Documentation/Nightly/Modules/AADImageFilter - Revision history

Acsenrafilho at 12:54, 25 July 2017

2017-07-25T12:54:32Z

Acsenrafilho at 16:26, 19 July 2017

2017-07-19T16:26:47Z

Acsenrafilho: COrrect minor parts of the text

2016-10-13T18:10:29Z

COrrect minor parts of the text

Acsenrafilho at 17:40, 27 April 2016

2016-04-27T17:40:30Z

Acsenrafilho at 17:33, 27 April 2016

2016-04-27T17:33:16Z

Acsenrafilho at 12:00, 22 April 2016

2016-04-22T12:00:41Z

Acsenrafilho: Created page with "{{documentation/versioncheck}} {{documentation/{{documentation/version}}/module-header}}

@@ Line 43: / Line 43: @@
 [[Image:aad_scalar_gui.png|thumb|380px|User Interface]]
-IO:
+'''IO:'''
-*Input Volume
+*'''Input Volume'''
 **Select the input image
-*Output Volume
+*'''Output Volume'''
 **Set the output image file which the filters should place the final result
-Diffusion Parameters:
+'''Diffusion Parameters:'''
-*Conductance
+*'''Conductance'''
 **The conductance regulates the diffusion intensity in the neighborhood area. Choose a higher conductance if the input image has strong noise seem in the whole image space.
-*Use Auto Conductance
+*'''Use Auto Conductance'''
 **Choose if you want to use an automatic adjustment of conductance parameter. If this is checked, the inserted value is ignored and the optimization function below is used.
-*Optimization Function
+*'''Optimization Function'''
 **A set of optimization function for automatic estimation of conductance parameter. This is helpful is you do not have an initial guess on what value is appropriate to the conductance setting. (Canny, MAD and Morphological). Please see the [http://www.insight-journal.org/browse/publication/983 Insight-Journal article] that explain each of these automatic conductance adjustment methods.
-*Number of Iteractions
+*'''Number of Iteractions'''
 **The number of iterations regulates the numerical simulation of the anomalous process over the image. This parameters is also related with the de-noising intensity, however it is more sensible to the noise intensity. Choose the higher number of iterations if the image presents high intensity noise which is not well treated by the conductance parameter.
-*Time Step
+*'''Time Step'''
 **The time step is a normalization parameters for the numerical simulation. The maximum value, given as default, is set to 3D images. Lower time step restrict the numerical simulation of the anomalous process.
-*Anomalous parameter
+*'''Anomalous parameter'''
 **The anomalous parameter (or q value) is the generalization parameters responsible to give the anomalous process approach on the diffusion equation. See the reference paper<ref>Da S Senra Filho, A. C., Garrido Salmon, C. E., & Murta Junior, L. O. (2015). Anomalous diffusion process applied to magnetic resonance image enhancement. Physics in Medicine and Biology, 60(6), 2355–2373. doi:10.1088/0031-9155/60/6/2355</ref> to choose the appropriate q value (at moment, only tested in MRI T1 and T2 weighted images).
@@ Line 70: / Line 70: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|References}}
 * da S Senra Filho, A.C., Garrido Salmon, C.E. & Murta Junior, L.O., 2015. Anomalous diffusion process applied to magnetic resonance image enhancement. Physics in Medicine and Biology, 60(6), pp.2355–2373. DOI: 10.1088/0031-9155/60/6/2355
 * Filho, A.C. da S.S. et al., 2014. Anisotropic Anomalous Diffusion Filtering Applied to Relaxation Time Estimation in Magnetic Resonance Imaging. In Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, pp. 3893–3896.

@@ Line 32: / Line 32: @@
 * Use Case 3: Noise reduction as part of image processing pipeline
 **Could offer a better segmentation and classification on specific brain image analysis such as in Multiple Sclerosis lesion segmentation
-<gallery widths="200px" perrow="3">
 Image:MRI_raw.png|Raw T1 weighted MRI Image
 Image:MRI_AAD.png|T1 weighted MRI Image with AAD filter (q=1.2)
@@ Line 50: / Line 51: @@
 Diffusion Parameters:
 *Conductance
-**The conductance regulates the diffusion intensity in the neighbourhood area. Choose a higher conductance if the input image has strong noise seem in the whole image space.
+**The conductance regulates the diffusion intensity in the neighborhood area. Choose a higher conductance if the input image has strong noise seem in the whole image space.
 *Number of Iteractions
 **The number of iterations regulates the numerical simulation of the anomalous process over the image. This parameters is also related with the de-noising intensity, however it is more sensible to the noise intensity. Choose the higher number of iterations if the image presents high intensity noise which is not well treated by the conductance parameter.

@@ Line 19: / Line 19: @@
 }}
 {{documentation/{{documentation/version}}/module-introduction-end}}
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Module Description}}
-This module aims to ...
+This module offer a simple application to the Anisotropic Anomalous Diffusion (AAD) filter, which is able to increase the image SNR and preserve fine object's details around the image space. This method was studied on MRI structural images (T1 and T2), which other imaging modalities could be properly investigated in the future.
 <!-- ---------------------------- -->
@@ Line 38: / Line 36: @@
 Image:MRI_AAD.png|T1 weighted MRI Image with AAD filter (q=1.2)
 </gallery>
-<!-- ---------------------------- -->
 <!-- ---------------------------- -->

@@ Line 46: / Line 46: @@
 [[Image:aad_scalar_gui.png|thumb|380px|User Interface]]
+IO:
 *Input Volume
 **Select the input image
 *Output Volume
 **Set the output image file which the filters should place the final result
 *Conductance
 **The conductance regulates the diffusion intensity in the neighbourhood area. Choose a higher conductance if the input image has strong noise seem in the whole image space.
-*Number of interactions
+*Number of Iteractions
 **The number of iterations regulates the numerical simulation of the anomalous process over the image. This parameters is also related with the de-noising intensity, however it is more sensible to the noise intensity. Choose the higher number of iterations if the image presents high intensity noise which is not well treated by the conductance parameter.
-*Time step
+*Time Step
 **The time step is a normalization parameters for the numerical simulation. The maximum value, given as default, is set to 3D images. Lower time step restrict the numerical simulation of the anomalous process.
 *Anomalous parameter

@@ Line 19: / Line 19: @@
 }}
 {{documentation/{{documentation/version}}/module-introduction-end}}
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Module Description}}
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Use Cases}}
+* Use Case 1: Noise reduction as a preprocessing step for tissue segmentation
+**When dealing with single voxel classification schemes running noise reduction as a preprocessing scheme will reduce the number of single misclassified voxels.
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Tutorials}}
+N/A
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Panels and their use}}
-|[[Image:aad_scalar_gui.png|thumb|380px|User Interface]]
+[[Image:aad_scalar_gui.png|thumb|380px|User Interface]]
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Similar Modules}}
 *[[Documentation/{{documentation/version}}/Modules/IADImageFilter|IAD Image Filter]]
-*[[Documentation/{{documentation/version}}/Modules/AADDiffusionWeightedData|AAD on DWI Image]]
+*[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion|Gradient Anisotropic Image Filter]]
 <!-- ---------------------------- -->