Modules:ResampleVolume2-Documentation - Revision history

Fbudin: /* Module Description */

2008-12-12T16:06:03Z

Module Description

Fbudin: /* Quick Tour of Features and Use */

2008-09-17T17:48:34Z

Quick Tour of Features and Use

Fbudin: /* References */

2008-09-16T14:59:32Z

References

Fbudin: /* References */

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References

Sylvain: /* References */

2008-09-16T14:33:17Z

References

Sylvain: /* References */

2008-09-16T14:29:52Z

References

Sylvain at 14:28, 16 September 2008

2008-09-16T14:28:31Z

Fbudin: /* Module Name */

2008-09-16T03:52:36Z

Module Name

Fbudin: /* Quick Tour of Features and Use */

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Quick Tour of Features and Use

Fbudin: /* Examples, Use Cases & Tutorials */

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Examples, Use Cases & Tutorials

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 ===Module Description===
-This module implements image and vector-image resampling through the use of ITK Transforms. It can also handle diffusion weighted MRI image resampling. 'Resampling' is performed in space coordinates, not pixel/grid coordinates. It is quite important to ensure that image spacing is properly set on the images involved. The interpolator is required since the mapping from one space to the other will often require evaluation of the intensity of the image at non-grid positions.
+This module implements image and vector-image resampling through the use of ITK Transforms. It supports any transform that is implemented in ITK (rigid, affine, non-rigid such as BSpline, etc). It can also handle diffusion weighted MRI image resampling. 'Resampling' is performed in space coordinates, not pixel/grid coordinates. It is quite important to ensure that image spacing is properly set on the images involved. The interpolator is required since the mapping from one space to the other will often require evaluation of the intensity of the image at non-grid positions.
 == Usage ==

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 ** ''Transform Matrix:'' a 12-parameter affine transformation manually. The first 9 numbers represent a linear transformation matrix in column-major order (where the column index varies the fastest), the last 3 are a translation.
 ** ''Transform:'' forces the transform to be of rigid or affine type (affine is default)
-** ''Space:'' It should normally not be modified when using this module directly in Slicer3. It does not specify whether the matrix is expressed in LPS or RAS coordinate space but rather if everything is expressed in the same coordinate space. LPS means that everything is in the same space and RAS means that it is not the case. This option can be set to RAS if the given transform is in RAS coordinate space (respectively LPS) and the input volume is in LPS coordinate space (respectively RAS). '''Be careful''': When passing manually the transform, the coordinate space modification is directly applied on the given transform. However, when passing the transform through a file or a transform node, it is the input volume coordinate space that is modified and the transform is left unchanged (so that any kind of transform supported by ITK is also supported by this module). If one sets the output volume parameters manually, one has to pay attention to the fact that in that case the given parameters are considered to be in the transform coordinate space!!!
+** ''Space:'' It should normally not be modified when using this module directly in Slicer3 with a transform node. It does not specify whether the matrix is expressed in LPS or RAS coordinate space but rather if everything is expressed in the same coordinate space. LPS means that everything is in the same space and RAS means that it is not the case. This option can be set to RAS if the given transform is in RAS coordinate space (respectively LPS) and the input volume is in LPS coordinate space (respectively RAS). '''Be careful''': When passing manually the transform, the coordinate space modification is directly applied on the given transform. However, when passing the transform through a file or a transform node, it is the input volume coordinate space that is modified and the transform is left unchanged (so that any kind of transform supported by ITK is also supported by this module). If one sets the output volume parameters manually, one has to pay attention to the fact that in that case the given parameters are considered to be in the transform coordinate space!!!
 * '''Rigid/Affine Parameters:'''
 ** ''Rotation Point:'' uses a fiducial to set a point around which the rotation defined in the transform needs to be performed.

← Older revision		Revision as of 14:59, 16 September 2008
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	[http://www.itk.org/ItkSoftwareGuide.pdf ITK software guide]. Sections "6.9 Geometric Transformations", "8.8 Transforms" and "8.9 Interpolators".		[http://www.itk.org/ItkSoftwareGuide.pdf ITK software guide]. Sections "6.9 Geometric Transformations", "8.8 Transforms" and "8.9 Interpolators".

−	[1] http://www.bic.mni.mcgill.ca/brainweb/	+	[1] [http://www.bic.mni.mcgill.ca/brainweb/ BrainWeb: Simulated Brain Database]

← Older revision		Revision as of 14:56, 16 September 2008
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	===References===		===References===
	[http://www.itk.org/ItkSoftwareGuide.pdf ITK software guide]. Sections "6.9 Geometric Transformations", "8.8 Transforms" and "8.9 Interpolators".		[http://www.itk.org/ItkSoftwareGuide.pdf ITK software guide]. Sections "6.9 Geometric Transformations", "8.8 Transforms" and "8.9 Interpolators".
		+
		+	[1] http://www.bic.mni.mcgill.ca/brainweb/

← Older revision		Revision as of 14:33, 16 September 2008
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	===References===		===References===
−	[http://www.itk.org/ItkSoftwareGuide.pdf ITK software guide]. Sections	+	[http://www.itk.org/ItkSoftwareGuide.pdf ITK software guide]. Sections "6.9 Geometric Transformations", "8.8 Transforms" and "8.9 Interpolators".

← Older revision		Revision as of 14:29, 16 September 2008
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	===References===		===References===
−	[http://www.itk.org/ItkSoftwareGuide.pdf ITK software guide]	+	[http://www.itk.org/ItkSoftwareGuide.pdf ITK software guide]. Sections

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 ===Acknowledgment===
-Include funding and other support here.
+This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics].
 ===References===
-Publications related to this module go here. Links to pdfs would be useful.
+[http://www.itk.org/ItkSoftwareGuide.pdf ITK software guide]

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 [[Documentation|Return to Slicer Documentation]]
 __NOTOC__
-===Module Name===
+===ResampleVolume2===
 {|

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 * This module is especially appropriate when one needs to resample an image and already knows the transform to apply to it. Its principal advantages resides in the fact that one can apply any kind of transform supported by ITK (rigid, affine and non-rigid) and can choose between the most commonly used interpolators.
-* The transform can be passed as an ITK Transform file using the command line, or directly as a transform in Slicer3. In the latter case, the transform can only be rigid or affine.
+* The transform can be passed as an ITK Transform file using the command line, or directly as a transform node in Slicer3. In the latter case, the transform can only be rigid or affine.
-* It also allows changing the spacing, the orientation, the size or the origin of the image.
+* It also allows changing the spacing, the orientation, the size and the origin of the image.
 ===Quick Tour of Features and Use===