Documentation/4.3/Modules/Growing

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Growing

Growing

User Interface

Baseline CBCT Scan - Input Scan

Follow up CBCT Scan - Input Scan

Baseline Segmentation Mask - Input Seg

Followup Segmentation Mask - Input Seg

thumb|280px|Baseline and Followup CBCT Scans - Baseline Input Scan + Followup Input Scan

Baseline and Followup CBCT Scans Registered - Baseline Input Scan + Output Scan

General Information

Module Type & Category

Type: CLI

Category: Diffusion.NIRALPipeline

Authors, Collaborators & Contact

Author: Casey Goodlett

Contributors:

Contact: name, email

Module Description

Program title	Growing
Program description
Program version	1.1.0
Program documentation-url	http://www.nitrc.org/forum/?group_id=527

Usage

Quick Tour of Features and Use

A list panels in the interface, their features, what they mean, and how to use them.

Input/Ouput: DWI Image [----dwi_image] : DWI image volume (required) Tensor Output [----tensor_output] : Tensor OutputImage Baseline Image (optional) [----B0] : Baseline image, average of all baseline images IDWI (optional) [----idwi] : idwi output image. Image with isotropic diffusion-weighted information = geometric mean of diffusion images Mask created by thresholded B0 (optional) [----B0_mask_output] : B0 mask used for the estimation. B0 thresholded either with the -t option value or the automatic OTSU value Input masks: Brain Mask [----brain_mask] [-M]: Brain mask. Image where for every voxel == 0 the tensors are not estimated Bad Region Mask [----bad_region_mask] [-B]: Bad region mask. Image where for every voxel > 0 the tensors are not estimated Options: Method [----method] [-m]: Esitmation method (lls:linear least squares, wls:weighted least squares, nls:non-linear least squares, ml:maximum likelihood) Default value: lls Threshold [----threshold] [-t]: Baseline threshold for estimation. If not specified calculated using an OTSU threshold on the baseline image Default value: -1 Weight Iterations [----weight_iterations] : Number of iterations to recaluate weightings from tensor estimate Default value: 1 Step Size [----step] [-S]: Gradient descent step size (for nls and ml methods) Default value: .00000001 Sigma [----sigma] [-s]: Default value: -1.0 DTI double (do not use in 3D Slicer) [----DTI_double] : Tensor components are saved as doubles (cannot be visualized in Slicer) Default value: false Verbose [----verbose] [-v]: produce verbose output Default value: 0

User Interface

More Information

More information is available on the project webpage: http://www.nitrc.org/forum/?group_id=527