Documentation:Nightly:Registration:RegistrationLibrary:RegLib C38 - Revision history

Meier at 14:02, 3 September 2013

2013-09-03T14:02:11Z

Meier: /* Procedure */

2013-09-03T14:00:37Z

Procedure

Meier at 13:59, 3 September 2013

2013-09-03T13:59:08Z

Meier: /* Procedure */

2013-09-03T13:55:22Z

Procedure

Meier at 13:51, 3 September 2013

2013-09-03T13:51:10Z

Meier: /* Input */

2013-07-01T22:26:23Z

Input

Meier: /* Video Screencasts */

2013-07-01T22:25:57Z

Video Screencasts

Meier: /* Procedure */

2013-07-01T22:25:23Z

Procedure

Meier: /* Procedure */

2013-07-01T22:23:48Z

Procedure

Meier at 22:23, 1 July 2013

2013-07-01T22:23:28Z

@@ Line 27: / Line 27: @@
 == Description ==
-This is an example of a multi-contrast dataset acquired for traumatic brain injury (TBI). We have many scans we seek to align to a common reference. Since all scans are acquired in short succession, they have only little initial misalignment, but they may differ significantly in contrast and field of view.
+This is an example of a multi-contrast dataset acquired for traumatic brain injury (TBI). We have many scans we seek to align to a common reference. Since all scans are acquired in short succession, they have only little initial misalignment, but they may differ significantly in contrast and field of view. <br>
 == Modules used ==
@@ Line 37: / Line 38: @@
 == Video Screencasts ==
 #[[Media:RegLib_C38.mov|registering all other images to T1, apply transform without resampling and save.]] (8.5 min, 37MB)
 == Procedure ==

@@ Line 55: / Line 55: @@
 ##leave all other settings at defaults
 ##click: Apply; runtime < 10 sec (MacPro QuadCore 2.4GHz)
-#this will generate the alignment transform. The demo screencast above shows how to apply the result transforms without resampling and then saving the images under a new name. It also shows where in the saved image the new orientation is stored.
+#this will generate the alignment transform. The demo screencast above shows how to apply the result transforms without resampling and then saving the images under a new name. It also shows where in the saved image the new orientation is stored. Note that the screencast was done for version 4.2.0. If you're using a more recent version, the BRAINS registration tool may automatically place the moving image into the result transform.
 #repeat steps above for all the other images: FLAIR, T1post, SWI,EP . The only 2 settings to change are the ''Moving Image'' and the ''Result Transform''

@@ Line 56: / Line 56: @@
 ##click: Apply; runtime < 10 sec (MacPro QuadCore 2.4GHz)
 #this will generate the alignment transform. The demo screencast above shows how to apply the result transforms without resampling and then saving the images under a new name. It also shows where in the saved image the new orientation is stored.
-#repeat steps above for all the other images: SWI, . The only 2 settings to change are the ''Moving Image'' and the ''Result Transform''
+#repeat steps above for all the other images: FLAIR, T1post, SWI,EP . The only 2 settings to change are the ''Moving Image'' and the ''Result Transform''
 == Registration Results==
 [[Image:RegLib_C38_unregistered.gif|300px|unregistered]] unregistered <br>
 [[Image:RegLib_C38_registered.gif|300px|registered]] registered

@@ Line 56: / Line 56: @@
 ##click: Apply; runtime < 10 sec (MacPro QuadCore 2.4GHz)
 #this will generate the alignment transform. The demo screencast above shows how to apply the result transforms without resampling and then saving the images under a new name. It also shows where in the saved image the new orientation is stored.
 == Registration Results==
 [[Image:RegLib_C38_unregistered.gif|300px|unregistered]] unregistered <br>
 [[Image:RegLib_C38_registered.gif|300px|registered]] registered

@@ Line 25: / Line 25: @@
 |EP100
 |}
 == Modules used ==
@@ Line 52: / Line 55: @@
 ##leave all other settings at defaults
 ##click: Apply; runtime < 10 sec (MacPro QuadCore 2.4GHz)
-#this will generate the alignment transform. Note that the Slicer4.1 version of BRAINS registration does '''not''' automatically place the moving volume inside the result transform, as it did for Slicer 3.6. In order to see the result, you must either go to the [[Documentation/Nightly/Modules/Data|''Data'' module]] and drag the moving volume inside the transform node, or when calculating the registration, select to generate a resampled ''Output Volume''. The demo screencast above shows how to apply the result transforms without resampling and then saving the images under a new name. It also shows where in the saved image the new orientation is stored.
+#this will generate the alignment transform. The demo screencast above shows how to apply the result transforms without resampling and then saving the images under a new name. It also shows where in the saved image the new orientation is stored.
 == Registration Results==
 [[Image:RegLib_C38_unregistered.gif|300px|unregistered]] unregistered <br>
 [[Image:RegLib_C38_registered.gif|300px|registered]] registered

@@ Line 11: / Line 11: @@
 |[[Image:RegLib_C38_Thumb4.png|100px]]
 |[[Image:RegLib_C38_Thumb5.png|100px]]
 |[[Image:RegLib_C38_Thumb6.png|100px]]
 |[[Image:RegLib_C38_Thumb7.png|100px]]
@@ Line 22: / Line 21: @@
 |coronal T2
 |SWI
 |EP50
 |EP75

@@ Line 35: / Line 35: @@
 == Video Screencasts ==
-#[[Media:RegLib_C38.mov|registering all other images to T1, apply transform without resampling and save.]] (5 min, 22MB)
+#[[Media:RegLib_C38.mov|registering all other images to T1, apply transform without resampling and save.]] (8.5 min, 37MB)
 ===Key Strategies===

@@ Line 1: / Line 1: @@
 =  Slicer Registration Library Case 38: TBI   =
@@ Line 27: / Line 29: @@
 == Modules used ==
-*[[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|''N4ITKBiasFieldCorrection'' ]] module
+*[[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
 == Download (from NAMIC MIDAS) ==
@@ Line 42: / Line 44: @@
 #Load all datasets via drag&drop or via "AddData / AddVolume" ... do not center the volumes, since they have reasonable alignment at the outset
 #the registration procedure below is identical for all other scans in the sequence, i.e. just replace the ''Moving Volume'' and the ''Slicer Linear Transform", everything else can stay at default
-#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS) module]
+#open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
 ##''Fixed Image Volume'': T1
 ##''Moving Image Volume'': T2
@@ Line 52: / Line 54: @@
 ##leave all other settings at defaults
 ##click: Apply; runtime < 10 sec (MacPro QuadCore 2.4GHz)
-#this will generate the alignment transform. Note that the Slicer4.1 version of BRAINS registration does '''not''' automatically place the moving volume inside the result transform, as it did for Slicer 3.6. In order to see the result, you must either go to the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Data ''Data module''] and drag the moving volume inside the transform node, or select to generate a resampled ''Output Volume'', as done above. The demo movies you can download here show how to do this.
+#this will generate the alignment transform. Note that the Slicer4.1 version of BRAINS registration does '''not''' automatically place the moving volume inside the result transform, as it did for Slicer 3.6. In order to see the result, you must either go to the [[Documentation/Nightly/Modules/Data|''Data'' module]]and drag the moving volume inside the transform node, or select to generate a resampled ''Output Volume'', as done above. The demo movies you can download here show how to do this.
 == Registration Results==
 [[Image:RegLib_C38_unregistered.gif|300px|unregistered]] unregistered <br>
 [[Image:RegLib_C38_registered.gif|300px|registered]] registered