Documentation:Nightly:Registration:RegistrationLibrary:RegLib C27 - Revision history

Meier at 13:37, 3 September 2013

2013-09-03T13:37:46Z

2013-06-27T16:54:47Z

Download (from NAMIC MIDAS)

2013-06-27T16:47:17Z

Registration Results

2013-06-27T16:46:59Z

Registration Results

2013-06-27T16:45:23Z

Download (from NAMIC MIDAS)

2013-05-14T14:57:49Z

Registration Results

2013-05-14T14:57:11Z

Registration Results

2013-05-14T14:56:04Z

Procedures

2013-05-14T14:54:24Z

Procedures

2013-05-14T14:52:41Z

Procedures

@@ Line 18: / Line 18: @@
 |moving image<br>DTI tensor
 |}
 == Modules used ==
 *[[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]
 *[[Documentation/Nightly/Modules/ResampleDTI|''Resample DTI Volume'']]
 == Download (from NAMIC MIDAS) ==

@@ Line 30: / Line 30: @@
 == 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=100678 '''RegLib_C27.mrb''']  <small>(input data, Slicer mrb file 50MB)</small><br>
 *[http://slicer.kitware.com/midas3/download/?items=95493 '''RegLib_C27_full.mrb'''] <small>(input data + results, Slicer mrb file 114MB) </small>

@@ Line 97: / Line 97: @@
 {|cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C27_Result1.gif|300px]] ||original and registered pair of FLAIR and DTI (click to enlarge)
+|[[Image:RegLib_C27_Result1.gif|400px]] ||original and registered pair of FLAIR and DTI (click to enlarge)
 |-
-|[[Image:RegLib_C27_Result2.gif|300px]]||original and registered pair of T1 and DTI (click to enlarge)
+|[[Image:RegLib_C27_Result2.gif|400px]]||original and registered pair of T1 and DTI (click to enlarge)
 |}

@@ Line 95: / Line 95: @@
 == Registration Results==
-[[Image:RegLib_C27_Result2.gif|500px|Registered DTI superimposed on FLAIR]] original and registered pair of T1 and DTI (animated gif, click to animate)<br>
+{|cellpadding="10" cellspacing="0" border="0"
-<br>
+|[[Image:RegLib_C27_Result1.gif|300px]] ||original and registered pair of FLAIR and DTI (click to enlarge)

@@ Line 31: / Line 31: @@
 == 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>
-*[http://slicer.kitware.com/midas3/download/?items=95265,1 '''RegLib_C27_raw.mrb''': raw data only, use this to run the tutorial from the start <small>(Slicer mrb file. 75 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=100678 '''RegLib_C27.mrb''']  <small>(input data, Slicer mrb file 50MB)</small><br>
-*[http://slicer.kitware.com/midas3/download/?items=95057,1 '''RegLib_C27.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 130 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=95493 '''RegLib_C27_full.mrb'''] <small>(input data + results, Slicer mrb file 114MB) </small>
 == Keywords ==

@@ Line 82: / Line 82: @@
 *'''Phase 3: resample DTI'''
-#Open the [[Documentation/Nightly/Modules/ResampleDTI|''Resample DTI Volume'' module]  (under ''All Modules'' menu; note this is distinct from the ResampleScalarVectorDWIVolume used above)]]
+#Open the [[Documentation/Nightly/Modules/ResampleDTI|''Resample DTI Volume'' module]  (under ''All Modules'' menu; note this is distinct from the ResampleScalarVectorDWIVolume)]]. We '''must''' use the ResampleDTI module to process tensor images to correctly resample the tensor data.
 ##''Input Volume'': DTI
 ##''Output Volume'': create new DTI Volume, rename to ''DTI_Xf2''

@@ Line 47: / Line 47: @@
 == Procedures ==
-*'''Phase 1:  Register DTI'''
+*'''Phase 1:  register DTI'''
 #open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
 ##''Fixed Image Volume'': FLAIR
@@ Line 75: / Line 75: @@
 ##Leave all other settings at default
 ##click: Apply; runtime < 10 sec (MacPro QuadCore 2.4GHz) -> This only generates the transform. We still need to apply it to the image
-#open the  [[Documentation/Nightly/Modules/Data| Data module]]
+#Apply the transform to the T1 image: open the  [[Documentation/Nightly/Modules/Data| Data module]]
 ##locate the transform generated above "Xf2_T1-FLAIR" and the T1 image. Drag the T1 image node onto the transform. A little + sign should appear next to the transform. Click on it to verify the T1 image was placed under the transform.
 ##right-click on the T1 image node, from the pop-up menu select ''Harden Transform''. The T1 node moves back out to the main level
@@ Line 81: / Line 81: @@
 #Save Results
-*'''Phase 3: Resample DTI'''
+*'''Phase 3: resample DTI'''
 #Open the [[Documentation/Nightly/Modules/ResampleDTI|''Resample DTI Volume'' module]  (under ''All Modules'' menu; note this is distinct from the ResampleScalarVectorDWIVolume used above)]]
 ##''Input Volume'': DTI