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

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|[[Image:BaselineSegmentationMaskCMFreg.png|thumb|280px|Baseline Segmentation Mask - Input Seg]]
 
|[[Image:BaselineSegmentationMaskCMFreg.png|thumb|280px|Baseline Segmentation Mask - Input Seg]]
 
|[[Image:FollowupSegmentationMaskCMFreg.png|thumb|280px|Followup Segmentation Mask - Input Seg]]
 
|[[Image:FollowupSegmentationMaskCMFreg.png|thumb|280px|Followup Segmentation Mask - Input Seg]]
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|[[BaselineFollowupSCANCMFreg.png|thumb|280px|Baseline and Followup CBCT Scans - Baseline Input Scan + Followup Input Scan]]
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|[[Image:BaselineFollowupSCANRegisteredCMFreg.png|thumb|280px|Baseline Input Scan + Followup Input Scan]]
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|[[Image:BaselineFollowupSCANRegisteredCMFreg.png|thumb|280px|Baseline and Followup CBCT Scans Registered - Baseline Input Scan + Output Scan]]
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|[[Image:BaselineFollowupSCANRegisteredCMFreg2.png|thumb|280px|Baseline and Followup CBCT Scans - Baseline and Followup CBCT Scans Registered - Baseline Input Scan + Output Scan]]
 
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===Module Type & Category===
 
===Module Type & Category===
  
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Type: CLI
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Type: Extension
  
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Category: Diffusion.NIRALPipeline
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Category: CBCT Scan Registration
  
  
 
===Authors, Collaborators & Contact===
 
===Authors, Collaborators & Contact===
  
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Author: Casey Goodlett
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Author: Vinicius Boen
  
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Contributors:
+
Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)
  
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Contact: name, email
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Contact: vboen@umich.edu
  
 
===Module Description===
 
===Module Description===
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{| style="color:green" border="1"
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* <span style="color:blue">'''''Input Parameters'''''</span>:  
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|Program title || Growing
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** <span style="color:green">'''Baseline Scan (fixed)'''</span> [<span style="color:orange">-f --fixedVolume</span>] : The fixed scan image for registration.
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|-
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** <span style="color:green">'''Follow up Scan (moving)'''</span> [<span style="color:orange">-m --movingVolume</span>] : The moving scan image for registration.
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|Program description || 
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** <span style="color:green">'''Baseline Segmentation (fixed)'''</span> [<span style="color:orange">--fixedBinaryVolume</span>] : The fixed one label segmentation image for registration used to specify the region of interest.
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|-
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** <span style="color:green">'''Follow up Segmentation (moving)'''</span> [<span style="color:orange">--movingBinaryVolume</span>] : The moving one label segmentation image for registration used to specify the region of interest.
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|Program version || 1.1.0
 
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|-
 
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|Program documentation-url || http://www.nitrc.org/forum/?group_id=527
 
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|-
 
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|}
 
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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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|
 
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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:blue">'''''Voxel Based Registration Options'''''</span>:
 +
** <span style="color:green">'''Rigid + Scale (7DOF)'''</span> [<span style="color:orange">--useScaleVersor3D</span>] : Perform a ScaleVersor3D registration as part of the sequential registration steps.
 +
** <span style="color:green">'''Rigid + Skew + Scale (10DOF)'''</span> [<span style="color:orange">--useScaleSkewVersor3D</span>] : Perform a ScaleSkewVersor3D registration as part of the sequential registration steps.
 +
** <span style="color:green">'''Affine (12DOF)'''</span> [<span style="color:orange">--useAffine</span>] : Perform an Affine registration as part of the sequential registration steps.
  
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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">'''''Output Registration Matrix'''''</span>:  
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** <span style="color:green">'''Registration Matrix'''</span> [<span style="color:orange">-t --transformPath</span>] : File name for the rigid component of the estimated registration matrix. Can be used to rigidly register the moving image to the fixed image.
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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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* <span style="color:blue">'''''Apply Registration Matrix'''''</span>:
 +
** <span style="color:green">'''Input Segmentatiton to be Registered'''</span> [<span style="color:orange">--segmentation</span>] : Input segmentation image to be modified with the registration matrix.
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** <span style="color:green">'''Output Registered Scan'''</span> [<span style="color:orange">--segmentationOut</span>] : Output segmentation image. This segmentaiton image is the 'Input Segmentation to be Registered' with the registration matrix already applied.
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** <span style="color:green">'''Output Registered Scan'''</span> [<span style="color:orange">--outputVolume</span>] : Output image for registration. This image is the Follow up Scan with the registration matrix already applied.
  
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More information is available on the project webpage: http://www.nitrc.org/forum/?group_id=527
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[[Image:GrowingInterface.png|thumb|280px|User Interface]]

Latest revision as of 19:01, 20 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
Baseline Input Scan + Followup Input Scan
Baseline and Followup CBCT Scans - Baseline and Followup CBCT Scans Registered - Baseline Input Scan + Output Scan

General Information

Module Type & Category

Type: Extension

Category: CBCT Scan Registration


Authors, Collaborators & Contact

Author: Vinicius Boen

Contributors: Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University Of North Carolina), Beatriz Paniagua (NIRAL, University Of North Carolina), Lucia Cevidanes (University of Michigan - School of Dentistry)

Contact: vboen@umich.edu

Module Description

  • Input Parameters:
    • Baseline Scan (fixed) [-f --fixedVolume] : The fixed scan image for registration.
    • Follow up Scan (moving) [-m --movingVolume] : The moving scan image for registration.
    • Baseline Segmentation (fixed) [--fixedBinaryVolume] : The fixed one label segmentation image for registration used to specify the region of interest.
    • Follow up Segmentation (moving) [--movingBinaryVolume] : The moving one label segmentation image for registration used to specify the region of interest.
  • Voxel Based Registration Options:
    • Rigid + Scale (7DOF) [--useScaleVersor3D] : Perform a ScaleVersor3D registration as part of the sequential registration steps.
    • Rigid + Skew + Scale (10DOF) [--useScaleSkewVersor3D] : Perform a ScaleSkewVersor3D registration as part of the sequential registration steps.
    • Affine (12DOF) [--useAffine] : Perform an Affine registration as part of the sequential registration steps.
  • Output Registration Matrix:
    • Registration Matrix [-t --transformPath] : File name for the rigid component of the estimated registration matrix. Can be used to rigidly register the moving image to the fixed image.
  • Apply Registration Matrix:
    • Input Segmentatiton to be Registered [--segmentation] : Input segmentation image to be modified with the registration matrix.
    • Output Registered Scan [--segmentationOut] : Output segmentation image. This segmentaiton image is the 'Input Segmentation to be Registered' with the registration matrix already applied.
    • Output Registered Scan [--outputVolume] : Output image for registration. This image is the Follow up Scan with the registration matrix already applied.
User Interface
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