Documentation:Nightly:Registration:RegistrationLibrary:RegLib C21 - Revision history

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Meier at 13:35, 3 September 2013

2013-09-03T13:35:22Z

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

2013-08-19T15:45:01Z

Download (from NAMIC MIDAS)

Meier at 15:34, 19 August 2013

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Meier at 15:31, 19 August 2013

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Meier at 15:28, 19 August 2013

2013-08-19T15:28:35Z

Meier at 15:28, 19 August 2013

2013-08-19T15:28:08Z

Meier: Created page with 'Back to Registration Library
= Slicer Registration Library Case #21: Align knee MRI of two different subjects = =…'

2013-08-19T15:11:10Z

Created page with 'Back to Registration Library = Slicer Registration Library Case #21: Align knee MRI of two different subjects = =…'

New page

[[Documentation/Nightly/Registration/RegistrationLibrary|Back to Registration Library]] 
= Slicer Registration Library Case #21: Align knee MRI of two different subjects =
== Input ==
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C21_Thumb1.png|150px|lleft|this is the fixed MRI reference image.]]
|[[Image:RegArrow_Nonrigid.png|100px|lleft]]
|[[Image:RegLib_C21_Thumb2.png|150px|lleft|this is the moving image, to be aligned with the reference MRI on the left]]
|-
|fixed image/target MRI
|
|moving image MRI
|}

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

== Download (from NAMIC MIDAS) ==
*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C21.mrb''': input data only, use this to run the tutorial from the start (Slicer mrb file. 12 MB). ]

== Keywords ==
MRI, knee, inter-subject, nonrigid

== Procedure ==
It is possible to perform all 3 steps of rigid, 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 a rigid registration, then use that to compute an affine registration, and finally use the affine as starting point for a BSpline registration. For the last one we will need to generate a quick mask to prevent aliasing artifacts in the image from influencing the result. The masks are available in the download set.
#'''Compute Rigid Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
##''Input Images: Fixed Image Volume'': MRI_58
##'''Input Images: Moving Image Volume'': MRI_64
##''Output Settings'':
###''Slicer Linear Transform'' (create new transform, rename to: "Xf1_Rigid")
###''Output Image Volume'' none (we need no resampled volume at this stage, only the transform)
##''Registration Phases'': select/check ''Rigid''
##''Main Parameters'':
###increase ''Number Of Samples'' to 200,000
##Leave all other settings at default
##click: ''Apply''; runtime < 1 min.
##check the result
###Place "MRI_58" in the background and "MRI_64" in the foreground
###switch to the [[Documentation/Nightly/Modules/Data|''Data'' module]], locate the "MRI_64" node, and drag it onto the newly created "Xf1_Affine" node.
###fade between background and foreground to judge the alignment.
###for better visibility, you can change the colormaps of the two volumes, as used in the examples shown here. Switch to the [[Documentation/Nightly/Modules/Volumes|''Volumes'' #'''Compute Affine Registration''': return to the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
##''Input Images: Fixed Image Volume'': MRI_58
##'''Input Images: Moving Image Volume'': MRI_64
##''Output Settings'':
###''Slicer Linear Transform'' (create new transform, rename to: "Xf2_Affine")
###''Output Image Volume'' none (we need no resampled volume at this stage, only the transform)
##''Initialization'': for the ''Initialization transform'' select the "Xf1_Rigid" transform created above.
##''Initialize Transform Mode'': switch to ''Off''
##''Registration Phases'': '''un'''check ''Rigid'' and select ''Rigid+Scale" and ''Affine'' only
##''Main Parameters'':
###leave ''Number Of Samples'' to 200,000
##Leave all other settings at default
##click: ''Apply''; runtime < 1 min.
##check the result
###Place "MRI_58" in the background and "MRI_64" in the foreground
###switch to the [[Documentation/Nightly/Modules/Data|''Data'' module]], locate the "MRI_64" node, and drag it onto the newly created "Xf1_Affine" node.
###fade between background and foreground to judge the alignment.
###for better visibility, you can change the colormaps of the two volumes, as used in the examples shown here. Switch to the [[Documentation/Nightly/Modules/Volumes|''Volumes'' module]], select "MRI_58" and then select "Green" from the ''Lookup Table'' menu. Similarly select "Cyan" for "MRI_64".
#'''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_C21_Unregistered.png|300px]] ||before registration (click to enlarge)
|-
|[[Image:RegLib_C21_Rigid.png|300px]]||after rigid registration (click to enlarge)
|-
|[[Image:RegLib_C21_Affine.png|300px]]||after affine registration (click to enlarge)
|-
|[[Image:RegLib_C21_BSpline.png|300px]]||after BSpline registration (click to enlarge)
|-
|[[Image:RegLib_C21_registered.gif|300px]]||animated gif showing the progression of all 3 steps(click to enlarge)
|}

=== Acknowledgments ===

@@ Line 14: / Line 14: @@
 == Description ==
 This case shows knee MRI of two different individuals. We explore the possibility of aligning those complex structures via intensity-based automated registration. Because we have two different anatomies, nonrigid registration is necessary. Also no perfect solution exists for such a case. Usually there is a particular target structure of interest, for which alignment is more relevant than for the rest of the image. Masking those regions tends to produce better results, provided there is enough matching image content remaining to keep the registration stable. <br>
-'''Approach:''' we will perform registrations of increasing degrees of freedom (DOF) in individual steps. This way we can verify progress. While it is possible to run all steps in a single pass, it is difficult to judge where thing went wrong should registration fail. We will also use more sample points for this example, because some of the key structures (e.g. cartilage) are small and we want to be sure enough points are sampled from this region to get a good result (remember sample points are drawn randomly from the entire image area). Sample sizes therefore depend critically on the image size.  [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_many_sample_points_should_I_choose_for_my_registration.3F See here for an illustration of what typical sampling sizes look like.]
+'''Approach:''' we will perform registrations of increasing degrees of freedom (DOF) in individual steps. This way we can verify progress. While it is possible to run all steps in a single pass, it is difficult to judge where thing went wrong should registration fail. We will also use more sample points for this example, because some of the key structures (e.g. cartilage) are small and we want to be sure enough points are sampled from this region to get a good result (remember sample points are drawn randomly from the entire image area). Sample sizes therefore depend critically on the image size.  [[Documentation/Nightly/FAQ#How_many_sample_points_should_I_choose_for_my_registration.3F|See here for an illustration of what typical sampling sizes look like.]]
 == Modules used ==

← Older revision		Revision as of 13:35, 3 September 2013
Line 12:		Line 12:
	\|}		\|}

		+	== Description ==
		+	This case shows knee MRI of two different individuals. We explore the possibility of aligning those complex structures via intensity-based automated registration. Because we have two different anatomies, nonrigid registration is necessary. Also no perfect solution exists for such a case. Usually there is a particular target structure of interest, for which alignment is more relevant than for the rest of the image. Masking those regions tends to produce better results, provided there is enough matching image content remaining to keep the registration stable. <br>
		+	'''Approach:''' we will perform registrations of increasing degrees of freedom (DOF) in individual steps. This way we can verify progress. While it is possible to run all steps in a single pass, it is difficult to judge where thing went wrong should registration fail. We will also use more sample points for this example, because some of the key structures (e.g. cartilage) are small and we want to be sure enough points are sampled from this region to get a good result (remember sample points are drawn randomly from the entire image area). Sample sizes therefore depend critically on the image size. [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#How_many_sample_points_should_I_choose_for_my_registration.3F See here for an illustration of what typical sampling sizes look like.]

	== Modules used ==		== Modules used ==

@@ Line 17: / Line 17: @@
 == Download (from NAMIC MIDAS) ==
-*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C21.mrb''':  input data, masks and result transforms <small>(Slicer mrb file. 12 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=115179 '''RegLib_C21.mrb''':  input data, masks and result transforms <small>(Slicer mrb file. 12 MB). </small>]
 == Keywords ==

@@ Line 17: / Line 17: @@
 == Download (from NAMIC MIDAS) ==
-*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C21.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 12 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C21.mrb''':  input data, masks and result transforms <small>(Slicer mrb file. 12 MB). </small>]
 == Keywords ==
@@ Line 71: / Line 71: @@
 ###increase ''Number Of Samples'' to 400,000
 ###set ''B-Spline Grid Size'' to 5,5,3
 ##Leave all other settings at default
 ##click: ''Apply''; runtime for this will be more than 1 minute, depending on CPU.

@@ Line 75: / Line 75: @@
 ##check the result
 ###Place "MRI_58" in the background and "MRI_64_Xf3" in the foreground
-#Apply and save transforms
+#'''Apply and save transforms'''
 ##To apply the rigid and affine transforms you need not resample the volume. Simply drag the MRI_64 volume into the transform node (Xf1_Rigid or Xf2_Affine), and then right click on the "MRI_64" volume node 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. '''Note that now you have a reoriented volume although the name is the same. It is advisable to immediately rename the node to document this fact. Then save it as a new file under a new name.'''
 ##To apply the nonrigid transform resampling is required. You already have a resampled volume "MRI_64_Xf3" from above. This uses linear interpolation and float as default. You can change these settings under the ''Advanced Output Settings'' tab. For this example "short" as Pixel Type and "Windowed Sinc" is recommended. To obtain a new resampled copy without repeating the whole registration step, use the [[Documentation/Nightly/Modules/BRAINSResample|''BRAINSResample'' module]]

@@ Line 3: / Line 3: @@
 == Input ==
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C21_Thumb1.png|150px|lleft|this is the fixed MRI reference image.]]
+|[[Image:RegLib_C21_Thumb1.png|150px|left|this is the fixed MRI reference image.]]
-|[[Image:RegArrow_Nonrigid.png|100px|lleft]]
+|[[Image:RegArrow_NonRigid.png|100px|left]]
-|[[Image:RegLib_C21_Thumb2.png|150px|lleft|this is the moving image, to be aligned with the reference MRI on the left]]
+|[[Image:RegLib_C21_Thumb2.png|150px|left|this is the moving image, to be aligned with the reference MRI on the left]]
 |-
 |fixed image/target<br>MRI

@@ Line 26: / Line 26: @@
 #'''Compute Rigid Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
 ##''Input Images: Fixed Image Volume'': MRI_58
-##'''Input Images: Moving Image Volume'': MRI_64
+##''Input Images: Moving Image Volume'': MRI_64
 ##''Output Settings'':
-###''Slicer Linear Transform'' (create new transform, rename to: "Xf1_Rigid")
+###''Slicer Linear Transform'': (create new transform, rename to: "Xf1_Rigid")
-###''Output Image Volume'' none (we need no resampled volume at this stage, only the transform)
+###''Output Image Volume'': none (we need no resampled volume at this stage, only the transform)
 ##''Registration Phases'':  select/check ''Rigid''
 ##''Main Parameters'':
@@ Line 37: / Line 37: @@
 ##check the result
 ###Place "MRI_58" in the background and "MRI_64" in the foreground
-###switch to the [[Documentation/Nightly/Modules/Data|''Data'' module]], locate the "MRI_64" node, and drag it onto the newly created "Xf1_Affine" node.
+###switch to the [[Documentation/Nightly/Modules/Data|''Data'' module]], locate the "MRI_64" node, and drag it onto the newly created "Xf1_Rigid" node.
 ###fade between background and foreground to judge the alignment.
-###for better visibility, you can change the colormaps of the two volumes, as used in the examples shown here. Switch to the [[Documentation/Nightly/Modules/Volumes|''Volumes'' #'''Compute Affine Registration''': return to the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
+###for better visibility, you can change the colormaps of the two volumes, as used in the examples shown here. Switch to the [[Documentation/Nightly/Modules/Volumes|''Volumes'' module]], select "MRI_58" and then select "Green" from the ''Lookup Table'' menu. Similarly select "Cyan" for "MRI_64".
 ##''Input Images: Fixed Image Volume'': MRI_58
-##'''Input Images: Moving Image Volume'': MRI_64
+##''Input Images: Moving Image Volume'': MRI_64
 ##''Output Settings'':
-###''Slicer Linear Transform'' (create new transform, rename to: "Xf2_Affine")
+###''Slicer Linear Transform'': (create new transform, rename to: "Xf2_Affine")
-###''Output Image Volume'' none (we need no resampled volume at this stage, only the transform)
+###''Output Image Volume'': none (we need no resampled volume at this stage, only the transform)
 ##''Initialization'':  for the ''Initialization transform'' select the "Xf1_Rigid" transform created above.
 ##''Initialize Transform Mode'': switch to ''Off''
-##''Registration Phases'':  '''un'''check ''Rigid'' and select ''Rigid+Scale" and ''Affine'' only
+##''Registration Phases'':  '''un'''check ''Rigid'' and select ''Rigid+Scale'' and ''Affine'' only
 ##''Main Parameters'':
 ###leave ''Number Of Samples'' to 200,000
@@ Line 57: / Line 58: @@
 ###fade between background and foreground to judge the alignment.
 ###for better visibility, you can change the colormaps of the two volumes, as used in the examples shown here. Switch to the [[Documentation/Nightly/Modules/Volumes|''Volumes'' module]], select "MRI_58" and then select "Green" from the ''Lookup Table'' menu. Similarly select "Cyan" for "MRI_64".
-#'''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.
+#'''Compute BSpline Registration''': return to the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
-##Go to the [[Documentation/Nightly/Modules/Data|''Data'']] module
+##''Input Images: Fixed Image Volume'': MRI_58
-###Find the original PET image, labeled as "PET"
+##''Input Images: Moving Image Volume'': MRI_64
-###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.
+##''Output Settings'':
-###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.
+###''Slicer BSpline Transform'': Create and rename new. Rename to "MRI_64_Xf3"
-###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.
+###''Slicer Linear Transform'': set to ''none''
-##Click on the Save icon and save the new "PET" image under a new name.
+###''Output Image Volume'': Create and rename new. Rename to "MRI_64_Xf3"
 ==Registration Results==

Documentation:Nightly:Registration:RegistrationLibrary:RegLib C21 - Revision history

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

Meier at 13:35, 3 September 2013

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

Meier at 15:34, 19 August 2013

Meier at 15:31, 19 August 2013

Meier at 15:28, 19 August 2013

Meier at 15:28, 19 August 2013

Meier: Created page with 'Back to Registration Library = Slicer Registration Library Case #21: Align knee MRI of two different subjects = =…'

Meier: Created page with 'Back to Registration Library
= Slicer Registration Library Case #21: Align knee MRI of two different subjects = =…'