Documentation/4.8/FAQ/Registration - Revision history

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UpdateBot: Nightly -> 4.8

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@@ Line 455: / Line 455: @@
 '''2.Automated registration:''' the basic concept here is to pad the image with duplicated slices in the 3rd dimension to provide the appearance of a 3D object (e.g. using the Resample module), and  then try to lock all degrees of freedom pertaining to the 3rd dimension (e.g. by masking), i.e. out-of-plane rotation or translation. Because the amount of data is very limited in 2D, automated registration is likely going to fail if the images are too far apart or to dissimilar in content.
 An example of 2D registration can be found in our case library:
-http://wiki.slicer.org/slicerWiki/index.php/Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C46
+https://www.slicer.org/wiki/Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C46 === What's the BSpline Grid Size? ===
 The BSpline grid is the basic structure of the deformation model applied when transforming one image to match the other. A uniform grid is placed over the entire image and the grid-points are allowed to move freely. These node displacements are then interpolated over the remainder of the grid. The image below shows an example of a 3x3x3 grid. An additional row of grid points is created at the boundary of the image (red). Those points are locked and do not move. They provide a boundary constraint to keep the grid from shifting. The interior points (green) are free to move in any direction (blue arrows), which gives 3 degrees of freedom (DOF) per grid-point. So a 3x3x3 grid translates into a transform with 27 DOF, a 5x5x5 grid will have 125 DOF. For comparison a rigid transform has 6 DOF, an affine transform has 12.
 When specifying a grid, be aware of your image resolution and anisotropy. For example if your image has substantially fewer voxels in one direction, it may be wise to also request fewer grid-points in that dimension, to avoid over fitting.<br>

@@ Line 576: / Line 576: @@
   referenceVolumeNode=slicer.util.getNode('MRHead')
   slicer.modules.transforms.logic().CreateDisplacementVolumeFromTransform(transformNode, referenceVolumeNode, False)
-The new volume can then be saved or used for ROI analysis with the [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/LabelStatistics Label Statistics module].
+The new volume can then be saved or used for ROI analysis with the [[Documentation/Nightly/Modules/LabelStatistics|Label Statistics module]].
 === Physical Space vs. Image Space: how do I align two registered images to the same image grid? ===

@@ Line 560: / Line 560: @@
 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 [[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 [[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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 === 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]
+[[Documentation/Nightly/RegistrationVideoTutorials|Registration Video Tutorials]]
 <br>
 Basically you can use any segmentation tool in Slicer that produces a labelmap.
@@ Line 286: / Line 286: @@
 * 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 [[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)]
+*[[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)]
+*[[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)]
+*[[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)]
+*[[Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C17|Case 17 (interventional MRI-CT)]]
 === Which registration methods offer masking? ===
@@ Line 451: / Line 451: @@
 Slicer is designed to work with 3D images. Since it operates in physical space, all objects must have a physical dimension (e.g. thickness).
 It is possible to still run a 2D registration with the 3D tools, with limitations. The two options are: <br>
-'''1.manual registration:''' the manual registration can easily be restricted to 2D. Simply do not use the sliders that control out-of plane rotation or translation. For more info on manual registration see  [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ#Can_I_manually_adjust_or_correct_a_registration.3F '''FAQ on manual registration'''] and also [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Registration/RegistrationLibrary the '''Registration Library''']
+'''1.manual registration:''' the manual registration can easily be restricted to 2D. Simply do not use the sliders that control out-of plane rotation or translation. For more info on manual registration see  [[Documentation/Nightly/FAQ#Can_I_manually_adjust_or_correct_a_registration.3F|'''FAQ on manual registration''']] and also [[Documentation/Nightly/Registration/RegistrationLibrary|the '''Registration Library''']]
 <br>
 '''2.Automated registration:''' the basic concept here is to pad the image with duplicated slices in the 3rd dimension to provide the appearance of a 3D object (e.g. using the Resample module), and  then try to lock all degrees of freedom pertaining to the 3rd dimension (e.g. by masking), i.e. out-of-plane rotation or translation. Because the amount of data is very limited in 2D, automated registration is likely going to fail if the images are too far apart or to dissimilar in content.
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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 [[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)