Documentation:Nightly:Registration:RegistrationLibrary:RegLib C03 - Revision history

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

2019-11-27T02:21:00Z

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

2016-07-01T15:15:25Z

Procedure: Update parameter names to Slicer 4.4

2013-09-03T13:26:12Z

Description

2013-09-03T13:25:15Z

Objective / Background

2013-08-28T18:26:12Z

Objective / Background

2013-08-28T18:24:24Z

Procedure

2013-08-19T15:30:50Z

2013-06-27T16:54:24Z

Download (from NAMIC MIDAS)

2013-06-27T16:42:49Z

Registration Results

2013-06-27T16:42:18Z

Registration Results

@@ Line 39: / Line 39: @@
 == Procedure ==
-This assumes you have the following: 1) a T2 reference image, 2) a DTI baseline image and  3) the DTI volume (both obtained from the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation module]). If you do not have a baseline image, generate a scalar Trace image from the DTI, using the ''Diffusion Tensor Scalar Measurements'' module:
+This assumes you have the following: 1) a T2 reference image, 2) a DTI baseline image and  3) the DTI volume (both obtained from the  [[Documentation/4.1/Modules/DiffusionTensorEstimation|Diffusion Tensor Estimation module]]). If you do not have a baseline image, generate a scalar Trace image from the DTI, using the ''Diffusion Tensor Scalar Measurements'' module:
 #'''Compute Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
 ##''Input Images: Fixed Image Volume'': T2

@@ Line 49: / Line 49: @@
 ##''Registration Phases'':  select/check ''Rigid'' , ''Rigid+Scale'', ''Affine'', ''BSpline''
 ##''Main Parameters'':
-###increase ''Number Of Samples'' to 300,000
+###increase ''Percentage of Samples'' to 0.006
 ###set  ''B-Spline Grid Size'' to 7,7,5 (we have lower resolution in the IS-direction (z), hence we set a smaller (5) grid size there)
 ##Leave all other settings at default

@@ Line 16: / Line 16: @@
 == Description ==
 This is a simple case of diffusion MRI. Goal is to align the Diffusion Tensor Image (DTI) with the structural reference T2 scan that provides accuracte anatomical reference.<br>
-'''Approach''': we compute the registration transform using a scalar DTI_baseline scan and then apply this transform to the DTI tensor image. Because reorienting tensor data requires a different form of resampling, we must use a dedicated module for this purpose.
+'''Approach''': we compute the registration transform using a scalar DTI_baseline scan and then apply this transform to the DTI tensor image. Because reorienting tensor data requires a different form of resampling, we must use a dedicated module for this purpose. Because DTI acquisitions tend to contain strong geometric distortions, we apply a nonrigid transform to the DTI, which makes resampling necessary.
 == Modules used ==

@@ Line 14: / Line 14: @@
 |}
-==Objective / Background ==
+== Description ==
-Goal is to align the DTI image with the structural reference T2 scan that provides accuracte anatomical reference.<br>
+This is a simple case of diffusion MRI. Goal is to align the Diffusion Tensor Image (DTI) with the structural reference T2 scan that provides accuracte anatomical reference.<br>
 '''Approach''': we compute the registration transform using a scalar DTI_baseline scan and then apply this transform to the DTI tensor image. Because reorienting tensor data requires a different form of resampling, we must use a dedicated module for this purpose.

@@ Line 15: / Line 15: @@
 ==Objective / Background ==
-Goal is to align the DTI image with the structural reference T2 scan that provides accuracte anatomical reference.
+Goal is to align the DTI image with the structural reference T2 scan that provides accuracte anatomical reference.<br>
 == Modules used ==

@@ Line 41: / Line 41: @@
 #'''Compute Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
 ##''Input Images: Fixed Image Volume'': T2
-##'''Input Images: Moving Image Volume'': DTI_baseline
+##''Input Images: Moving Image Volume'': DTI_baseline
 ##''Output Settings'':
 ###''Slicer BSpline Transform'' (create new transform, rename to: "Xf1_DTbase-T2_BSpline")

@@ Line 3: / Line 3: @@
 == Input ==
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C03_thumb1.png|150px|lleft|this is the fixed T2 reference image. All images are aligned into this space]]
+|[[Image:RegLib_C03_thumb1.png|150px|left|this is the fixed T2 reference image. All images are aligned into this space]]
-|[[Image:RegArrow_NonRigid.png|100px|lleft]]
+|[[Image:RegArrow_NonRigid.png|100px|left]]
-|[[Image:RegLib_C03_thumb2.png|150px|lleft|this is the DTI Baseline scan, to be registered with the T2]]
+|[[Image:RegLib_C03_thumb2.png|150px|left|this is the DTI Baseline scan, to be registered with the T2]]
-|[[Image:RegLib_C03_thumb3.png|150px|lleft|this is the DTI tensor image, in the same orientation as the DTI Baseline]]
+|[[Image:RegLib_C03_thumb3.png|150px|left|this is the DTI tensor image, in the same orientation as the DTI Baseline]]
 |-
 |fixed image 1/target<br>T2

@@ Line 27: / Line 27: @@
 == Download (from NAMIC MIDAS) ==
-<small>''Why 2 sets of files?  The mrb for the full dataset includes Slicer nodes for intermediate files. If you plan on running the procedure yourself it can get difficult to distinguish the old data from the new one you generated yourself. So to keep things uncluttered we recommend to start from the raw dataset when running the tutorial, and to use the full dataset to verify/compare.''</small>
+<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=95490 '''RegLib_C03.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=95491 '''RegLib_C03_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 108 MB). </small>]

@@ Line 66: / Line 66: @@
 {|cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C03_baseline_unregistered.gif]] ||baseline & T2 before registration
+|[[Image:RegLib_C03_baseline_unregistered.gif|300px]] ||baseline & T2 before registration (click to enlarge)
 |-
-|[[Image:RegLib_C03_baseline_registered.gif]]||baseline to T2 after affine+nonrigid alignment
+|[[Image:RegLib_C03_baseline_registered.gif|300px]]||baseline to T2 after affine+nonrigid alignment (click to enlarge)
 |-
-|[[Image:RegLib_C03_DTI_registered.gif|200px]]||DTI and T2 before & after registration
+|[[Image:RegLib_C03_DTI_registered.gif|300px]]||DTI and T2 before & after registration (click to enlarge)
 |}