Documentation:Nightly:Registration:RegistrationLibrary:RegLib C10 - Revision history

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

2013-09-04T18:51:28Z

Download (from NAMIC MIDAS)

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

2013-09-04T18:44:56Z

Download (from NAMIC MIDAS)

Meier: /* Registration Results */

2013-09-04T18:39:52Z

Registration Results

Meier: /* Registration Results */

2013-09-04T18:39:34Z

Registration Results

Meier: /* Procedure */

2013-09-04T18:24:30Z

Procedure

Meier: /* Procedure */

2013-09-04T18:23:53Z

Procedure

Meier at 17:26, 4 September 2013

2013-09-04T17:26:10Z

Meier: /* Input */

2013-09-04T17:09:58Z

Input

Meier: Created page with 'Back to Registration Library
= Slicer Registration Library Case #10: group atlas to structural MRI = == Input == …'

2013-09-04T17:07:06Z

Created page with 'Back to Registration Library = Slicer Registration Library Case #10: group atlas to structural MRI = == Input == …'

New page

[[Documentation/Nightly/Registration/RegistrationLibrary|Back to Registration Library]] 
= Slicer Registration Library Case #10: group atlas to structural MRI =
== Input ==

==Description ==
This shows registration of an fMRI baseline scan to a structural reference T1. The fMRI suffers from low SNR and bad distortions we seek to correct.
'''Approach''': we first compute a rigid alignment of the fMRI to the T1. We then expand this to a nonrigid transform, which we constrain either by explicit limits on the absolute deformation amount or via a mask. Constraints are necessary because the skull present in the T1 would otherwise negatively affect the registration result.

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

== 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=116858 '''RegLib_C09.mrb''': input data only, use this to run the tutorial from the start (Slicer mrb file. 40 MB). ]
*[http://slicer.kitware.com/midas3/download/?items=116857 '''RegLib_C09_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify (Slicer mrb file. 182 MB). ]

== Keywords ==
MRI, fMRI, brain, head, intra-subject

== Video Screencasts ==
#[[Media:RegLib_C09_1_Rigid+BSpline.mov|Movie/screencast showing rigid + BSpline registration]]
#[[Media:RegLib_C09_2_SwissSkullStripper.mov|Movie/screencast showing installation and use of the "SwissSkullStripper" for generating a T1 mask]]
#[[Media:RegLib_C09_3_BSpline_masked.mov|Movie/screencast showing an alternative BSpline registration using masks instead of an explicit deformation limit]]

== Procedure ==
#'''Rigid Registration''': register fMRI to T1 [[Media:RegLib_C09_1_Rigid+BSpline.mov|(screencast for this step)]]
##open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
##''Fixed Image Volume'': T1 (SPGR)
##''Moving Image Volume'': fMRI
##Output Settings:
###''Slicer BSpline Transform": none
###''Slicer Linear Transform'': create & rename new transform: Xf1_Rigid.tfm
###''Output Image Volume'': none
##''Registration Phases'': check box for ''Rigid''
##''Main Parameters''
###'''Number of Samples''': 200,000
##click: Apply; runtime < 10 sec (MacPro QuadCore 2.4GHz)
#'''Nonrigid BSpline Registration'''
##''Fixed Image Volume'': T1 SPGR
##''Moving Image Volume'': fMRI
###''Slicer BSpline Transform": create & rename new transform: Xf2_BSpline.tfm
##''Slicer Linear Transform'': none
###''Output Image Volume'': create & rename new: fMRI_Xf2
##''Initialization Transform'':select "Xf1_Rigid" created above
##''Initialization Transform Mode'': off
##''Registration Phases'': uncheck boxe for ''Rigid'' and instead check ''BSpline''
##''Main Parameters'': '''Number of Samples''': 200,000
##''Advanced Output Settings'': '''Maximum B-Spline Displacement''': 3
##click: Apply

'''Alternate Option: Masking'''
#if not yet present, install the [[Documentation/Nightly/Modules/SwissSkullStripper| ''SwissSkullStripper'']] module: [[Media:RegLib_C09_2_SwissSkullStripper.mov|(screencast for this step)]]
##open the [[Documentation/Nightly/SlicerApplication/ExtensionsManager| ''ExtensionsManager'']] [[Image:ExtensionManagerIcon.png|50px]]
##locate the ''SwissSkullStripper" extension (under segmentation). 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 the data and open the [[Documentation/Nightly/Modules/SwissSkullStripper| ''SwissSkullStripper'']] module (under Segmentation)
##You will need to download an atlas image and its mask. Link is here: [[Documentation/Nightly/Modules/SwissSkullStripper| ''SwissSkullStripper'']]
##''Atlas Volume'': select the atlas image you downloaded.
##''Atlas Mask Volume'': select the atlas mask image you downloaded.
##''Patient Volume'': select the T1 SPGR
##''Patient Output Volume'': create and rename new: "T1_stripped" or similar
##''Patient Mask Label'': : create and rename new: "T1_mask"
##''Apply''
##go to the [[Documentation/Nightly/Modules/Editor| ''Editor'']]
##''Merge Volume'': "T1_mask"
##select the "Dilation" tool. Click "Apply" 2-3 times to extend the mask beyond the brain surface
#'''Build Mask for fMRI''': [[Media:RegLib_C09_3_BSpline_masked.mov|(screencast for this step)]]
##open the [[Documentation/Nightly/Modules/Editor| ''Editor'']]
##''Master Volume'': fMRI
##''Merge Volume'': create new: fMRI_label
##select the ''Threshold tool'', reduce threshold until entire brain is selected.
##click "Apply"
##select the "Dilation" tool. Click "Apply" 2-3 times to extend the mask beyond the brain surface
#'''Masked BSpline Registration''': [[Media:RegLib_C09_3_BSpline_masked.mov|(screencast for this step)]]
##repeat the BSpline registration above, with the following changes:
##Turn off the deformation Limit: ''Advanced Output Settings'': '''Maximum B-Spline Displacement''': '''0'''
##''Mask Option'': select ''ROI'' button
###''ROI Masking input fixed'': select "T1_mask" generated above
###''ROI Masking input moving'': select "fMRI_mask" generated above
##Apply

==Registration Results==

{|cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C09_unregistered.png|300px]] unregistered (click to enlarge)
|-
|[[Image:RegLib_C09_registered1_rigid.gif|300px]] after rigid registration (click to enlarge)
|-
|[[Image:RegLib_C09_registered2_BSpline.gif|300px]] after nonrigid BSpline registration (click to enlarge)
|}

=== Acknowledgments ===

@@ Line 21: / Line 21: @@
 == 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_C10.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=116868 '''RegLib_C10.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_C10_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 50 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=116867 '''RegLib_C10_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 50 MB). </small>]
 == Keywords ==

@@ Line 21: / Line 21: @@
 == 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_C10.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 40 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C10.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_C10_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 182 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C10_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 50 MB). </small>]
 == Keywords ==

@@ Line 72: / Line 72: @@
 |[[Image:RegLib_C10_unregistered.png|300px]]  unregistered (click to enlarge)
 |-
-|[[Image:RegLib_C10_registered1_Affine.png|300px]] after affine registration (click to enlarge)
+|[[Image:RegLib_C10_registered1_Affine.png|300px]] after affine registration (click to enlarge)<br>
 |[[Image:RegLib_C10_registered2_Affine.gif|300px]] after affine registration (click to enlarge)
 |-

@@ Line 72: / Line 72: @@
 |[[Image:RegLib_C10_unregistered.png|300px]]  unregistered (click to enlarge)
 |-
-|[[Image:RegLib_C10_registered1_Affine.gif|300px]] after affine registration (click to enlarge)
+|[[Image:RegLib_C10_registered1_Affine.png|300px]] after affine registration (click to enlarge)
 |-
-|[[Image:RegLib_C10_registered2_BSpline2.gif|300px]] after nonrigid BSpline (5x5x3)  registration (click to enlarge)
+|[[Image:RegLib_C10_registered3_BSpline.gif|300px]] after nonrigid BSpline (5x5x3)  registration (click to enlarge)
 |-
-|[[Image:RegLib_C10_registered3_BSpline3.gif|300px]] after nonrigid BSpline (7x7x5)  registration (click to enlarge)
+|[[Image:RegLib_C10_registered4_BSpline2.gif|300px]] after nonrigid BSpline (7x7x5)  registration (click to enlarge)
 |}
 === Acknowledgments ===

@@ Line 65: / Line 65: @@
 ##''BSpline Grid Size'':7,7,5
 ##click: Apply
-#"further increase DOF'': you can continue exploring how far the direct approach (from Affine direct to high DOF BSpline) remains stable, by increasing the BSpline grid size until results become too distorted. Alternatively you can use the lower DOF result (e.g. Atlas_Xf2) as input to the next higher DOF transform. This enables a stable progression to higher DOF, but it also includes multiple resampling and accompanied data loss from interpolation blurring.
+#''further increase DOF'': you can continue exploring how far the direct approach (from Affine direct to high DOF BSpline) remains stable, by increasing the BSpline grid size until results become too distorted. Alternatively you can use the lower DOF result (e.g. Atlas_Xf2) as input to the next higher DOF transform. This enables a stable progression to higher DOF, but it also includes multiple resampling and accompanied data loss from interpolation blurring.
 ==Registration Results==

@@ Line 44: / Line 44: @@
 ##click: Apply; runtime < 10 sec (MacPro QuadCore 2.4GHz)
 #'''Nonrigid BSpline Registration'''
 ##''Fixed Image Volume'': T1ref
 ##''Moving Image Volume'': Atlas

@@ Line 13: / Line 13: @@
 ==Description ==
-This shows registration of an fMRI baseline scan to a structural reference T1. The fMRI suffers from low SNR and bad distortions we seek to correct.
+This is an example of inter-subject registration; we seek to align a group atlas image with a structural reference T1.
-'''Approach''': we first compute a rigid alignment of the fMRI to the T1. We then expand this to a nonrigid transform, which we constrain either by explicit limits on the absolute deformation amount or via a mask. Constraints are necessary because the skull present in the T1 would otherwise negatively affect the registration result.
+'''Approach''': we first compute an affine alignment of the atlas to the T1. We then proceed to nonrigid registrations of higher and higher DOF, stopping at the DOF where deformations become unreasonable. We can constrain the deformation by either explicit limits on the absolute deformation amount or via a mask. Constraints become increasingly critical as DOF increases.
 == Modules used ==
 *[[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]
 == 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=116858 '''RegLib_C09.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 40 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C10.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 40 MB). </small>]
-*[http://slicer.kitware.com/midas3/download/?items=116857 '''RegLib_C09_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 182 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C10_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 182 MB). </small>]
 == Keywords ==
-MRI, fMRI, brain, head, intra-subject
+MRI, atlas, brain, head, inter-subject
 == Video Screencasts ==
-#[[Media:RegLib_C09_1_Rigid+BSpline.mov|Movie/screencast showing rigid + BSpline registration]]
+#[[Media:RegLib_C10_Affine+BSpline.mov|Movie/screencast showing rigid + BSpline registration]]
 == Procedure ==
-#'''Rigid Registration''': register fMRI to T1  [[Media:RegLib_C09_1_Rigid+BSpline.mov|(screencast for this step)]]
+#'''Affine Registration''': register atlas to T1
 ##open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
-##''Fixed Image Volume'': T1 (SPGR)
+##''Fixed Image Volume'': T1ref
-##''Moving Image Volume'': fMRI
+##''Moving Image Volume'': Atlas
 ##Output Settings:
 ###''Slicer BSpline Transform": none
-###''Slicer Linear Transform'': create & rename new transform: Xf1_Rigid.tfm
+###''Slicer Linear Transform'': create & rename new transform: Xf1_Affine.tfm
 ###''Output Image Volume'': none
-##''Registration Phases'': check box for ''Rigid''
+##''Registration Phases'': check box for "Rigid"', "Rigid+Scale" and "Affine"
 ##''Main Parameters''
 ###'''Number of Samples''': 200,000
 ##click: Apply; runtime < 10 sec (MacPro QuadCore 2.4GHz)
 #'''Nonrigid BSpline Registration'''
-##''Fixed Image Volume'': T1 SPGR
+##''Fixed Image Volume'': T1ref
-##''Moving Image Volume'': fMRI
+##''Moving Image Volume'': Atlas
 ###''Slicer BSpline Transform": create & rename new transform: Xf2_BSpline.tfm
 ##''Slicer Linear Transform'': none
-###''Output Image Volume'': create & rename new: fMRI_Xf2
+###''Output Image Volume'': create & rename new: Atlas_Xf2
-##''Initialization Transform'':select "Xf1_Rigid" created above
+##''Initialization Transform'':select "Xf1_Affine" created above
 ##''Initialization Transform Mode'': off
 ##''Registration Phases'': uncheck boxe for ''Rigid''  and instead check ''BSpline''
-##''Main Parameters'': '''Number of Samples''': 200,000
+##''Main Parameters'': '''Number of Samples''': 300,000
-##''Advanced Output Settings'': '''Maximum B-Spline Displacement''': 3
+##''BSpline Grid Size'':5,5,3
 ##click: Apply
+#'''Increasing DOF'''
-'''Alternate Option: Masking'''
+##repeat the above with a larger BSpline grid:
-#if not yet present, install the [[Documentation/Nightly/Modules/SwissSkullStripper| ''SwissSkullStripper'']] module: [[Media:RegLib_C09_2_SwissSkullStripper.mov|(screencast for this step)]]
+###''Slicer BSpline Transform": create & rename new transform: Xf3_BSpline2.tfm
-##open the [[Documentation/Nightly/SlicerApplication/ExtensionsManager| ''ExtensionsManager'']] [[Image:ExtensionManagerIcon.png|50px]]
+###''Output Image Volume'': create & rename new: Atlas_Xf3
-##locate the ''SwissSkullStripper" extension (under segmentation). Click on the "Install" button
+##''Initialization Transform'':select "Xf1_Affine" created above
-##you will need to restart Slicer to complete the installation. '''Make sure to save all your work before restarting.'''
+##''Initialization Transform Mode'': off
-##upon restart, reload the data and open the [[Documentation/Nightly/Modules/SwissSkullStripper| ''SwissSkullStripper'']] module (under Segmentation)
+##''Main Parameters'': '''Number of Samples''': 400,000
-##You will need to download an atlas image and its mask. Link is here: [[Documentation/Nightly/Modules/SwissSkullStripper| ''SwissSkullStripper'']]
+##''BSpline Grid Size'':7,7,5
-##''Atlas Volume'': select the atlas image you downloaded.
+##click: Apply
-##''Atlas Mask Volume'': select the atlas mask image you downloaded.
+#"further increase DOF'': you can continue exploring how far the direct approach (from Affine direct to high DOF BSpline) remains stable, by increasing the BSpline grid size until results become too distorted. Alternatively you can use the lower DOF result (e.g. Atlas_Xf2) as input to the next higher DOF transform. This enables a stable progression to higher DOF, but it also includes multiple resampling and accompanied data loss from interpolation blurring.
 ==Registration Results==
 {|cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C09_unregistered.png|300px]]  unregistered (click to enlarge)
+|[[Image:RegLib_C10_unregistered.png|300px]]  unregistered (click to enlarge)
 |-
-|[[Image:RegLib_C09_registered1_rigid.gif|300px]] after rigid registration (click to enlarge)
+|[[Image:RegLib_C10_registered2_BSpline2.gif|300px]] after nonrigid BSpline (5x5x3)  registration (click to enlarge)
 |-
-|[[Image:RegLib_C09_registered2_BSpline.gif|300px]] after nonrigid BSpline registration (click to enlarge)
+|[[Image:RegLib_C10_registered3_BSpline3.gif|300px]] after nonrigid BSpline (7x7x5)  registration (click to enlarge)
 |}
 === Acknowledgments ===

@@ Line 2: / Line 2: @@
 =  Slicer Registration Library Case #10: group atlas to structural MRI =
 == Input ==
 ==Description ==

Documentation:Nightly:Registration:RegistrationLibrary:RegLib C10 - Revision history

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

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

Meier: /* Registration Results */

Meier: /* Registration Results */

Meier: /* Procedure */

Meier: /* Procedure */

Meier at 17:26, 4 September 2013

Meier: /* Input */

Meier: Created page with 'Back to Registration Library = Slicer Registration Library Case #10: group atlas to structural MRI = == Input == …'

Meier: Created page with 'Back to Registration Library
= Slicer Registration Library Case #10: group atlas to structural MRI = == Input == …'