Slicer3:Module:Rician Noise Removal - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T17:26:10Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Marianna: Protected "Slicer3:Module:Rician Noise Removal" [edit=sysop:move=sysop]

2008-05-22T14:52:53Z

Protected "Slicer3:Module:Rician Noise Removal" [edit=sysop:move=sysop]

Marianna: Replacing page with ''''Note:''' We are migrating this content to the slicer.org domain - The newer page is [http://www.slicer.org/slicerWiki/index.php/Slicer3:Module:Rici...'

2008-05-22T14:52:38Z

Replacing page with '<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [http://www.slicer.org/slicerWiki/index.php/Slicer3:Module:Rici...'

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Fletcher: /* Module Description */

2007-09-19T17:05:25Z

Module Description

Fletcher: /* Authors, Collaborators & Contact */

2007-09-19T16:56:06Z

Authors, Collaborators & Contact

Sgouttard at 16:17, 19 September 2007

2007-09-19T16:17:00Z

Sgouttard at 16:16, 19 September 2007

2007-09-19T16:16:41Z

Sgouttard at 16:07, 19 September 2007

2007-09-19T16:07:09Z

Sgouttard at 16:05, 19 September 2007

2007-09-19T16:05:24Z

Sgouttard at 15:58, 19 September 2007

2007-09-19T15:58:51Z

← Older revision		Revision as of 17:26, 10 July 2017
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−	<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [~~http~~://www.slicer.org/~~slicerWiki/index.php~~/Slicer3:Module:Rician_Noise_Removal here]</font></big>	+	<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/Slicer3:Module:Rician_Noise_Removal here]</font></big>

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 ===Module Description===
-Rician noise introduces a bias into MRI measurements that
+Rician noise introduces a bias into MRI measurements that can have a signiﬁcant impact on the shapes and orientations of tensors in diﬀusion tensor magnetic resonance images. This is less of a problem in structural MRI, because this bias is signal dependent and it does not seriously impair tissue identiﬁcation or clinical diagnoses. However, diﬀusion imaging is used extensively for quantitative evaluations, and the tensors used in those evaluations are biased in ways that depend on orientation and signal levels. This module implements the algorithm developed by Basu, et al. for ﬁltering diﬀusion tensor magnetic resonance images. The method is a maximum a posteriori estimation technique that operates directly on the diﬀusion weighted images and accounts for the biases introduced by Rician noise. We account for Rician noise through a data likelihood term that is combined with a spatial smoothing prior. Also included in the module are several other approaches from the literature, including methods that ﬁlter diffusion weighted imagery and those that operate directly on the diﬀusion tensors. These methods are compared in [Basu, et al. 2006], where it is shown that the Rician filter gives the best overall results.
 == Usage ==

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 ===Authors, Collaborators & Contact===
 * Saurav Basu: University of Utah
-* Thomas Fletcher, University of Utah
+* Tom Fletcher, University of Utah
-* Ross Withaker, University of Utah
+* Ross Whitaker, University of Utah
-* Contact: Thomas Fletcher
+* Sylvain Gouttard, University of Utah
 ===Module Description===

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 {|
 |[[Image:RicianTensorCorrectionImage.png|thumb|280px|Caption 1]]
 |}

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 {|
-|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
+|[[Image:RicianTensorCorrectionImage.png|thumb|280px|Caption 1]]
 |[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
 |[[Image:screenshotBlank.png|thumb|280px|Caption 3]]

← Older revision	Revision as of 14:52, 22 May 2008
(No difference)

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 means perform simple anisotropic diffusion
-* 1 means perform Chi-Squared smoothing (square the image and perform anisotropic diffusion and then subtract the variance of the noise, and take square root. (The square of a Rice distribution is a Chi Squared distribution with known bias equal to the variance of the noise) (Refer:Max likelihood Est. of Rician Ditribution Parameters. Sijbers et. al)
+* - 1 means perform Chi-Squared smoothing (square the image and perform anisotropic diffusion and then subtract the variance of the noise, and take square root. (The square of a Rice distribution is a Chi Squared distribution with known bias equal to the variance of the noise) (Refer:Max likelihood Est. of Rician Ditribution Parameters. Sijbers et. al)
-* 2 means Perform Rician bias correction filtering.(Refer: Rician Noise Removal in DT-MRI.)
+* - 2 means Perform Rician bias correction filtering.(Refer: Rician Noise Removal in DT-MRI.)
-* 3 is same as 2 except use a Gaussian Attachment Term .
+* - 3 is same as 2 except use a Gaussian Attachment Term .
 <Sigma>
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 Argument 6 is the name of the output tensor file
-Example Usage:
+EXAMPLE
 --------------
 tensorFilter 2 1 0.0625 1.0 noisyTensor_10.nhdr FilteredTensor.nhrd
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 == Development ==
 ===Known bugs===

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 ===Module Name===
-Rician Noise Removal in Diffusion Tensor MRI
+Rician Noise Removal in Diffusion Tensor MRI (DWI and tensors)
 {|
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 The filtered image is filteredDWI.nhdr.
-* Note use cases for which this module is especially appropriate, and/or link to examples.
+===Tensor filtering===
-* Link to examples of the module's use
-* Link to any existing tutorials
+Usage
 ===Quick Tour of Features and Use===
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 ===Acknowledgement===
-Include funding and other support here.
+This work is part of the National Alliance for Medical Image Computing
 ===References===
-Publications related to this module go here. Links to pdfs would be useful.
+Basu, S., Fletcher, P.T., Whitaker, R.T. Rician Noise Removal in Diffusion Tensor MRI. In Medical Image Computing and Computer Assisted Intervention (MICCAI), LNCS 4190, pp. 117-125, October, 2006.

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 ====Examples, Use Cases & Tutorials====
-USAGE:dwiFilter <arguments>
+USAGE
 Arguments:
 . Input File Name
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 <Filter Type>
-   Can Take 3 values:
+Can Take 3 values:
 means perform simple anisotropic diffusion
-means perform Chi-Squared smoothing (square the image and
+* 1 means perform Chi-Squared smoothing (square the image and perform anisotropic diffusion and then subtract the variance of the noise, and take square root. (The square of a Rice distribution is a Chi Squared distribution with known bias equal to the variance of the noise) (Refer:Max likelihood Est. of Rician Ditribution Parameters. Sijbers et. al)
-   perform anisotropic diffusion and then subtract the variance
+* 2 means Perform Rician bias correction filtering.(Refer: Rician Noise Removal in DT-MRI.)
-   of the noise, and take square root. (The square of a Rice
+* 3 is same as 2 except use a Gaussian Attachment Term .
 <Sigma>
@@ Line 121: / Line 114: @@
 weight of 100. The estimate of noise in the input image is a sigma of 10
 The filtered image is filteredDWI.nhdr.
 * Note use cases for which this module is especially appropriate, and/or link to examples.
 * Link to examples of the module's use