Documentation/Nightly/Registration/RegistrationLibrary/RegLib C29 - Revision history

Meier: /* Description */

2013-09-03T13:48:01Z

Description

Meier: /* Description */

2013-09-03T13:43:33Z

Description

Meier at 13:42, 3 September 2013

2013-09-03T13:42:41Z

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

2013-06-27T16:54:11Z

Download (from NAMIC MIDAS)

Meier: /* Registration Results */

2013-06-27T16:50:13Z

Registration Results

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

2013-06-27T16:48:55Z

Download (from NAMIC MIDAS)

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

2013-06-27T16:48:43Z

Download (from NAMIC MIDAS)

UpdateBot: Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

2013-06-14T08:02:29Z

Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

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

2013-05-13T21:31:00Z

Download (from NAMIC MIDAS)

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

2013-05-13T21:29:10Z

Download (from NAMIC MIDAS)

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 == Description ==
-This is a classic case of a multi-sequence MRI exam we wish to spatially align to the anatomical reference scan (T1-SPGR). The scan of interest is the DTI image to be aligned for surgical planning/reference.  Unlike CaseXX this one does contain both a T1 and a T2 image. The T2 image being closer in contrast to the DWI/DTI baseline, it makes for the better registration reference. However the T1 contains the tissue contrast of interest. <br>
+This is a classic case of a multi-sequence MRI exam we wish to spatially align to the anatomical reference scan (T1-SPGR). The scan of interest is the DTI image to be aligned for surgical planning/reference.  Unlike [[Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C27 |Case 27]]  this one does contain both a T1 and a T2 image. The T2 image being closer in contrast to the DWI/DTI baseline, it makes for the better registration reference. However the T1 contains the tissue contrast of interest. <br>
 '''Approach:''' we can use either T1 or T2 as the spatial reference. Ultimately we seek to overlay the DTI information onto the T1 image. But the T2 makes for a better registration reference because it matches better the DTI baseline contrast. Hence we will use the T2 as the reference and align the T1 to the T2 in a separate registration step. The typical DTI challenges are present here also:
 :*The DWI sequence (EPI) contains distortions we seek to correct via non-rigid alignment

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 == Description ==
 This is a classic case of a multi-sequence MRI exam we wish to spatially align to the anatomical reference scan (T1-SPGR). The scan of interest is the DTI image to be aligned for surgical planning/reference.  Unlike CaseXX this one does contain both a T1 and a T2 image. The T2 image being closer in contrast to the DWI/DTI baseline, it makes for the better registration reference. However the T1 contains the tissue contrast of interest. <br>
-'''Approach:''' we can use either T1 or T2 as the spatial reference. Ultimately we seek to overlay the DTI information onto the T1 image. But the T2 makes for a better registration reference because it matches better the DTI baseline contrast. Hence we will use the T2 as the reference and align the T1 to the T2 in a separate registration step.
+'''Approach:''' we can use either T1 or T2 as the spatial reference. Ultimately we seek to overlay the DTI information onto the T1 image. But the T2 makes for a better registration reference because it matches better the DTI baseline contrast. Hence we will use the T2 as the reference and align the T1 to the T2 in a separate registration step. The typical DTI challenges are present here also:
+:*The DWI sequence (EPI) contains distortions we seek to correct via non-rigid alignment
-*The DWI sequence (EPI) contains distortions we seek to correct via non-rigid alignment
+:*The DWI sequence also contains intensity inhomogeneity (coil bias)
-*The DWI sequence also contains intensity inhomogeneity (coil bias)
+:*the DTI baseline is similar in contrast to a T2, albeit at much lower resolution
-*the DTI baseline is similar in contrast to a T2, albeit at much lower resolution
+:*we have different amounts of voxel-anisotropy
 == Modules used ==

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 |moving image<br>DTI baseline+DTI tensor
 |}
 == Modules used ==
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 *[[Documentation/{{documentation/version}}/Modules/BRAINSFit| ''General Registration (BRAINS)'']]
 *[[Documentation/{{documentation/version}}/Modules/ResampleDTI|''Resample DTI Volume'']]
 == Download (from NAMIC MIDAS) ==

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 == 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=95265 '''RegLib_C29_raw.mrb'''] <small>(input data, Slicer mrb file. 71 MB). </small> <br>
 *[http://slicer.kitware.com/midas3/download/?items=95058 '''RegLib_C29_full.mrb'''] <small>(input data+results, Slicer mrb file. 124 MB). </small>

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 == Registration Results==
-[[Image:RegLib_C29_registered.gif|500px|Registered DTI superimposed on SPGR and T2]] original and registered pair of T1 and DTI (animated gif, may have to be opened to animate)<br>
+{|cellpadding="10" cellspacing="0" border="0"
-<br>
+|[[Image:RegLib_C29_registered.gif|400px]] ||original and registered pair of T1 and DTI (click to enlarge)

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 == 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_C29_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=95265 '''RegLib_C29_raw.mrb'''] <br><small>(input data, Slicer mrb file. 71 MB). </small> <br>
-*[http://slicer.kitware.com/midas3/download/?items=95057,1 '''RegLib_C29.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=95058 '''RegLib_C29_full.mrb'''] <br><small>(input data+results, Slicer mrb file. 124 MB). </small>
 == Keywords ==

← Older revision		Revision as of 08:02, 14 June 2013
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	[[Documentation/Nightly/Registration/RegistrationLibrary\|Back to Registration Library]] <br>		[[Documentation/Nightly/Registration/RegistrationLibrary\|Back to Registration Library]] <br>
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