Documentation:Nightly:Registration:RegistrationLibrary:RegLib C02 - Revision history

Meier at 06:13, 1 July 2016

2016-07-01T06:13:41Z

2016-07-01T06:13:18Z

2013-09-03T13:24:08Z

Description

2013-09-03T13:22:03Z

Objective / Background

2013-08-28T18:23:44Z

Objective / Background

2013-08-20T14:57:13Z

Download (from NAMIC MIDAS)

2013-08-20T14:37:06Z

Procedure

2013-08-20T14:13:46Z

Procedure

2013-08-20T14:13:28Z

Procedure

2013-08-20T14:12:13Z

Input

@@ Line 24: / Line 24: @@
 <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=115374 '''RegLib_C02.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 19 MB). </small>]
-*[http://slicer.kitware.com/midas3/download/?items= 244969 '''RegLib_C02_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 30 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=244969 '''RegLib_C02_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 30 MB). </small>]
 == Keywords ==

@@ Line 24: / Line 24: @@
 <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=115374 '''RegLib_C02.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 19 MB). </small>]
-*[http://slicer.kitware.com/midas3/download/?items=115373 '''RegLib_C02_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 30 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items= 244969 '''RegLib_C02_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 30 MB). </small>]
 == Keywords ==

@@ Line 16: / Line 16: @@
 == Description ==
 This case contains a structural T1-weighted MRI scan and a lesion segmentation obtained from another (FLAIR) scan. Goal is to align the FLAIR image and its segmentation labelmap with the structural reference T1 scan. <br>
-'''Approach''': we first compute the registration from the T1-FLAIR pair and then apply this transform to the lesion segmentation.
+'''Approach''': we first compute the registration from the T1-FLAIR pair and then apply this transform to the lesion segmentation. To follow a "non-destructive" processing philosophy we will avoid resampling the data where possible. Instead we will integrate the new orientation of the images in the image header, which does not change the image data itself.
 == Modules used ==

@@ Line 14: / Line 14: @@
 |}
-==Objective / Background ==
+== Description ==
-We have a structural T1-weighted MRI scan and a lesion segmentation obtained from another (FLAIR) scan. Goal is to align the FLAIR image and its segmentation labelmap with the structural reference T1 scan. <br>
+This case contains a structural T1-weighted MRI scan and a lesion segmentation obtained from another (FLAIR) scan. Goal is to align the FLAIR image and its segmentation labelmap with the structural reference T1 scan. <br>
 '''Approach''': we first compute the registration from the T1-FLAIR pair and then apply this transform to the lesion segmentation.

@@ Line 15: / Line 15: @@
 ==Objective / Background ==
-Goal is to align the FLAIR image and its segmentation labelmap with the structural reference T1 scan.
+We have a structural T1-weighted MRI scan and a lesion segmentation obtained from another (FLAIR) scan. Goal is to align the FLAIR image and its segmentation labelmap with the structural reference T1 scan. <br>
 == Modules used ==

@@ Line 48: / Line 48: @@
 ###the "FLAIR" image should already be placed within the transform "Xf1_Affine", that was done by the registration module. If not, left click on the "FLAIR" node and drag it onto the "Xf1_Affine" node. You will see a "+" sign appear indicating that the image is placed within the transform.
 ###Do the same for the "LesionSeg" node, i.e. drag it into the "Xf1_Affine" transform.
 ==Registration Results==

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 ##Leave all other settings at default
 ##click: ''Apply''; runtime < 1 min.
-#'''Align LabelmapI:''' We have now computed the registration transform. To reorient both FLAIR and its label map, we place both volumes inside the transform.
+#'''Align Labelmap:''' We have now computed the registration transform. To reorient both FLAIR and its label map, we place both volumes inside the transform.
 ###Place "T1" in the background and "FLAIR" in the foreground. Select "LesionSeg" as the labelmap to display.
 ##Go to the [[Documentation/Nightly/Modules/Data|''Data'']] module

@@ Line 34: / Line 34: @@
 #'''Compute Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
 ##''Input Images: Fixed Image Volume'': T1
-##'''Input Images: Moving Image Volume'': FLAIR
+##''Input Images: Moving Image Volume'': FLAIR
 ##''Output Settings'':
 ###''Slicer Linear Transform'' (create new transform, rename to: "Xf1_Affine")

@@ Line 4: / Line 4: @@
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
 |[[Image:RegLib_C02_Thumb1.png|150px|left|this is the fixed MRI reference image. All images are aligned into this space]]
-|[[Image:RegArrow_NonRigid.png|100px|left]]
+|[[Image:RegArrow_Affine.png|100px|left]]
 |[[Image:RegLib_C02_Thumb2.png|150px|left|this is the moving image, to be aligned with the reference on the left]]
 |[[Image:RegLib_C02_Thumb3.png|150px|left|this is a segmentation labelmap in the same space as the moving image. To be registered also]]