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| | |Program description || | | |Program description || |
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| − | |Program version || 1.1.0
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| | |Program documentation-url || http://www.nitrc.org/forum/?group_id=527 | | |Program documentation-url || http://www.nitrc.org/forum/?group_id=527 |
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| − | == Usage ==
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| − | ===Quick Tour of Features and Use===
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| − | A list panels in the interface, their features, what they mean, and how to use them.
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| − | {|
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| − | * <span style="color:blue">'''''Input/Ouput'''''</span>:
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| − | ** <span style="color:green">'''DWI Image'''</span> [<span style="color:orange">----dwi_image</span>] : DWI image volume (required)
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| − | ** <span style="color:green">'''Tensor Output'''</span> [<span style="color:orange">----tensor_output</span>] : Tensor OutputImage
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| − | ** <span style="color:green">'''Baseline Image (optional)'''</span> [<span style="color:orange">----B0</span>] : Baseline image, average of all baseline images
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| − | ** <span style="color:green">'''IDWI (optional)'''</span> [<span style="color:orange">----idwi</span>] : idwi output image. Image with isotropic diffusion-weighted information = geometric mean of diffusion images
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| − | ** <span style="color:green">'''Mask created by thresholded B0 (optional)'''</span> [<span style="color:orange">----B0_mask_output</span>] : B0 mask used for the estimation. B0 thresholded either with the -t option value or the automatic OTSU value
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| − | * <span style="color:blue">'''''Input masks'''''</span>:
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| − | ** <span style="color:green">'''Brain Mask'''</span> [<span style="color:orange">----brain_mask</span>] [<span style="color:pink">-M</span>]: Brain mask. Image where for every voxel == 0 the tensors are not estimated
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| − | ** <span style="color:green">'''Bad Region Mask'''</span> [<span style="color:orange">----bad_region_mask</span>] [<span style="color:pink">-B</span>]: Bad region mask. Image where for every voxel > 0 the tensors are not estimated
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| − | * <span style="color:blue">'''''Options'''''</span>:
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| − | ** <span style="color:green">'''Method'''</span> [<span style="color:orange">----method</span>] [<span style="color:pink">-m</span>]: Esitmation method (lls:linear least squares, wls:weighted least squares, nls:non-linear least squares, ml:maximum likelihood) ''Default value: lls''
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| − | ** <span style="color:green">'''Threshold'''</span> [<span style="color:orange">----threshold</span>] [<span style="color:pink">-t</span>]: Baseline threshold for estimation. If not specified calculated using an OTSU threshold on the baseline image ''Default value: -1''
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| − | ** <span style="color:green">'''Weight Iterations'''</span> [<span style="color:orange">----weight_iterations</span>] : Number of iterations to recaluate weightings from tensor estimate ''Default value: 1''
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| − | ** <span style="color:green">'''Step Size'''</span> [<span style="color:orange">----step</span>] [<span style="color:pink">-S</span>]: Gradient descent step size (for nls and ml methods) ''Default value: .00000001''
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| − | ** <span style="color:green">'''Sigma'''</span> [<span style="color:orange">----sigma</span>] [<span style="color:pink">-s</span>]: ''Default value: -1.0''
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| − | ** <span style="color:green">'''DTI double (do not use in 3D Slicer)'''</span> [<span style="color:orange">----DTI_double</span>] : Tensor components are saved as doubles (cannot be visualized in Slicer) ''Default value: false''
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| − | ** <span style="color:green">'''Verbose'''</span> [<span style="color:orange">----verbose</span>] [<span style="color:pink">-v</span>]: produce verbose output ''Default value: 0''
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| − | |[[Image:GrowingInterface.png|thumb|280px|User Interface]]
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| − | |}
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| − | == More Information ==
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| − | More information is available on the project webpage: http://www.nitrc.org/forum/?group_id=527
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