Documentation/Nightly/Modules/Resampling - Revision history

Grundlett: Text replacement - "\[http:\/\/wiki\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:12:45Z

Text replacement - "\[http:\/\/wiki\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Meier: /* Nesting & Hardening Transforms */

2014-05-06T21:01:36Z

Nesting & Hardening Transforms

Meier: /* Nesting & Hardening Transforms */

2014-05-06T21:01:06Z

Nesting & Hardening Transforms

Meier: /* Nesting & Hardening Transforms */

2014-05-06T21:00:41Z

Nesting & Hardening Transforms

Meier: /* Nesting & Hardening Transforms */

2014-05-06T20:59:36Z

Nesting & Hardening Transforms

Meier at 20:46, 6 May 2014

2014-05-06T20:46:16Z

Meier: /* Nesting Transforms */

2014-05-06T20:39:43Z

Nesting Transforms

Meier: /* Nesting Transforms */

2014-05-06T20:37:40Z

Nesting Transforms

Meier: /* Nesting Transforms */

2014-05-06T20:37:20Z

Nesting Transforms

Meier at 20:22, 6 May 2014

2014-05-06T20:22:22Z

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 <noinclude>{{documentation/versioncheck}}</noinclude>
-This page discusses Resampling of image and model data. [http://wiki.slicer.org/slicerWiki/index.php/Category:Documentation/{{documentation/version}}/Modules/Registration '''See here for an overview of registration methods'''].
+This page discusses Resampling of image and model data. [[Category:Documentation/{{documentation/version}}/Modules/Registration|'''See here for an overview of registration methods''']].
 = Transforms and how they are displayed in 3DSlicer =

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 *'''hardening is not the same as resampling''': in case of linear transforms, the new orientation is added to the physical orientation stored in the image header, without actually resampling the data itself. This is preferable in most cases as it avoids data degradation from interpolation artifacts associated with resampling. If you '''do''' need the transformed dataset resampled, use one of the resampling modules described below.
 *'''hardening''' is currently supported for volumes inside BSpline transforms, but '''not''' for the transform itself, i.e. the image on the right shows which hardening will work and which will not. Hardening cannot currently be used to concatenate linear and BSpline or multiple BSpline transforms.
 <br>

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 = Nesting & Hardening Transforms =
 [[Image:Registration_TransformNesting.png|200px|right|example of nested transforms for an affine followed by a BSpline. Note that the order matters]]
 "Nesting" transforms is a term we use to describe the joining / concatenation of multiple transforms. This is supported in Slicer to some degree. The important thing to remember is that '''the order matters''', i.e. A*B is '''not''' the same as B*A. For example, a typical application is that you first perform a rigid or affine registration, followed by a separate nonrigid BSpline registration. Although you can combine both in one, there are cases where it is useful to separate the two, e.g. if robustness is an issue and there is a chance the linear portion might fail, or for visualization, when you want to look at the deformations incurring from the BSpline, you need to have them separate from the global "bulk" transform to see detail. So in this case you need to nest the '''Affine''' inside the '''BSpline''', not vice versa. If this seems counter-intuitive, remember that hierarchies are read/applied from the inside out, i.e. the first transform applied is the Affine and '''then''' the BSpline. So the arrangement within the data-module should look as shown on the image on the right (example of an MRI registered to a CT in 2 steps of first affine, then BSpline).<br>
 '''Hardening''' is a term used to describe applying a transform or effect to a dataset. In the  [[Documentation/{{documentation/version}}/Modules/Data|''Data'' module]] a right-click onto a node produces a context-menu, which lists ''Harden Transform'' as an option if a nesting is present. Two important points to remember about this option:
 *'''hardening is not the same as resampling''': in case of linear transforms, the new orientation is added to the physical orientation stored in the image header, without actually resampling the data itself. This is preferable in most cases as it avoids data degradation from interpolation artifacts associated with resampling. If you '''do''' need the transformed dataset resampled, use one of the resampling modules described below.

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 '''Hardening''' is a term used to describe applying a transform or effect to a dataset. In the  [[Documentation/{{documentation/version}}/Modules/Data|''Data'' module]] a right-click onto a node produces a context-menu, which lists ''Harden Transform'' as an option if a nesting is present. Two important points to remember about this option:
 *'''hardening is not the same as resampling''': in case of linear transforms, the new orientation is added to the physical orientation stored in the image header, without actually resampling the data itself. This is preferable in most cases as it avoids data degradation from interpolation artifacts associated with resampling. If you '''do''' need the transformed dataset resampled, use one of the resampling modules described below.
-*'''hardening''' is currently supported for volumes inside BSpline transforms, but '''not''' for the transform itself, i.e. the image on the right shows which hardening will work and which will not. Hardening cannot be used to concatenate linear and BSpline or multiple BSpline transforms.
+*'''hardening''' is currently supported for volumes inside BSpline transforms, but '''not''' for the transform itself, i.e. the image on the right shows which hardening will work and which will not. Hardening cannot currently be used to concatenate linear and BSpline or multiple BSpline transforms.
 = What we mean by ''Resampling'' =

@@ Line 33: / Line 33: @@
 [[Image:Registration_TransformNesting.png|200px|right|example of nested transforms for an affine followed by a BSpline. Note that the order matters]]
 "Nesting" transforms is a term we use to describe the joining / concatenation of multiple transforms. This is supported in Slicer to some degree. The important thing to remember is that '''the order matters''', i.e. A*B is '''not''' the same as B*A. For example, a typical application is that you first perform a rigid or affine registration, followed by a separate nonrigid BSpline registration. Although you can combine both in one, there are cases where it is useful to separate the two, e.g. if robustness is an issue and there is a chance the linear portion might fail, or for visualization, when you want to look at the deformations incurring from the BSpline, you need to have them separate from the global "bulk" transform to see detail. So in this case you need to nest the '''Affine''' inside the '''BSpline''', not vice versa. If this seems counter-intuitive, remember that hierarchies are read/applied from the inside out, i.e. the first transform applied is the Affine and '''then''' the BSpline. So the arrangement within the data-module should look as shown on the image on the right (example of an MRI registered to a CT in 2 steps of first affine, then BSpline).<br>
 '''Hardening''' is a term used to describe applying a transform or effect to a dataset. In the  [[Documentation/{{documentation/version}}/Modules/Data|''Data'' module]] a right-click onto a node produces a context-menu, which lists ''Harden Transform'' as an option if a nesting is present. Two important points to remember about this option:
 *'''hardening is not the same as resampling''': in case of linear transforms, the new orientation is added to the physical orientation stored in the image header, without actually resampling the data itself. This is preferable in most cases as it avoids data degradation from interpolation artifacts associated with resampling. If you '''do''' need the transformed dataset resampled, use one of the resampling modules described below.
 *'''hardening''' is currently supported for volumes inside BSpline transforms, but '''not''' for the transform itself, i.e. the image on the right shows which hardening will work and which will not. Hardening cannot be used to concatenate linear and BSpline or multiple BSpline transforms.
 = What we mean by ''Resampling'' =

← Older revision		Revision as of 20:22, 6 May 2014
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	So the effect of a linear transform is therefore visible right away. '''Nonlinear (BSpline) transforms are not visualized on the fly and must be resampled to see.''' Hence if you calculate a BSpline transform inside BRAINSfit and then place a volume inside this transform, you will '''not''' see an effect, because the Viewer can apply only linear transforms directly. So to see a nonrigid transform you must resample the image. We therefore recommend to always select an output volume when running a nonrigid registration. To apply a transform and resample an image see the [[Documentation/{{documentation/version}}/Modules/Resampling#Resampling_via_a_spatial_transform\|resampling via a spatial transform]]section below.		So the effect of a linear transform is therefore visible right away. '''Nonlinear (BSpline) transforms are not visualized on the fly and must be resampled to see.''' Hence if you calculate a BSpline transform inside BRAINSfit and then place a volume inside this transform, you will '''not''' see an effect, because the Viewer can apply only linear transforms directly. So to see a nonrigid transform you must resample the image. We therefore recommend to always select an output volume when running a nonrigid registration. To apply a transform and resample an image see the [[Documentation/{{documentation/version}}/Modules/Resampling#Resampling_via_a_spatial_transform\|resampling via a spatial transform]]section below.
		+
		+	= Nesting Transforms =
		+	"Nesting" transforms is a term we use to describe the joining / concatenation of multiple transforms. This is supported in Slicer to some degree. The important thing to remember is that '''the order matters''', i.e. AB is '''not''' the same as BA. For example, a typical application is that you first perform a rigid or affine registration, followed by a separate nonrigid BSpline registration. Although you can combine both in one, there are cases where it is useful to separate the two, e.g. if robustness is an issue and there is a chance the linear portion might fail, or for visualization, when you want to look at the deformations incurring from the BSpline, you need to have them separate from the global "bulk" transform to see detail. So in this case you need to nest the '''Affine''' inside the '''BSpline''', not vice versa. If this seems counter-intuitive, remember that hierarchies are read/applied from the inside out, i.e. the first transform applied is the Affine and '''then''' the BSpline. So the arrangement within the data-module should look like this:
		+

	= What we mean by ''Resampling'' =		= What we mean by ''Resampling'' =