Difference between revisions of "Documentation/4.3/Modules/Growing"

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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''
 
** <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''
 
** <span style="color:green">'''Verbose'''</span> [<span style="color:orange">----verbose</span>] [<span style="color:pink">-v</span>]: produce verbose output ''Default value: 0''
 
** <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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Revision as of 22:35, 17 September 2013

Home < Documentation < 4.3 < Modules < Growing


For the latest Slicer documentation, visit the read-the-docs.



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

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