Documentation:Nightly:Registration:RegistrationLibrary:RegLib C01 - Revision history

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

2018-05-23T20:42:31Z

Download (from NAMIC MIDAS)

2018-05-23T20:40:32Z

2018-05-23T20:34:35Z

2013-09-03T13:21:14Z

Description

2013-09-03T13:17:55Z

Objective / Background

2013-08-20T14:34:52Z

Procedure

2013-08-20T14:32:55Z

Procedure

2013-08-20T14:32:03Z

Procedure

2013-08-19T20:45:28Z

Registration Results

2013-08-19T20:45:14Z

Download (from NAMIC MIDAS)

← Older revision		Revision as of 20:42, 23 May 2018
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	== Download (from NAMIC MIDAS) ==		== Download (from NAMIC MIDAS) ==
−	*Case1.zip
	*[http://slicer.kitware.com/midas3/download/?items=115233 '''RegLib_C01.mrb''': includes raw data + all solutions and intermediate files <small>(Slicer mrb file. 13 MB). </small>]		*[http://slicer.kitware.com/midas3/download/?items=115233 '''RegLib_C01.mrb''': includes raw data + all solutions and intermediate files <small>(Slicer mrb file. 13 MB). </small>]

← Older revision		Revision as of 20:40, 23 May 2018
Line 20:		Line 20:

	== Download (from NAMIC MIDAS) ==		== Download (from NAMIC MIDAS) ==
		+	*Case1.zip
	*[http://slicer.kitware.com/midas3/download/?items=115233 '''RegLib_C01.mrb''': includes raw data + all solutions and intermediate files <small>(Slicer mrb file. 13 MB). </small>]		*[http://slicer.kitware.com/midas3/download/?items=115233 '''RegLib_C01.mrb''': includes raw data + all solutions and intermediate files <small>(Slicer mrb file. 13 MB). </small>]

@@ Line 31: / Line 31: @@
 == Procedure ==
 #'''Rigid Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
-##''Input Images: Fixed Image Volume'': MRMeningioma_1
+##''Input Images: Fixed Image Volume'': MR_1_baseline image
-##'''Input Images: Moving Image Volume'': MRMeningioma_2
+##'''Input Images: Moving Image Volume'': MR_2_followup image
 ##''Output Settings'':
 ###''Slicer Linear Transform'' (create new transform, rename to: "Xf1_Rigid")

@@ Line 14: / Line 14: @@
 == Description ==
 This case contains a baseline-followup pair of brain MRI. Goal is to align the follow-up image with the reference/baseline scan to assess changes, particularly in the tumor region. <br>
-'''Approach:''' Since image contrast and content is very similar in both images, and there is a good amount of initial overlap, the standard Slicer automated registration should work fine "out of the box" (i.e. with default parameters).
+'''Approach:''' Since image contrast and content is very similar in both images, and there is a good amount of initial overlap, the standard Slicer automated registration should work well for this. If possible, and affine registration would be preferable to a rigid one to address the typical distortions that occur in MRI and often vary between scans. However to assure the tumor and tumor changes do not influence the result, we will build a mask that excludes the tumor region from participating (i.e. actively contributing toward the result transform). We also use this case as an example to illustrate how to quickly generate masks for registration.
 == Modules used ==

@@ Line 12: / Line 12: @@
 |}
-==Objective / Background ==
+== Description ==
-Goal is to align the follow-up image with the reference/baseline scan to assess changes.
+This case contains a baseline-followup pair of brain MRI. Goal is to align the follow-up image with the reference/baseline scan to assess changes, particularly in the tumor region. <br>
 == Modules used ==

@@ Line 86: / Line 86: @@
 ##Go to the [[Documentation/Nightly/Modules/Data|''Data'' module]]
 ###Drag "MR_2_followup" into the "Xf2_Affine" transform node, if it isn't there already.
-#'''Apply the transforms / Save result images'''
+#'''Apply the transforms without resampling / Save result images'''
 ##for linear (rigid to affine) transforms you have two options for generating a result image in the new orientation: with and without resampling. The method without resampling leaves the original image data untouched and writes the new orientation into the image header. This preserves the full original image quality and is the preferred method, provided that the software using the result image can read the spatial information in the header correctly. If you open an image with a software that does not account for this header information, the image will appear in its original orientation. The resampling method will create a new image volume by interpolating the data into the new space. This has the advantage that your registered volume will have matching size and resolution as your reference image, but it is associated with some data loss from the interpolation during resampling.
 ##''Apply Transform without resampling'':

@@ Line 93: / Line 93: @@
 ##right click on the image node and from the pop-up menu, select ''Harden Transform''. This will apply the transform and move the image node back outside onto the main level.
 ##double click on the image node and rename it to document that this is no longer the original image but the reoriented one. Note that the image in its original position is replaced in memory and no longer accessible. There is no "undo" for this step, so if you wish to return to the original image, you must reload it from the original file. '''Be careful not to accidentally overwrite the original image file with the resampled one. Use a new filename when saving the image'''.
-##''Apply Transform with resampling'':
+#Alternative: '''Apply Transform with resampling''':
 ##Go to the [[Documentation/Nightly/Modules/BRAINSResample|''BRAINSResample'' module]]
 ###''Image To Warp'': select MR_2_followup

@@ Line 92: / Line 92: @@
 |[[Image:RegLib_C01_unregistered.png|300px]] ||baseline and follow-up before registration (click to enlarge)
 |-
-|[[Image:RegLib_C01_rigid|300px]]||after rigid alignment. Note the residual shape differences (click to enlarge)
+|[[Image:RegLib_C01_rigid.png|300px]]||after rigid alignment. Note the residual shape differences (click to enlarge)
 |-
 |[[Image:RegLib_C01_affine.png|300px]]||after affine registration (click to enlarge)

@@ Line 19: / Line 19: @@
 == Download (from NAMIC MIDAS) ==
-*[http://slicer.kitware.com/midas3/download/?items=115233 '''RegLib_C03.mrb''':  includes raw data + all solutions and intermediate files <small>(Slicer mrb file. 13 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=115233 '''RegLib_C01.mrb''':  includes raw data + all solutions and intermediate files <small>(Slicer mrb file. 13 MB). </small>]
 == Keywords ==