRI
+##in a slice view, locate the anterior commissure (sagittal view recommended).
-##'''Input Images: Moving Image Volume'': PET
+##Click on the Fiducial placement button in the toolbar. This declares the next left mouseclick to be a fiducial selection.
-##''Output Settings'':
+##click (left mouse button) in the image to place the fiducial. You should see an annotation being placed at the location.
-###''Slicer Linear Transform'' (create new transform, rename to: "Xf1_Affine")
+##Locate the prosterior commissure and repeat fiducial placement above.
-###''Output Image Volume'' (create new volume, rename to: "PET_Xf1" or similar. We need this for visualization only. You may leave this at None and just use the transform result.
+##In the ''Fiducial'' module, make sure the two created landmarks are in the same hierarchy. Rename the hierarchy "AC-PC" or similar
-##''Registration Phases'':  select/check ''Rigid'' , ''Rigid+Scale'', ''Affine''
+##Create a new fiducial hierarchy. Rename to "Midline"
-##''Main Parameters'':
+##in the axial view, place 4-5 landmarks along the interhemispheral midline (same as above)
-###increase ''Number Of Samples'' to 200,000
+##n the ''Fiducial'' module, make sure the above created midline landmarks are all in the same '"Midline" hierarchy.
-##Leave all other settings at default
+##The "AC-PC" hierarchy should only contain 2 landmarks for AC and PC, respectively
-##click: ''Apply''; runtime < 1 min.
+##The "Midline" hierarchy should only contain 4 or more landmarks defining the interhemispheral midline
-#'''Apply transform to PET:''' We have now computed the registration transform, but we still need to apply this transform to the PET image. The preferred way to do this is without resampling the image, i.e. by applying the linear transform to the spatieal orientation information in the image header. You can of course also create a resampled version, like the MRI_Xf1 output volume produced above.
+#Open the  [[Documentation/Nightly/Modules/ACPCTransform|''ACPC Transform'' module]]
 ##Go to the [[Documentation/Nightly/Modules/Data|''Data'']] module
-###Find the original PET image, labeled as "PET"
+###Find the original image, labeled as "MRI"
-###drag the "PET" node '''onto''' the transform node, labeled "Xf1_Affine". You should see a small + appear next to the transform node. When you click it you should see the "PET" image now residing inside the transform. If you have the PET image in one of the Slice views, it should show you now the aligned position of the PET image.
+###drag the "MRI" node '''onto''' the transform node, labeled "Xf1_ACPC". You should see a small + appear next to the transform node. When you click it you should see the image now residing inside the transform. If you have the Slice views, it should show you now the aligned position of the MRI image.
-###apply the transform: right click on the "PET" image and from the pop-up menu, select ''Harden Transform''. This will apply the transform '''without resampling''' and move it back to the main hierarchy level.
+###apply the transform: right click on the "MRI" image and from the pop-up menu, select ''Harden Transform''. This will apply the transform '''without resampling''' and move it back to the main hierarchy level.
-###double click on the PET node and rename it to something like "PET_registered" or "PET_XF1applied" 3etc. to document that this image has now a transform applied to it.
+###double click on the PET node and rename it to something like "MRI_ACPCAligned" or similar, to document that this image has now a transform applied to it.
-##Click on the Save icon and save the new "PET" image under a new name.
+##Click on the Save icon and save the new image under a new name.
 ==Registration Results==

Documentation:Nightly:Registration:RegistrationLibrary:RegLib C15 - Revision history

Meier: /* Slicer Registration Library Case #15: Align brain MRI along anatomical AC-PC line */

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

Meier at 19:53, 1 July 2013

Meier at 19:52, 1 July 2013

Meier: /* Procedure */

Meier: /* Procedure */

Meier: /* Procedure */

Meier: /* Procedure */

Meier: /* Procedure */

Meier: Created page with 'Back to Registration Library = Slicer Registration Library Case #15: Align brain MRI along anatomical AC-PC line …'

Meier: Created page with 'Back to Registration Library
= Slicer Registration Library Case #15: Align brain MRI along anatomical AC-PC line …'