Line 16:

|Image:CSIM-logo.png|CSIM Laboratory  

|Image:CSIM-logo.png|CSIM Laboratory  

|Image:USP-logo.png|University of Sao Paulo

|Image:USP-logo.png|University of Sao Paulo

−

|Image:CAPES-logo.png|CAPES Brazil

+

|Image:CNPqOrig-logo.png|CNPq Brazil

}}

}}

{{documentation/{{documentation/version}}/module-introduction-end}}

{{documentation/{{documentation/version}}/module-introduction-end}}

Line 23:

{{documentation/{{documentation/version}}/module-section|Module Description}}

{{documentation/{{documentation/version}}/module-section|Module Description}}

−

This module offers a simple application of the [[Documentation/Nightly/Modules/AADImageFilter|AAD filter]] on general echo-planar imaging (EPI) data, e.g. functional-MRI and arterial spin labeling (ASL). Since the noise through the image space is present in the tensorial acquisition, the AAD filter could be applied in order to decrease the noise amplitude and maintain the geometrical details of the image.

+

This module offers a simple application of the [[Documentation/Nightly/Modules/AADImageFilter|AAD filter]] on general echo-planar imaging (EPI) data. This approach could be useful to images such as, but not limited to, functional-MRI and arterial spin labelling (ASL). Since the image noise pattern is considered spread through the image space, the AAD filter could be a promising in order to decrease the noise amplitude and maintain the geometrical details of the image.

−

'''NOTE:''' This module works with NRRD DWI volumes. If your diffusion data is on different file formats (e.g. FSL output files), please convert then in advance. A useful tool to do that on 3D Slicer is the [[Documentation/Nightly/Modules/DWIConverter|DWI Converter]]

+

'''NOTE:''' The full compatibility of 4D volumes (usually adopted in fMRI and ASL data) is made by specific external modules, which means that the data loading process should be processed in advance to the actual AADEPI module application. The ... modules can be helpful.

+

'''NOTE:''' Although DWI and DTI images are also considered as EPI-like data, a specific module was also provided to these type of data. Please see [[Documentation/Nightly/Modules/AADDiffusionWeightedData|AAD Diffusion Weighted Data]] module.

<!-- ---------------------------- -->

<!-- ---------------------------- -->

{{documentation/{{documentation/version}}/module-section|Use Cases}}

{{documentation/{{documentation/version}}/module-section|Use Cases}}

*Use Case 1: Decrease noise in a general EPI data

*Use Case 1: Decrease noise in a general EPI data

−

** The raw DWI data could be filtered using the AAD approach, which was previously applied on structural MRI data<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> and Diffusion Tensor Imaging images as well<ref>Senra Filho, A. C. da S. et al. (2017) Enhancing quality in Diffusion Tensor Imaging with anisotropic anomalous diffusion filter, Research on Biomedical Engineering. doi: 10.1590/2446-4740.02017.</ref>

+

** fMRI and ASL data usually present low signal to noise ratio, offering practical difficulties for true positive signal detection. For the case of ASL processing, the AAD filtering application was discussed<ref>doi:...</ref>  

<gallery widths="300px" heights="300px" perrow="2">

<gallery widths="300px" heights="300px" perrow="2">

−

Image:EPI_ASL_raw.png|Raw DTI FA map

+

Image:EPI_ASL_raw.png|A single volume from a conventional ASL data

−

Image:EPI_ASL_AAD.png|DTI FA map filtered with AAD filter (q=1.2)

+

Image:EPI_ASL_AAD.png|The same volume filtered with AAD filter (q=...)

−

Image:Tractography_AAD.png|Tractography example using filtered FA map

+

Image:Tractography_AAD.png|The cerebral blood flow (CBF) map resulted from the filtered ASL data showing more precise cortical delineation and true positive findings even in challenging cortical areas.

</gallery>

</gallery>

Line 47:

Line 49:

'''IO:'''

'''IO:'''

*'''Input Volume'''

*'''Input Volume'''

−

**Select the DWI input image

+

**Select the EPI input image

−

*'''Output Volume'''

+

−

**Set the output DWI image file which the filters should place the final result

−

'''Diffusion Parameters:'''

+

''' Parameters:'''

*'''Conductance'''

*'''Conductance'''

**A float value for edge preservation adjustment. 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. If you want an automatic evaluation to conductance variable, please select the following methods

**A float value for edge preservation adjustment. 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. If you want an automatic evaluation to conductance variable, please select the following methods

Documentation/Nightly/Modules/AADEPIData - Revision history

Acsenrafilho at 18:06, 9 November 2017

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