Unknown user: Text replacement - "slicerWiki/index.php" to "wiki"

2019-11-21T17:34:28Z

Text replacement - "slicerWiki/index.php" to "wiki"

JChris.FillionR at 16:22, 15 July 2015

2015-07-15T16:22:59Z

UpdateBot: Nightly -> 4.4

2014-12-25T06:55:10Z

Nightly -> 4.4

Show changes

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 === How do I generate a mask and what should it look like ? ===
 The purpose of masking (see above) is to exclude any parts of the image that are present in only one of the images yet large enough to distract the registration algorithm as it is trying to find a match for something that doesn't exist. So your mask should focus on excluding those (irrelevant) aspects of the image. Also if you have deformations in the image and care about accuracy in one region more than another you would center the mask around that region. There is a set of screencasts dedicated to quick mask building here:
-[http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/RegistrationVideoTutorials Registration Video Tutorials]
+[http://wiki.slicer.org/wiki/Documentation/Nightly/RegistrationVideoTutorials Registration Video Tutorials]
 <br>
 Basically you can use any segmentation tool in Slicer that produces a labelmap.
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 * you need a mask for both the fixed and the moving image.
-There are many example cases in the [http://wiki.slicer.org/slicerWiki/index.php/Documentation:Nightly:Registration:RegistrationLibrary '''Slicer Registration Library'''] that demonstrate the use of masks, e.g.:
+There are many example cases in the [http://wiki.slicer.org/wiki/Documentation:Nightly:Registration:RegistrationLibrary '''Slicer Registration Library'''] that demonstrate the use of masks, e.g.:
-*[http://wiki.slicer.org/slicerWiki/index.php/Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C06 Case 06 (Breast MRI)]
+*[http://wiki.slicer.org/wiki/Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C06 Case 06 (Breast MRI)]
-*[http://wiki.slicer.org/slicerWiki/index.php/Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C07 Case 07 (prostate MRI)]
+*[http://wiki.slicer.org/wiki/Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C07 Case 07 (prostate MRI)]
-*[http://wiki.slicer.org/slicerWiki/index.php/Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C12 Case 12 (abdominal CT)]
+*[http://wiki.slicer.org/wiki/Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C12 Case 12 (abdominal CT)]
-*[http://wiki.slicer.org/slicerWiki/index.php/Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C17 Case 17 (interventional MRI-CT)]
+*[http://wiki.slicer.org/wiki/Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C17 Case 17 (interventional MRI-CT)]
 === Which registration methods offer masking? ===
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 === How do I register images via landmarks/fiducials? ===
-There are two fiducial registration tools available within Slicer. The default is within the Registration menu, and an alternative version is found in the SlicerIGT extension as "Fiducial Registration Wizard". A detailed case example using both tools is available in the [http://wiki.slicer.org/slicerWiki/index.php/Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C48 Case 48 in the Registration Case Library]. A brief screencast on selecting landmarks and running either tools are also here:
+There are two fiducial registration tools available within Slicer. The default is within the Registration menu, and an alternative version is found in the SlicerIGT extension as "Fiducial Registration Wizard". A detailed case example using both tools is available in the [http://wiki.slicer.org/wiki/Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C48 Case 48 in the Registration Case Library]. A brief screencast on selecting landmarks and running either tools are also here:
 #[[Media:RegLib_C48_FiducialRegistration.mov|'''fiducial-based registration''']]
 #[[Media:RegLib_C48_FiducialRegistration_IGT.mov|'''alternative tool: using SlicerIGT's fiducial-based registration''']] (shows extension download and module execution only, for the landmark selection see movie above)
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 Slice views: Slicer sets the overall field of view based on the image selected as "background". If the image in the foreground extends beyond that region it will be clipped. You can easily fix/test that by switching foreground and background volumes.
 If you already created a resampled version of the registered image, that may also have been cropped,because it sets the field of view based on the reference image (which is the fixed image usually). If you place your resampled image in the background and still see cropped edges, then that's what happened. In that case either use a different reference image for resampling or no reference at all and specify the result sizes manually, or use the  crop tool to expand the FOV as described below:
-#use the [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Crop_Volume CropVolume module] to over-crop the reference image (define ROI to cover the field of view you want to have in the resampled volume). You will need to use interpolated crop mode, so the resolution will not match the original reference volume.
+#use the [http://www.slicer.org/wiki/Documentation/Nightly/Modules/Crop_Volume CropVolume module] to over-crop the reference image (define ROI to cover the field of view you want to have in the resampled volume). You will need to use interpolated crop mode, so the resolution will not match the original reference volume.
-#Use the result of the cropping operation as the reference for [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/BRAINSResample BRAINSResample module] (you will need to specify the moving volume, output volume, and the transform produced by the BRAINS registration module).
+#Use the result of the cropping operation as the reference for [http://www.slicer.org/wiki/Documentation/Nightly/Modules/BRAINSResample BRAINSResample module] (you will need to specify the moving volume, output volume, and the transform produced by the BRAINS registration module).

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 <noinclude>__TOC__
 ={{#titleparts: {{PAGENAME}} | | -1 }}=</noinclude><includeonly>
-='''User FAQ: {{{1}}}'''=
+{{#ifeq: {{#titleparts: {{PAGENAME}} | 3 }} | Documentation/{{documentation/version}}/Developers | | ='''User FAQ: {{{1}}}'''=}}
 </includeonly>

Documentation/4.4/FAQ/Registration - Revision history

Unknown user: Text replacement - "slicerWiki/index.php" to "wiki"

JChris.FillionR at 16:22, 15 July 2015

UpdateBot: Nightly -> 4.4