Documentation:Nightly:Registration:RegistrationLibrary:RegLib C50 - Revision history

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

2014-01-23T20:30:32Z

Download (from NAMIC MIDAS)

Meier: /* Registration Results */

2014-01-23T20:07:45Z

Registration Results

Meier at 20:05, 23 January 2014

2014-01-23T20:05:15Z

Meier: Created page with 'Back to Registration Library
= Slicer Registration Library Case #50: Mouse micro-CT = == Input == {| style="color…'

2014-01-23T20:02:19Z

Created page with 'Back to Registration Library = Slicer Registration Library Case #50: Mouse micro-CT = == Input == {| style="color…'

New page

[[Documentation/Nightly/Registration/RegistrationLibrary|Back to Registration Library]] 
= Slicer Registration Library Case #50: Mouse micro-CT =
== Input ==
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C50_Thumb1.png|150px|left|this is the fixed DTI FA image. We want to align all images into this space]]
|[[Image:RegArrow_NonRigid.png|100px|left]]
|[[Image:RegLib_C50_Thumb2.png|150px|left|this is the moving MR image, to be aligned with the reference on the left]]
|-
|fixed image/target baseline CT
|
|moving image CT after fixation + staining
|}

== Description ==
Goal is to align the two CT images pre/post fixation. The fixation process altered the tissue appearance and also caused distortions we seek to correct with non-rigid registration.

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

== 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=xx '''RegLib_C50.mrb''': input data only, use this to run the tutorial from the start (Slicer mrb file. 50 MB). ]
*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C50_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify (Slicer mrb file. 82 MB). ]

== Keywords ==
micro-CT, animal, mouse, brain, intra-subject,

== Video Screencasts ==
#[[Media:RegLib_C50_01_Affine.mov|'''RegLib_C50 Registration Screencast (I. Affine Registration)''']]
#[[Media:RegLib_C50_02_BSpline.mov|'''RegLib_C50 Registration Screencast (II. BSpline Registration)''']]

== Procedure ==
#'''Affine Register'''
##go to the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
##''Input Images: Fixed Image Volume'': baseline
##''Input Images: Moving Image Volume'': stained
##''Output Settings'':
###''Slicer Linear Transform'' (create new transform, rename to: "Xf1_Affine")
###''Output Image Volume'' none. No resampling required for linear transforms
##''Registration Phases'': select/check ''Rigid'' , ''Rigid+Scale'', ''Affine''
##''Main Parameters'':
###increase ''Number Of Samples'' to 300,000
##click: ''Apply''; runtime ~ 1 min.
#'''BSpline Register'''
##leave baseline and stained as fixed and moving volumes
##''Output Settings'':
###''Slicer Linear Transform'' select None
###''Slicer BSpline Transform'' create new, rename to "Xf2_BSpline" or similar
###''Output Image Volume'': create new and rename to "stained_Xf2". Resampling '''is''' required for nonrigid transforms.
##''Registration Phases'': unchheck ''Rigid'' , ''Rigid+Scale'', ''Affine'' and check "BSpline" only
##''Main Parameters'':
###increase ''Number Of Samples'' to at least 300,000
###''BSpline Grid Size'': set to 7,7,7 or similar.
##click: ''Apply''; runtime < 3 min.

==Registration Results==

{|cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C50_unregistered.png|300px]] | before registration (click to enlarge)
|-
|[[Image:RegLib_C50_registered1_BSpline.gif|300px]]| after affine+nonrigid alignment (click to enlarge)
|}

=== Acknowledgments ===
Many thanks to Dr.Murat Maga from xx for sharing the example data.

@@ Line 20: / Line 20: @@
 == 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_C50.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=127956 '''RegLib_C50.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=xx '''RegLib_C50_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=127955 '''RegLib_C50_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 82 MB). </small>]
 == Keywords ==

← Older revision		Revision as of 20:05, 23 January 2014
Line 63:		Line 63:

	=== Acknowledgments ===		=== Acknowledgments ===
−	Many thanks to Dr.Murat Maga ~~from xx~~ for sharing the example data.	+	Many thanks to Dr.Murat Maga from [http://www.seattlechildrens.org/research/developmental-biology-regenerative-medicine Center for Developmental Biology and Regenerative Medicine in Seattle, WA] for sharing the example data.

@@ Line 57: / Line 57: @@
 {|cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C50_unregistered.png|300px]] | before registration (click to enlarge)
+|[[Image:RegLib_C50_unregistered.png|300px]] before registration (click to enlarge)
 |-
-|[[Image:RegLib_C50_registered1_BSpline.gif|300px]]| after affine+nonrigid alignment (click to enlarge)
+|[[Image:RegLib_C50_registered_BSpline.gif|300px]] after affine+nonrigid alignment (click to enlarge)
 |}
 === Acknowledgments ===
 Many thanks to Dr.Murat Maga from [http://www.seattlechildrens.org/research/developmental-biology-regenerative-medicine Center for Developmental Biology and Regenerative Medicine in Seattle, WA]  for sharing the example data.

Documentation:Nightly:Registration:RegistrationLibrary:RegLib C50 - Revision history

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

Meier: /* Registration Results */

Meier at 20:05, 23 January 2014

Meier: Created page with 'Back to Registration Library = Slicer Registration Library Case #50: Mouse micro-CT = == Input == {| style="color…'

Meier: Created page with 'Back to Registration Library
= Slicer Registration Library Case #50: Mouse micro-CT = == Input == {| style="color…'