Documentation:Nightly:Registration:RegistrationLibrary:RegLib C49 - Revision history

Meier: /* Acknowledgments */

2013-10-02T16:51:25Z

Acknowledgments

Meier: /* Acknowledgments */

2013-10-01T13:43:58Z

Acknowledgments

Meier: /* Description */

2013-09-18T17:16:44Z

Description

Meier: /* Registration Results */

2013-09-18T17:15:32Z

Registration Results

Meier: /* Input */

2013-09-18T17:13:59Z

Input

Meier at 17:11, 18 September 2013

2013-09-18T17:11:28Z

Meier at 16:52, 18 September 2013

2013-09-18T16:52:51Z

Meier at 16:45, 18 September 2013

2013-09-18T16:45:29Z

Meier at 16:43, 18 September 2013

2013-09-18T16:43:52Z

Meier: Created page with 'Back to Registration Library
= Slicer Registration Library Case #49: Pediatric Brain DTI = == Input == {| style="…'

2013-09-18T16:35:49Z

Created page with 'Back to Registration Library = Slicer Registration Library Case #49: Pediatric Brain DTI = == Input == {| style="…'

New page

[[Documentation/Nightly/Registration/RegistrationLibrary|Back to Registration Library]] 
= Slicer Registration Library Case #49: Pediatric Brain DTI =
== Input ==
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C17_Thumb1.png|150px|left|this is the fixed CT reference image. All images are aligned into this space]]
|[[Image:RegArrow_Rigid.png|100px|left]]
|[[Image:RegLib_C17_Thumb2.png|150px|left|this is the moving MR image, to be aligned with the reference on the left]]
|-
|fixed image/target intra-op CT
|
|moving image pre-op MRI
|}

== Description ==
Goal is to align the pre-op MRI to the intra-op interventional CT. The MR contains detail about location and extent of the pathology not apparent on the CT. Hence we register the MR to the CT to help guide the intervention. This is the same case as [[Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C17| Case# 17]], but here we demonstrate the use of the '''Fiducial Registration''' module. Fiducial registration can be useful in cases where the initial misalignment is too great or image appearance is too different for direct intensity-based registration to succeed. It can also b useful as a tool for an initial alignment to be refined with additional intensity-based methods. 
'''Approach:''' we use the fiducial registration method to obtain an initial alignment that corrects for the strong rotation and translation between the two images. This method requires two separate lists of fiducials that represent corresponding anatomical landmarks. The number and order of the fiducials in the two lists must be the same.

== Modules used ==
*[[Documentation/Nightly/Modules/Markups| ''Markups'']] (for generating fiducial lists)
*[[Documentation/Nightly/Modules/FiducialRegistration| ''Fiducial Registration'']]

== 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=118088 '''RegLib_C48.mrb''': input data only, use this to run the tutorial from the start (Slicer mrb file. 10 MB). ]
*[http://slicer.kitware.com/midas3/download/?items=118087 '''RegLib_C48_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify (Slicer mrb file. 12 MB). ]

== Keywords ==
MRI, CT, abdominal, image-guided surgery, interventional radiology, intra-subject, fiducial-based registration

== Video Screencasts ==
#[[Media:RegLib_C48_FiducialRegistration.mov|'''fiducial-based registration''']]

== Procedure ==
#'''Create CT fiducial list:''': see also movie above
##load the two datasets. Adjust brightness & contrast if necessary. Place the CT scan in the background and center the views.
##Open the [[Documentation/Nightly/Modules/Markups|''Markups'' module]]
##''List'': create and rename new list. Name to "fiducials_CT" or similar
##locate anatomical landmarks that is common to both images and readily identifiable. Smaller and distinctly shaped structures will likely carry less of a selection error than large uniform ones. It is also advisable to select fiducials from or near the region of interest.
##switch the mouse function to fiducial mode, by clicking the ''Fiducial'' button in the toolbar. [[Image:Slicer4_FiducialButton.png| ]]
##place a fiducial marker via left mouse-click
##you should see the fiducial appear in the list on the left. Double click the name field and rename the point with a descriptive name that will let you distinguish it from others. The fiducials we generate in the list '''must be in the same order''' in both lists (MR and CT), so it is important we can distinguish which fiducial is which.
##select 2-3 additional fiducials. The more fiducials we have, the more robust the registration. However, if you feel that the uncertainty/accuracy of a new landmark is significantly above the others, you may do better leaving it out and trying with a smaller set. For a rigid registration at least 3 fiducials are needed. Another advantage of having more than necessary, is that you can later easily test/revise the registration by removing individual points and recalculating the transform. Because the calculation is instant, you can see immediately if the match improves by leaving individual markers out. More on this in the discussion below.
##open the ''Advanced'' tab and change the colors for this list (both selected and unselected). This will help you keep the two lists apart, i.e. distingush the CT list from the MR list
##switch the MR image into the backrgound and recenter the views.
#'''Create MRI fiducial list''': see also movie above
##''List'': create and rename new list. Name to "fiducials_MRI" or similar
##repeat the selection of fiducials as above.
##in the ''Advanced'' tab, you can reshuffle the order of fiducials in the list. '''Important: remember that the fiducials in the two lists must be in the same order, i.e. the same anatomical loci must appear in both lists in the same order. If not you can use the shuffle buttons in the Advanced tab to rearrange.
##Save both lists. This will create ".csv" with fiducial names and coordinates
#'''Fiducial Registration:'''
##go to the [[Documentation/Nightly/Modules/Fiducial Registration ''Fiducial Registration'' module]] (menu: ''Registration / Specialized'')
##''Fixed Landmarks'': select "Fiducials_CT"
##''Moving Landmarks'': select "Fiducials_MR"
##''Save transform'': select "Create and rename new linear transform'', rename to "FiducialReg_Rigid" or similar.
##click ''Apply''. note that the calculation is instantaneous, but you will not see an effect on the image just yet.
##place the CT image in the background and center. Place the MR image in the foreground and set the fade slider halfway so you can see both images superimposed
##Go to the [[Documentation/Nightly/Modules/Data ''Data'' module]]
###you should see the newly created transform node in the MRML tree. Locate the MR image and drag its node onto the transform node (release the left mouse button when a box appears around the transform node). The MR image is placed inside the new transform. You should see the views update immediately.
###also drag the "fiducially_MR" node into the transform. Your data hierarchy should look similar to the image on the right. [[Image:RegLib_C48_DataHierarchy.png|right]]
###use the fade slider to judge the alignment.
##the 3D viewer will be very helpful here to assess the alignment of the fiducial pairs in space.
#'''optional: Revise registration / sensitivity test'''
##if you have more than the minimal (3) fiducial points available, you can test the effects of individual landmarks by recalculating the transform with individual points deleted.
##make sure you have both fiducial lists saved beforehand
##from the 3D or 3D views, identify a fiducial pair that shows the largest residual misalignment after registration (make sure the MR fiducial list is also within the transform)
##go back to the [[Documentation/Nightly/Modules/Markups|''Markups'' module]] and delete that fiducial from both lists.
##make sure you have the CT in the background and the MR in the foreground, the fade slider set to halfway and the MR image inside the result transform
##return to the [[Documentation/Nightly/Modules/Fiducial Registration ''Fiducial Registration'' module]] (menu: ''Registration / Specialized'') and rerun the registration, choosing the same transform result name.
##click apply. This will calculate a new transform with the updated fiducial list and replace the existing transform. You should see the difference immediately as the views update. You can use this to test if a registration can be improved by leaving out indiv. landmarks.

==Registration Results==

{|cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C17_unregistered.gif|300px]] ||MR/CT before registration (click to enlarge)
|-
|[[Image:RegLib_C48_registered.gif|300px]]||MR/CT after fiducial rigid alignment (click to enlarge)
|}

=== Acknowledgments ===

← Older revision		Revision as of 16:51, 2 October 2013
Line 123:		Line 123:

	=== Acknowledgments ===		=== Acknowledgments ===
−	Many thanks to Mojdeh Zamyadi and Dr. E. Widjaja's lab for sharing the example data.	+	Many thanks to Mojdeh Zamyadi and Dr. E. Widjaja's lab from the Hospital for Sick Children in Toronto, Canada, for sharing the example data.

← Older revision		Revision as of 13:43, 1 October 2013
Line 123:		Line 123:

	=== Acknowledgments ===		=== Acknowledgments ===
		+	Many thanks to Mojdeh Zamyadi and Dr. E. Widjaja's lab for sharing the example data.

@@ Line 17: / Line 17: @@
 == Description ==
-Goal is to align the structural T1 and T2 images with the DTI. Particularly the T1, which is associated with additional atlas/segmentation data (not shown). The DTI has strong distortions typical for EPI acquisitions. <br>
+Goal is to align the structural T1 and T2 images with the DTI. Particularly the T1, which is associated with additional atlas/segmentation data (not shown). The DTI has strong distortions typical for EPI acquisitions. Note that the T1 image had "defacing" applied for anonymization, but the brain portion of the image is unaffected.<br>
 '''Approach:''' Because the T2 matches the B0 contrast better than the T1, we will use the T2 as registration target. We will then register the T1 to the T2 and finally to the B0. Since the DTI contains strong distortions, a nonrigid registration is necessary. Workflow:
 #affine register T2-B0

@@ Line 116: / Line 116: @@
 |-
 |[[Image:RegLib_C49_registered1_T2B0.gif|300px]]|| alignment of T2 to B0 (click to enlarge)
 |[[Image:RegLib_C49_registered2_T1T2.gif|300px]]|| preliminary affine alignment of T1 to T2 (click to enlarge)
 |[[Image:RegLib_C49_registered3_T1B0.gif|300px]]|| final alignment of T1 to B0 (click to enlarge)
 |}
 === Acknowledgments ===

@@ Line 5: / Line 5: @@
 |[[Image:RegLib_C49_Thumb1.png|150px|left|this is the fixed DTI FA image. We want to align all images into this space]]
 |[[Image:RegLib_C49_Thumb2.png|150px|left|this is associated B0 image. Aligned with FA. Will use this as registration reference (fixed image)]]
-|[[Image:RegArrow_Nonrigid.png|100px|left]]
+|[[Image:RegArrow_NonRigid.png|100px|left]]
 |[[Image:RegLib_C49_Thumb3.png|150px|left|this is the moving MR image, to be aligned with the reference on the left]]
 |[[Image:RegLib_C49_Thumb4.png|150px|left|this is the moving MR image, to be aligned with the reference on the left]]

@@ Line 52: / Line 52: @@
 ##again select the Dilate tool and click "Dilate" 2-3 times. We can afford to dilate more here since the skull is very dark in the B0.
 #'''Affine Register T2-B0'''
-[[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
+##go to the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
+##''Input Images: Fixed Image Volume'': B0
+##''Input Images: Moving Image Volume'': T2
 ==Registration Results==
 {|cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C17_unregistered.gif|300px]] ||MR/CT before registration (click to enlarge)
+|[[Image:RegLib_C49_unregistered.gif|300px]] ||MR/CT before registration (click to enlarge)
 |-
-|[[Image:RegLib_C48_registered.gif|300px]]||MR/CT after fiducial rigid alignment (click to enlarge)
+|[[Image:RegLib_C49_registered1_T2B0.gif|300px]]|| alignment of T2 to B0 (click to enlarge)
 |}
 === Acknowledgments ===

@@ Line 31: / Line 31: @@
 == 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=118088 '''RegLib_C49.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 50 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=118347 '''RegLib_C49.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 50 MB). </small>]
-*[http://slicer.kitware.com/midas3/download/?items=118087 '''RegLib_C49_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 82 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=118346 '''RegLib_C49_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 82 MB). </small>]
 == Keywords ==
-MRI, CT, abdominal, image-guided surgery, interventional radiology, intra-subject, fiducial-based registration
+MRI, pediatric, brain, intra-subject, diffusion MRI, DWI, DTI
 == Video Screencasts ==
-#[[Media:RegLib_C48_FiducialRegistration.mov|'''fiducial-based registration''']]
+#[[Media:RegLib_C49.mov|'''RegLib_C49 Registration Screencast (start-finish)''']]
 == Procedure ==
-#'''Create CT fiducial list:''': see also movie above
+#'''Prepare Masks''': see also movie above
-##load the two datasets. Adjust brightness & contrast if necessary. Place the CT scan in the background and center the views.
+##two masks for the B0 and T2 are already provided with the dataset. For examples on how to obtain masks quickly from your image data see:
-##Open the [[Documentation/Nightly/Modules/Markups|''Markups'' module]]
+##We will use these masks for the registration. To ensure sufficient points outside the brain surface can participate in the registration, we dilate the two masks slightly to extend beyond the brain:
-##''List'': create and rename new list. Name to "fiducials_CT" or similar
+##go to the [[Documentation/Nightly/Modules/Editor ''Editor'' module]]
-##locate anatomical landmarks that is common to both images and readily identifiable. Smaller and distinctly shaped structures will likely carry less of a selection error than large uniform ones. It is also advisable to select fiducials from or near the region of interest.
+##''Master Volume'': T2
-##switch the mouse function to fiducial mode, by clicking the ''Fiducial'' button in the toolbar. [[Image:Slicer4_FiducialButton.png| ]]
+##''Merge Volume'': T2_mask
-##place a fiducial marker via left mouse-click
+##click on the ''Dilation Tool''. Set label to 1. Ensure T2_mask is visible in the slice views
-##you should see the fiducial appear in the list on the left. Double click the name field and rename the point with a descriptive name that will let you distinguish it from others. The fiducials we generate in the list '''must be in the same order''' in both lists (MR and CT), so it is important we can distinguish which fiducial is which.
+##click on the "Dilate" button once. You should see the boundary expand. Because there is little interstitial space/cortical CSF, we dilate only little to avoid including the skull in the ROI.
-##select 2-3 additional fiducials. The more fiducials we have, the more robust the registration. However, if you feel that the uncertainty/accuracy of a new landmark is significantly above the others, you may do better leaving it out and trying with a smaller set. For a rigid registration at least 3 fiducials are needed. Another advantage of having more than necessary, is that you can later easily test/revise the registration by removing individual points and recalculating the transform. Because the calculation is instant, you can see immediately if the match improves by leaving individual markers out. More on this in the discussion below.
+##switch ''MergeVolume'' to B0 and the ''Merge Volume'' to B0_mask
-##open the ''Advanced'' tab and change the colors for this list (both selected and unselected). This will help you keep the two lists apart, i.e. distingush the CT list from the MR list
+##again select the Dilate tool and click "Dilate" 2-3 times. We can afford to dilate more here since the skull is very dark in the B0.
-##switch the MR image into the backrgound and recenter the views.
+#'''Affine Register T2-B0'''
-#'''Create MRI fiducial list''': see also movie above
+[[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
-##''List'': create and rename new list. Name to "fiducials_MRI" or similar
-##repeat the selection of fiducials as above.
 ==Registration Results==

@@ Line 25: / Line 25: @@
 == Modules used ==
-*[[Documentation/Nightly/Modules/BRAINS| ''General (BRAINS) Registration'']]
+*[[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
 == 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=118088 '''RegLib_C48.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 10 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=118088 '''RegLib_C49.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 50 MB). </small>]
-*[http://slicer.kitware.com/midas3/download/?items=118087 '''RegLib_C48_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 12 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=118087 '''RegLib_C49_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 82 MB). </small>]
 == Keywords ==

@@ Line 3: / Line 3: @@
 == Input ==
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C17_Thumb1.png|150px|left|this is the fixed CT reference image. All images are aligned into this space]]
+|[[Image:RegLib_C49_Thumb1.png|150px|left|this is the fixed DTI FA image. We want to align all images into this space]]
-|[[Image:RegArrow_Rigid.png|100px|left]]
+|[[Image:RegLib_C49_Thumb2.png|150px|left|this is associated B0 image. Aligned with FA. Will use this as registration reference (fixed image)]]
-|[[Image:RegLib_C17_Thumb2.png|150px|left|this is the moving MR image, to be aligned with the reference on the left]]
+|[[Image:RegArrow_Nonrigid.png|100px|left]]
 |-
-|fixed image/target<br>intra-op CT
+|fixed image/target<br>DTI (FA)
+|
-|moving image <br>pre-op MRI
+|moving image <br>T2 MRI
 |}
 == Description ==
-Goal is to align the pre-op MRI to the intra-op interventional CT. The MR contains detail about location and extent of the pathology not apparent on the CT. Hence we register the MR to the CT to help guide the intervention.  This is the same case as [[Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C17| Case# 17]], but here we demonstrate the use of the '''Fiducial Registration''' module. Fiducial registration can be useful in cases where the initial misalignment is too great or image appearance is too different for direct intensity-based registration to succeed. It can also b useful as a tool for an initial alignment to be refined with additional intensity-based methods.<br>
+Goal is to align the structural T1 and T2 images with the DTI. Particularly the T1, which is associated with additional atlas/segmentation data (not shown). The DTI has strong distortions typical for EPI acquisitions. <br>
-'''Approach:''' we use the fiducial registration method to obtain an initial alignment that corrects for the strong rotation and translation between the two images. This method requires two separate lists of fiducials that represent corresponding anatomical landmarks. The number and order of the fiducials in the two lists must be the same.
+'''Approach:''' Because the T2 matches the B0 contrast better than the T1, we will use the T2 as registration target. We will then register the T1 to the T2 and finally to the B0. Since the DTI contains strong distortions, a nonrigid registration is necessary. Workflow:
 == Modules used ==
-*[[Documentation/Nightly/Modules/Markups| ''Markups'']] (for generating fiducial lists)
+*[[Documentation/Nightly/Modules/BRAINS| ''General (BRAINS) Registration'']]
 == Download (from NAMIC MIDAS) ==

Documentation:Nightly:Registration:RegistrationLibrary:RegLib C49 - Revision history

Meier: /* Acknowledgments */

Meier: /* Acknowledgments */

Meier: /* Description */

Meier: /* Registration Results */

Meier: /* Input */

Meier at 17:11, 18 September 2013

Meier at 16:52, 18 September 2013

Meier at 16:45, 18 September 2013

Meier at 16:43, 18 September 2013

Meier: Created page with 'Back to Registration Library = Slicer Registration Library Case #49: Pediatric Brain DTI = == Input == {| style="…'

Meier: Created page with 'Back to Registration Library
= Slicer Registration Library Case #49: Pediatric Brain DTI = == Input == {| style="…'