https://public.kitware.com/Wiki/api.php?action=feedcontributions&user=Christopher.mullins&feedformat=atomKitwarePublic - User contributions [en]2024-03-29T14:15:45ZUser contributionsMediaWiki 1.38.6https://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/TransformTubes&diff=57323TubeTK/Documentation/TransformTubes2015-01-07T19:39:12Z<p>Christopher.mullins: Created page with " Description: Applies a transform or displacement field to tubes (i.e., spatial objects). USAGE: ./TransformTubes [--returnparameterfile <std::string>]..."</p>
<hr />
<div> Description: Applies a transform or displacement field to tubes (i.e.,<br />
spatial objects).<br />
<br />
USAGE: <br />
<br />
./TransformTubes [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>] [--xml]<br />
[--echo] [--useInverseTransform] [--scale <double>]<br />
[--displacementField <std::string>] [--transformFile<br />
<std::string>] [--] [--version] [-h] <std::string><br />
<std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--useInverseTransform<br />
Instead of using the transform directly, compute its inverse and<br />
apply. For a displacement field, the user is responsible for inputting<br />
the inverse displacement field. (default: 0)<br />
<br />
--scale <double><br />
When --transformFile is specified, additional isotropic scaling can<br />
also be applied. (default: 1)<br />
<br />
--displacementField <std::string><br />
Specify the displacement field (e.g., generated using ANTS).<br />
<br />
--transformFile <std::string><br />
Transform to apply (in ITK format). When a displacement field is<br />
specified, any additional transforms are currently ignored.<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input tubes.<br />
<br />
<std::string><br />
(required) Output tubes.<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/TextCompareCommand&diff=57322TubeTK/Documentation/TextCompareCommand2015-01-07T19:38:40Z<p>Christopher.mullins: Created page with "Usage : ./TextCompareCommand System tags: [ -v ] or [ -h ] = List options in short format [ -V ] or [ -H ] = List options in long format [ -vxml ] or [..."</p>
<hr />
<div>Usage : ./TextCompareCommand<br />
System tags: <br />
[ -v ] or [ -h ]<br />
= List options in short format<br />
[ -V ] or [ -H ]<br />
= List options in long format<br />
[ -vxml ] or [ -hxml ] or [ -exportXML ]<br />
= List options in xml format for BatchMake<br />
[ --xml ]<br />
= List options in xml format for Slicer<br />
[ -vgad ] or [ -hgad ] or [ -exportGAD ]<br />
= List options in Grid Application Description format<br />
[ -version ]<br />
= return the version number<br />
[ -date ]<br />
= return the cvs checkout date<br />
Command tags: <br />
[ -d < value > ]<br />
= Acceptable differences in numeric values in the files<br />
[ -n < value > ]<br />
= Number of differences that are acceptable to have intensity differences<br />
-t < filename > <br />
= Filename of the text file to be tested against the baseline images<br />
[ -B < filename > ]<br />
= List of baseline text files <N> <image1> <image2>...<imageN><br />
[ -b < filename > ]<br />
= Baseline text file filename<br />
You must provide a -BaselineFile or -BaselineFiles option</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/SubSampleTubes&diff=57321TubeTK/Documentation/SubSampleTubes2015-01-07T19:38:19Z<p>Christopher.mullins: Created page with " Description: Sub-samples the points comprising a tube tree. USAGE: ./SubSampleTubes [--returnparameterfile <std::string>] [--processinformationa..."</p>
<hr />
<div> Description: Sub-samples the points comprising a tube tree.<br />
<br />
USAGE: <br />
<br />
./SubSampleTubes [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>] [--xml]<br />
[--echo] [-s <int>] [--] [--version] [-h]<br />
<std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-s <int>, --samplingFactor <int><br />
Sub-sampling decimation factor. (default: 1)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input tubes.<br />
<br />
<std::string><br />
(required) Output tubes.<br />
<br />
Author(s): Matthew M. McCormick (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/SimulateAcquisitionArtifactsUsingPrior&diff=57320TubeTK/Documentation/SimulateAcquisitionArtifactsUsingPrior2015-01-07T19:37:46Z<p>Christopher.mullins: Created page with " Description: Given an image and a mask, process the mask to match the image. USAGE: ./SimulateAcquisitionArtifactsUsingPrior [--returnparameterfile..."</p>
<hr />
<div> Description: Given an image and a mask, process the mask to match the<br />
image.<br />
<br />
USAGE: <br />
<br />
./SimulateAcquisitionArtifactsUsingPrior [--returnparameterfile<br />
<std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo] [-S<br />
<int>] [-n] [-B <std::vector<int>>]<br />
[-r] [--loadTransform<br />
<std::string>] [--saveTransform<br />
<std::string>] [-o] [-s <float>]<br />
[-g <float>] [-d <int>] [-e <int>]<br />
[-m <std::string>] [-b <float>] [-f<br />
<float>] [--] [--version] [-h]<br />
<std::string> <std::string><br />
<std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-S <int>, --seed <int><br />
Seed for random processes in the method (0 = no seed). (default: 0)<br />
<br />
-n, --disableNormalize<br />
Disable attempt to match mask intensity range with volume intensity<br />
range. (default: 0)<br />
<br />
-B <std::vector<int>>, --outputBoundary <std::vector<int>><br />
Size of boundary to be excluded from match computation and then<br />
cropped.<br />
<br />
-r, --disableParameterOptimization<br />
Turn off the optimization of the erode, dilate, blur parameters.<br />
(default: 0)<br />
<br />
--loadTransform <std::string><br />
Load the transform to be used instead of registration.<br />
<br />
--saveTransform <std::string><br />
Save the registration transform.<br />
<br />
-o, --disableRegistrationOptimization<br />
Turn off the optimization of the registration of the prior to the<br />
image. (default: 0)<br />
<br />
-s <float>, --samplingRate <float><br />
Portion of voxels to use when computing image-match metric. (default:<br />
0.1)<br />
<br />
-g <float>, --gaussianBlur <float><br />
Radius to use for blurring to simulate tomosynthesis. (default: 9)<br />
<br />
-d <int>, --dilate <int><br />
Radius to use for dilation (after erosion) to simulate tomosynthesis.<br />
(default: 10)<br />
<br />
-e <int>, --erode <int><br />
Radius to use for erosion to simulate tomosynthesis. (default: 6)<br />
<br />
-m <std::string>, --metricMask <std::string><br />
Points with non-zero values in this mask are used in match<br />
computations.<br />
<br />
-b <float>, --background <float><br />
Background intensity value. (default: 0)<br />
<br />
-f <float>, --foreground <float><br />
Foreground intensity value, i.e., object value. (default: 255)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume.<br />
<br />
<std::string><br />
(required) Input mask.<br />
<br />
<std::string><br />
(required) Output volume.<br />
<br />
<std::string><br />
(required) Output mask.<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware. It<br />
was funded in part by USC:EXPOSE.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ShrinkImage&diff=57319TubeTK/Documentation/ShrinkImage2015-01-07T19:37:13Z<p>Christopher.mullins: Created page with " Description: Project an image into fewer slices. Integration uses the 'max' function. USAGE: ./ShrinkImage [--returnparameterfile <std::string>]..."</p>
<hr />
<div> Description: Project an image into fewer slices. Integration uses the<br />
'max' function.<br />
<br />
USAGE: <br />
<br />
./ShrinkImage [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>] [--xml]<br />
[--echo] [-p <std::string>] [-o <std::vector<int>>] [-n<br />
<std::vector<int>>] [-d <std::vector<int>>] [--]<br />
[--version] [-h] <std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-p <std::string>, --pointImage <std::string><br />
Save a vector image containing physical point of chosen pixel's<br />
original location<br />
<br />
-o <std::vector<int>>, --overlap <std::vector<int>><br />
Amount each sliding window region should overlap (in pixels)<br />
<br />
-n <std::vector<int>>, --newSize <std::vector<int>><br />
Target size of each dimension (size/newSize must be an integer)<br />
<br />
-d <std::vector<int>>, --divideBy <std::vector<int>><br />
Size of each dimension is divide by this much (must be integers)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input image.<br />
<br />
<std::string><br />
(required) Output image.<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/SegmentUsingOtsuThreshold&diff=57318TubeTK/Documentation/SegmentUsingOtsuThreshold2015-01-07T19:36:42Z<p>Christopher.mullins: Created page with " Description: Run Otsu thresholding to automatically split the intensities in an image. USAGE: ./SegmentUsingOtsuThreshold [--returnparameterfile <std::string>]..."</p>
<hr />
<div> Description: Run Otsu thresholding to automatically split the<br />
intensities in an image.<br />
<br />
USAGE: <br />
<br />
./SegmentUsingOtsuThreshold [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>]<br />
[--xml] [--echo] [--mask <std::string>]<br />
[--] [--version] [-h] <std::string><br />
<std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--mask <std::string><br />
Mask volume.<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume.<br />
<br />
<std::string><br />
(required) Output volume.<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/SegmentTubes&diff=57317TubeTK/Documentation/SegmentTubes2015-01-07T19:36:09Z<p>Christopher.mullins: Created page with " Description: Extracts a 1D scaled ridge and estimate its radius in an ND image. USAGE: ./SegmentTubes [--returnparameterfile <std::string>] [--..."</p>
<hr />
<div> Description: Extracts a 1D scaled ridge and estimate its radius in an ND<br />
image.<br />
<br />
USAGE: <br />
<br />
./SegmentTubes [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>] [--xml]<br />
[--echo] [-o <std::string>] [-P <std::string>] [-b<br />
<double>] [-T <int>] [-S <std::string>] [-M<br />
<std::string>] [-p <std::vector<std::vector<float> >>]<br />
... [-i <std::vector<std::vector<float> >>] ... [-s<br />
<double>] [-f <std::string>] [--] [--version] [-h]<br />
<std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-o <std::string>, -- <std::string><br />
Output binary mask of extracted tubes<br />
<br />
-P <std::string>, --parametersFile <std::string><br />
Parameters for ridge and radius extraction<br />
<br />
-b <double>, --border <double><br />
Distance from edge (in voxels) to ignore (default: 5)<br />
<br />
-T <int>, --seedMaskStride <int><br />
Only use 1/stride seed points (default: 4)<br />
<br />
-S <std::string>, --scaleMask <std::string><br />
Intensity is initial extraction scale for that point<br />
<br />
-M <std::string>, --seedMask <std::string><br />
Image mask where non-zero values are used as seeds.<br />
<br />
-p <std::vector<std::vector<float> >>, --seedP<br />
<std::vector<std::vector<float> >> (accepted multiple times)<br />
Phisycal coordinate seed for ridge extraction<br />
<br />
-i <std::vector<std::vector<float> >>, --seedI<br />
<std::vector<std::vector<float> >> (accepted multiple times)<br />
Continuous index for starting ridge extraction<br />
<br />
-s <double>, --scale <double><br />
Scale used for ridge measures (default: 2)<br />
<br />
-f <std::string>, --seedList <std::string><br />
List seed points stored in a file<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume<br />
<br />
<std::string><br />
(required) Output tube file<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/SegmentConnectedComponentsUsingParzenPDFs&diff=57316TubeTK/Documentation/SegmentConnectedComponentsUsingParzenPDFs2015-01-07T18:58:52Z<p>Christopher.mullins: Created page with " Description: Given multiple, registered images and foreground and background masks, computes multivariate PDFs for inside and outside classes, and then performs compe..."</p>
<hr />
<div> Description: Given multiple, registered images and foreground and<br />
background masks, computes multivariate PDFs for inside and outside<br />
classes, and then performs competitive region growing.<br />
<br />
USAGE: <br />
<br />
./SegmentConnectedComponentsUsingParzenPDFs [--returnparameterfile<br />
<std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo]<br />
[--saveClassPDFBase <std::string>]<br />
[--loadClassPDFBase <std::string>]<br />
[--saveClassProbabilityVolumeBase<br />
<std::string>]<br />
[--forceClassification]<br />
[--reclassifyNotObjectLabels]<br />
[--reclassifyObjectLabels]<br />
[--draft]<br />
[--histogramSmoothingStdDev<br />
<double>]<br />
[--probImageSmoothingStdDev<br />
<double>] [--objectPDFWeight<br />
<std::vector<double>>]<br />
[--dilateFirst]<br />
[--holeFillIterations <int>]<br />
[--erodeRadius <int>] [--voidId<br />
<int>] [--objectId<br />
<std::vector<int>>] [--inputVolume4<br />
<std::string>] [--inputVolume3<br />
<std::string>] [--inputVolume2<br />
<std::string>] [--] [--version]<br />
[-h] <std::string> <std::string><br />
<std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--saveClassPDFBase <std::string><br />
Save images that represent probability density functions.<br />
<br />
--loadClassPDFBase <std::string><br />
Load images that represent probability density functions.<br />
<br />
--saveClassProbabilityVolumeBase <std::string><br />
Save images where each represents the probability of being a<br />
particular object at each voxel. Image files create =<br />
base.classNum.mha.<br />
<br />
--forceClassification<br />
Force classification using simple maximum likelihood. (default: 0)<br />
<br />
--reclassifyNotObjectLabels<br />
Perform classification on all non-void voxels. (default: 0)<br />
<br />
--reclassifyObjectLabels<br />
Perform classification on voxels within the object mask. (default: 0)<br />
<br />
--draft<br />
Generate draft results. (default: 0)<br />
<br />
--histogramSmoothingStdDev <double><br />
Standard deviation of blur applied to convert the histogram to a<br />
probability density function estimate (default: 5)<br />
<br />
--probImageSmoothingStdDev <double><br />
Standard deviation of blur applied to probability images prior to<br />
computing maximum likelihood of each class at each pixel (default: 1)<br />
<br />
--objectPDFWeight <std::vector<double>><br />
Relative weight (multiplier) of each PDF. (default: 1)<br />
<br />
--dilateFirst<br />
Performs dilation then erosion (versus opposite order) to help fill-in<br />
sparse models. (default: 0)<br />
<br />
--holeFillIterations <int><br />
Number of iterations for hole filling. (default: 1)<br />
<br />
--erodeRadius <int><br />
Radius of noise to clip from edges. (default: 1)<br />
<br />
--voidId <int><br />
Value that represents 'nothing' in the label map. (default: 0)<br />
<br />
--objectId <std::vector<int>><br />
List of values that represent the objects in the label map. (default:<br />
255,127)<br />
<br />
--inputVolume4 <std::string><br />
Input volume 4.<br />
<br />
--inputVolume3 <std::string><br />
Input volume 3.<br />
<br />
--inputVolume2 <std::string><br />
Input volume 2.<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume 1.<br />
<br />
<std::string><br />
(required) Label map that designates the object of interest and<br />
'other.'<br />
<br />
<std::string><br />
(required) Segmentation results.<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/SegmentConnectedComponents&diff=57315TubeTK/Documentation/SegmentConnectedComponents2015-01-07T18:58:14Z<p>Christopher.mullins: Created page with " Description: Label each connected region in a binary image with a unique value. USAGE: ./SegmentConnectedComponents [--returnparameterfile <std::string>]..."</p>
<hr />
<div> Description: Label each connected region in a binary image with a unique<br />
value.<br />
<br />
USAGE: <br />
<br />
./SegmentConnectedComponents [--returnparameterfile <std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo]<br />
[--seedMask <std::string>] [--minSize<br />
<double>] [--] [--version] [-h]<br />
<std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--seedMask <std::string><br />
Seed mask of connected components to keep.<br />
<br />
--minSize <double><br />
Any connected component whose size (in physical space) is less than<br />
this is ignored. (default: 0)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input mask.<br />
<br />
<std::string><br />
(required) Output mask of labeled connected components.<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/SegmentBinaryImageSkeleton&diff=57314TubeTK/Documentation/SegmentBinaryImageSkeleton2015-01-07T18:57:46Z<p>Christopher.mullins: Created page with " Description: Generate a skeleton from a binary mask. USAGE: ./SegmentBinaryImageSkeleton [--returnparameterfile <std::string>] [--pr..."</p>
<hr />
<div> Description: Generate a skeleton from a binary mask.<br />
<br />
USAGE: <br />
<br />
./SegmentBinaryImageSkeleton [--returnparameterfile <std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo] [-r <int>]<br />
[--] [--version] [-h] <std::string><br />
<std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-r <int>, --radius <int><br />
The radius used for dilation of the skeleton. (default: 0)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume.<br />
<br />
<std::string><br />
(required) Output volume.<br />
<br />
Author(s): Patrick Reynolds (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/SampleCLIApplication&diff=57313TubeTK/Documentation/SampleCLIApplication2015-01-07T18:57:14Z<p>Christopher.mullins: Created page with " Description: Demonstration of how to write a CLI application. Performs blurring. USAGE: ./SampleCLIApplication [--returnparameterfile <std::string>]..."</p>
<hr />
<div> Description: Demonstration of how to write a CLI application. Performs<br />
blurring.<br />
<br />
USAGE: <br />
<br />
./SampleCLIApplication [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>]<br />
[--xml] [--echo] [-g <double>] [--] [--version]<br />
[-h] <std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-g <double>, --gaussianBlurStdDev <double><br />
Standard deviation of the Gaussian kernel used to blur the binary<br />
mask. (default: 4)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input image.<br />
<br />
<std::string><br />
(required) Output image.<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ResampleImage&diff=57312TubeTK/Documentation/ResampleImage2015-01-07T18:56:40Z<p>Christopher.mullins: Created page with " Description: Resamples an image to match another image (origin, orientation, and spacing), to be isotropic, or to have a specific spacing. USAGE: ./ResampleImag..."</p>
<hr />
<div> Description: Resamples an image to match another image (origin,<br />
orientation, and spacing), to be isotropic, or to have a specific<br />
spacing.<br />
<br />
USAGE: <br />
<br />
./ResampleImage [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>] [--xml]<br />
[--echo] [--loadTransform <std::string>]<br />
[--interpolator <NearestNeighbor|Linear|BSpline>]<br />
[--makeIsotropic] [--resampleFactor<br />
<std::vector<double>>] [--index <std::vector<int>>]<br />
[--origin <std::vector<double>>] [--spacing<br />
<std::vector<double>>] [--matchImage <std::string>]<br />
[--] [--version] [-h] <std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--loadTransform <std::string><br />
Load the transform to be applied.<br />
<br />
--interpolator <NearestNeighbor|Linear|BSpline><br />
Type of interpolation to perform. (default: Linear)<br />
<br />
--makeIsotropic<br />
Make spacing isotropic. Overrides other matchImage and setSpacing.<br />
(default: 0)<br />
<br />
--resampleFactor <std::vector<double>><br />
Factor to increase size. 2,2,2 doubles size in each dimension. Should<br />
be an N-vector. Overrides matchImage and setSpacing.<br />
<br />
--index <std::vector<int>><br />
Index to be used. Should be an N-vector. Overrides matchImage.<br />
<br />
--origin <std::vector<double>><br />
Origin to be used. Should be an N-vector. Overrides matchImage.<br />
<br />
--spacing <std::vector<double>><br />
Spacing to be used. Should be an N-vector. Overrides matchImage.<br />
<br />
--matchImage <std::string><br />
The image from which origin, orientation, and spacing should be taken.<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume.<br />
<br />
<std::string><br />
(required) Resampling results.<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/RegisterUsingSlidingGeometries&diff=57311TubeTK/Documentation/RegisterUsingSlidingGeometries2015-01-07T18:55:52Z<p>Christopher.mullins: Created page with " Description: Performs registration between images depicting sliding organs, using an anisotropic diffusive regularization. USAGE: ./RegisterUsingSlidingGeometries..."</p>
<hr />
<div> Description: Performs registration between images depicting sliding<br />
organs, using an anisotropic diffusive regularization.<br />
<br />
USAGE: <br />
<br />
./RegisterUsingSlidingGeometries [--returnparameterfile <std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo] [-c<br />
<RAS|LPS>] [-u <SlidingOrgan<br />
|SparseSlidingOrgan>] [-a]<br />
[--doNotComputeIntensityDistanceTerm]<br />
[-r] [-g <double>] [-l <double>] [-z<br />
<std::string>] [-x <std::string>] [-v<br />
<std::string>] [-o <std::string>] [-d<br />
<std::string>]<br />
[--stoppingCriterionMask<br />
<std::string>] [--backgroundIntensity<br />
<double>] [-q <std::string>] [-t<br />
<std::string>] [-e <std::string>] [-w<br />
<std::string>] [-n <std::string>] [-p<br />
<std::string>] [-b <std::string>] [-m<br />
<double>] [--maximumTotalEnergyChange<br />
<double>] [--stoppingCriterionPeriod<br />
<int>] [-k <std::vector<double>>] [-s<br />
<double>] [-i <std::vector<int>>] [--]<br />
[--version] [-h] <std::string><br />
<std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-c <RAS|LPS>, --worldCoordinateSystem <RAS|LPS><br />
The world coordinate system. RAS if the images and model are aligned<br />
when visualized in 3D Slicer, LPS if the images and model are aligned<br />
when visualized in Paraview. (default: RAS)<br />
<br />
-u <SlidingOrgan|SparseSlidingOrgan>, --anisotropicRegistrationType<br />
<SlidingOrgan|SparseSlidingOrgan><br />
The type of the anisotropic registration. Each voxel has one normal in<br />
the 'sliding organ' type, and three normals in the 'sparse sliding<br />
organ' type. 'sparse sliding organ' is under development and not<br />
recommended. (default: SlidingOrgan)<br />
<br />
-a, --doNotUseAnisotropicRegularization<br />
Whether or not to use the anisotropic diffusive regularization (if<br />
true, uses the diffusive regularization (i.e. Gaussian smoothing).<br />
(default: 0)<br />
<br />
--doNotComputeIntensityDistanceTerm<br />
Whether or not to compute the intensity distance term. (default: 0)<br />
<br />
-r, --doNotPerformRegularization<br />
Whether or not to perform motion field regularization. (default: 0)<br />
<br />
-g <double>, --gamma <double><br />
Controls the Dirac-shaped function used to calculate the weight value<br />
as a function of the distance to the closest organ border point. Must<br />
be positive to use a Dirac-shaped function. If gamma = -1, then an<br />
exponential decay using lambda will be used instead (default<br />
behavior). (default: -1)<br />
<br />
-l <double>, --lambda <double><br />
Controls the function used to calculate the weight value as a function<br />
of the distance to the closest organ border point. If gamma = -1, then<br />
the function is exponential decay. Otherwise, the function is a<br />
Dirac-shaped function. Must be positive. (default: 0.1)<br />
<br />
-z <std::string>, --outputWeightStructuresImage <std::string><br />
Image specifying the the matrices weighting between plane, tube and<br />
point-like structures. This is applicable for sparse sliding organ<br />
registration only. This is in the space of the fixed image. Optional:<br />
allows you to save the weight image when providing an organ boundary<br />
surface. On later registrations, you can provide it instead of an<br />
organ boundary, so that it does not need to be recalculated.<br />
<br />
-x <std::string>, --outputWeightRegularizationsImage <std::string><br />
Image specifying the weights between the anisotropic diffusive<br />
regularization and the diffusive regularization, typically a function<br />
of distance to the organ boundary. This is in the space of the fixed<br />
image. Optional: allows you to save the weight image when providing an<br />
organ boundary surface. On later registrations, you can provide it<br />
instead of an organ boundary, so that it does not need to be<br />
recalculated.<br />
<br />
-v <std::string>, --outputNormalVectorImage <std::string><br />
Image specifying the normal vectors. This is in the space of the fixed<br />
image. Optional: allows you to save the normal vector image when<br />
providing an organ boundary surface. On later registrations, you can<br />
provide it instead of an organ boundary, so that it does not need to<br />
be recalculated. Gives the 0th column vector of the normal matrix if<br />
using the sparse registration.<br />
<br />
-o <std::string>, --outputResampledMovingFileName <std::string><br />
Resampled moving image to fixed image coordinate frame. Optional<br />
(specify an output deformation field or an output volume or both).<br />
<br />
-d <std::string>, --outputDeformationField <std::string><br />
Deformation field calculated that aligns the fixed and moving image.<br />
Maps positions from the fixed coordinate frame to the moving<br />
coordinate frame. Optional (specify an output deformation field or an<br />
output volume or both).<br />
<br />
--stoppingCriterionMask <std::string><br />
Mask specifying which voxels should be used in the stopping criterion.<br />
Only pixels with value zero WILL be included in the metric computation<br />
and stopping criterion.<br />
<br />
--backgroundIntensity <double><br />
Background intensity of the moving image. (default: 0)<br />
<br />
-q <std::string>, --initialTransformImage <std::string><br />
Initial transform for aligning the fixed and moving image, specified<br />
as a vector image. When applied to the moving image, should make it<br />
look closer to the fixed image. Optional. If both an 'initial<br />
transform' image and an 'initial transform' transform are given, the<br />
'initial transform' image will be used.<br />
<br />
-t <std::string>, --initialTransform <std::string><br />
Initial transform for aligning the fixed and moving image. When<br />
applied to the moving image, should make it look closer to the fixed<br />
image. Optional. If both an 'initial transform' image and an 'initial<br />
transform' transform are given, the 'initial transform' image will be<br />
used.<br />
<br />
-e <std::string>, --inputWeightStructuresImage <std::string><br />
Image specifying the the matrices weighting between plane, tube and<br />
point-like structures. This is applicable for sparse sliding organ<br />
registration only. This image should be in the space of the fixed<br />
image. Optional: supply a weight image or an organ boundary surface<br />
(and a lambda). If both are provided, the organ boundary surface is<br />
used.<br />
<br />
-w <std::string>, --inputWeightRegularizationsImage <std::string><br />
Image specifying the weights between the anisotropic diffusive<br />
regularization and the diffusive regularization, typically a function<br />
of distance to the organ boundary. This should be in the space of the<br />
fixed image. Optional: supply a weight image or an organ boundary<br />
surface (and a lambda). If both are provided, the organ boundary<br />
surface is used.<br />
<br />
-n <std::string>, --inputNormalVectorImage <std::string><br />
Image specifying the normal vectors. This should be in the space of<br />
the fixed image. Optional: supply a normal vector image or an organ<br />
boundary surface. If both are provided, the organ boundary surface is<br />
used.<br />
<br />
-p <std::string>, --tubeSpatialObject <std::string><br />
Filename of the tube spatial object (.tre). This should be in the<br />
space of the fixed image. Use for sparse anisotropic diffusion<br />
registration only.<br />
<br />
-b <std::string>, --organBoundary <std::string><br />
Filename of the organ boundary surface model. This should be in the<br />
space of the fixed image.<br />
<br />
-m <double>, --maximumRMSError <double><br />
If the RMS change in a registration iteration is less than the maximum<br />
RMS error threshold, the registration will be halted. Specify a larger<br />
value to halt faster. If using a multiresolution registration, the<br />
maximum RMS error condition will be tested at every level (i.e. will<br />
run at least one registration on each iteration). If zero, the RMS<br />
change stopping criterion is not used. (default: 0)<br />
<br />
--maximumTotalEnergyChange <double><br />
If the total energy change summed over the stopping criterion<br />
evaluation period is less than the maximum total energy change<br />
threshold, then the registration will be halted. Specify a larger<br />
value to halt faster. If zero, the total energy change stopping<br />
criterion is not used. (default: 0)<br />
<br />
--stoppingCriterionPeriod <int><br />
The number of iterations that elapse between evaluations of the total<br />
energy change stopping criterion. (default: 50)<br />
<br />
-k <std::vector<double>>, --regularizationWeightings<br />
<std::vector<double>><br />
Comma separated list of weightings to be applied to the regularization<br />
update term. The final update term will be ( itensityDistanceWeighting<br />
* intensityUpdateTerm ) + ( RegularizationWeighting *<br />
regularizationUpdateTerm ). Increase this value to increase the<br />
smoothness of the resulting displacement field. If using a<br />
multiresolution registration, you can set a different weighting for<br />
each level. If, on any multiresolution level, the current level is<br />
past the number of provided weights, the last weight will be used<br />
(allowing you to specify only one weight to be used on all levels).<br />
Default is 1.0 for each level. (default: 1.0)<br />
<br />
-s <double>, --timestep <double><br />
Time step duration. (default: 0.125)<br />
<br />
-i <std::vector<int>>, --iterations <std::vector<int>><br />
Comma separated list of iterations. The number of iterations specified<br />
dictates the number of levels of the multiresolution registration. The<br />
multiresolution shrink factors are halved in all three directions on<br />
each of the multiresolution levels. The registration will stop when<br />
either the maximum RMS error condition or the number of iterations<br />
condition is reached. (default: 20)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Fixed image to which to register.<br />
<br />
<std::string><br />
(required) Moving image.<br />
<br />
Author(s): Danielle F. Pace (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/RegisterUsingImageCenters&diff=57310TubeTK/Documentation/RegisterUsingImageCenters2015-01-07T18:55:09Z<p>Christopher.mullins: Created page with " Description: Center phantom data (e.g., image, label map) with respect to the center of a reference image's space. USAGE: ./RegisterUsingImageCenters [--returnpar..."</p>
<hr />
<div> Description: Center phantom data (e.g., image, label map) with respect<br />
to the center of a reference image's space.<br />
<br />
USAGE: <br />
<br />
./RegisterUsingImageCenters [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>]<br />
[--xml] [--echo] [--isLabelMap]<br />
[--centerOnZero] [--] [--version] [-h]<br />
<std::string> <std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--isLabelMap<br />
Specifies that the input phantom data contains discrete labels.<br />
(default: 0)<br />
<br />
--centerOnZero<br />
Set this to ensure that the output image will have origin = (0,0,0).<br />
(default: 0)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Phantom image (e.g., could be label map, or a T1-weighted<br />
MR image).<br />
<br />
<std::string><br />
(required) The reference image that is used for centering the phantom<br />
data.<br />
<br />
<std::string><br />
(required) The centered phantom data image.<br />
<br />
Author(s): Roland Kwitt (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/RegisterImages&diff=57309TubeTK/Documentation/RegisterImages2015-01-07T18:52:53Z<p>Christopher.mullins: Created page with " Description: Provides rigid, affine, and BSpline registration methods via a simple GUI USAGE: ./RegisterImages [--returnparameterfile <std::string>]..."</p>
<hr />
<div> Description: Provides rigid, affine, and BSpline registration methods<br />
via a simple GUI<br />
<br />
USAGE: <br />
<br />
./RegisterImages [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>] [--xml]<br />
[--echo] [--controlPointSpacing <int>]<br />
[--bsplineSamplingRatio <float>]<br />
[--bsplineMaxIterations <int>] [--affineSamplingRatio<br />
<float>] [--affineMaxIterations <int>]<br />
[--rigidSamplingRatio <float>] [--rigidMaxIterations<br />
<int>] [--movingLandmarks<br />
<std::vector<std::vector<float> >>] ... <br />
[--fixedLandmarks <std::vector<std::vector<float> >>]<br />
... [--interpolation <NearestNeighbor|Linear<br />
|BSpline>] [--minimizeMemory] [--numberOfThreads<br />
<int>] [--randomNumberSeed <int>] [--fixedImageMask<br />
<std::string>] [--sampleFromOverlap] [--verbosityLevel<br />
<Silent|Standard|Verbose>] [--expectedSkew <float>]<br />
[--expectedScale <float>] [--expectedRotation <float>]<br />
[--expectedOffset <float>] [--metric <MattesMI<br />
|NormCorr|MeanSqrd>] [--registration <None|Initial<br />
|Rigid|Affine|BSpline|PipelineRigid|PipelineAffine<br />
|PipelineBSpline>] [--initialization <None|Landmarks<br />
|ImageCenters|CentersOfMass|SecondMoments>]<br />
[--saveDisplacementField <std::string>]<br />
[--saveTransform <std::string>] [--loadTransform<br />
<std::string>] [--resampledImage <std::string>] [--]<br />
[--version] [-h] <std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--controlPointSpacing <int><br />
Number of pixels between control points (default: 40)<br />
<br />
--bsplineSamplingRatio <float><br />
Portion of the image to use in computing the metric during BSpline<br />
registration (default: 0.1)<br />
<br />
--bsplineMaxIterations <int><br />
Maximum number of bspline optimization iterations (default: 20)<br />
<br />
--affineSamplingRatio <float><br />
Portion of the image to use in computing the metric during affine<br />
registration (default: 0.02)<br />
<br />
--affineMaxIterations <int><br />
Maximum number of affine optimization iterations (default: 50)<br />
<br />
--rigidSamplingRatio <float><br />
Portion of the image to use in computing the metric during rigid<br />
registration (default: 0.01)<br />
<br />
--rigidMaxIterations <int><br />
Maximum number of rigid optimization iterations (default: 100)<br />
<br />
--movingLandmarks <std::vector<std::vector<float> >> (accepted multiple<br />
times)<br />
Ordered list of landmarks in the moving image<br />
<br />
--fixedLandmarks <std::vector<std::vector<float> >> (accepted multiple<br />
times)<br />
Ordered list of landmarks in the fixed image<br />
<br />
--interpolation <NearestNeighbor|Linear|BSpline><br />
Method for interpolation within the optimization process (default:<br />
Linear)<br />
<br />
--minimizeMemory<br />
Reduce the amount of memory required at the cost of increased<br />
computation time (default: 0)<br />
<br />
--numberOfThreads <int><br />
Number of CPU threads to use (default: 0)<br />
<br />
--randomNumberSeed <int><br />
Seed to generate a consistent random number sequence (default: 0)<br />
<br />
--fixedImageMask <std::string><br />
Image which defines a mask for the fixed image<br />
<br />
--sampleFromOverlap<br />
Limit metric evaluation to the fixed image region overlapped by the<br />
moving image (default: 0)<br />
<br />
--verbosityLevel <Silent|Standard|Verbose><br />
Level of detail of reporting progress (default: Standard)<br />
<br />
--expectedSkew <float><br />
Expected misalignment after initialization (default: 0.01)<br />
<br />
--expectedScale <float><br />
Expected misalignment after initialization (default: 0.05)<br />
<br />
--expectedRotation <float><br />
Expected misalignment after initialization (default: 0.1)<br />
<br />
--expectedOffset <float><br />
Expected misalignment after initialization (default: 10)<br />
<br />
--metric <MattesMI|NormCorr|MeanSqrd><br />
Method to quantify image match (default: MattesMI)<br />
<br />
--registration <None|Initial|Rigid|Affine|BSpline|PipelineRigid<br />
|PipelineAffine|PipelineBSpline><br />
Method for the registration process (default: PipelineAffine)<br />
<br />
--initialization <None|Landmarks|ImageCenters|CentersOfMass<br />
|SecondMoments><br />
Method to prime the registration process (default: CentersOfMass)<br />
<br />
--saveDisplacementField <std::string><br />
Save displacement field result from registration<br />
<br />
--saveTransform <std::string><br />
Save the transform that results from registration<br />
<br />
--loadTransform <std::string><br />
Load a transform that is immediately applied to the moving image<br />
<br />
--resampledImage <std::string><br />
Registration results<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Image which defines the space into which the moving image<br />
is registered<br />
<br />
<std::string><br />
(required) The transform goes from the fixed image's space into the<br />
moving image's space<br />
<br />
Author(s): Stephen R Aylward (Kitware), Casey B Goodlett<br />
(Kitware)<br />
<br />
Acknowledgements: This work is part of the National Alliance for Medical<br />
Image Computing (NAMIC), funded by the National Institutes of Health<br />
through the NIH Roadmap for Medical Research, Grant U54 EB005149.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/MergeTubeGraphs&diff=57308TubeTK/Documentation/MergeTubeGraphs2015-01-07T18:52:14Z<p>Christopher.mullins: Created page with " Description: Map multiple graphs into just one graph. USAGE: ./MergeTubeGraphs [--returnparameterfile <std::string>] [--processinformationaddre..."</p>
<hr />
<div> Description: Map multiple graphs into just one graph.<br />
<br />
USAGE: <br />
<br />
./MergeTubeGraphs [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>] [--xml]<br />
[--echo] [--] [--version] [-h] <std::string><br />
<std::string> <int><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Object document file containing subject-specifc graphs.<br />
<br />
<std::string><br />
(required) Ouput graph.<br />
<br />
<int><br />
(required) Number of centroids (of CVT) used to compute the<br />
subject-specific graphs.<br />
<br />
Author(s): Stephen R. Aylward, Roland Kwitt (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/MergeAdjacentImages&diff=57307TubeTK/Documentation/MergeAdjacentImages2015-01-07T18:51:41Z<p>Christopher.mullins: Created page with " Description: Merge the second image into the space of the first. USAGE: ./MergeAdjacentImages [--returnparameterfile <std::string>] [--p..."</p>
<hr />
<div> Description: Merge the second image into the space of the<br />
first.<br />
<br />
USAGE: <br />
<br />
./MergeAdjacentImages [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>]<br />
[--xml] [--echo] [-f] [-a] [-L <std::string>] [-S<br />
<std::string>] [-s <float>] [-r <float>] [-o<br />
<float>] [-b <std::vector<int>>] [-i <int>] [-M]<br />
[-k <double>] [--] [--version] [-h] <std::string><br />
<std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-f, --useFastBlending<br />
Use experimental method for blending. (default: 0)<br />
<br />
-a, --averageOverlap<br />
Use average of overlapping pixels instead of blending. (default: 0)<br />
<br />
-L <std::string>, --loadTransform <std::string><br />
Filename to load the transform from.<br />
<br />
-S <std::string>, --saveTransform <std::string><br />
Filename to save the transform to.<br />
<br />
-s <float>, --samplingRatio <float><br />
Portion of pixels to use for registration. (default: 0.01)<br />
<br />
-r <float>, --expectedRotation <float><br />
Expected initial mis-registration between the images. (default: 0.001)<br />
<br />
-o <float>, --expectedOffset <float><br />
Expected initial mis-registration between the images. (default: 20)<br />
<br />
-b <std::vector<int>>, --boundary <std::vector<int>><br />
Pixels to be added around the second image as padding (account for<br />
registration movement). (default: 0)<br />
<br />
-i <int>, --iterations <int><br />
Number of iterations (0=no registration). (default: 300)<br />
<br />
-M, --mask<br />
Zero-valued input pixels are ignored. (default: 0)<br />
<br />
-k <double>, --background <double><br />
Value to assign to pixels in the output image that do not intersect an<br />
input image. (default: 0)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume 1.<br />
<br />
<std::string><br />
(required) Input volume 2.<br />
<br />
<std::string><br />
(required) Output volume.<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/JsonCompareCommand&diff=57306TubeTK/Documentation/JsonCompareCommand2015-01-07T18:51:08Z<p>Christopher.mullins: Created page with "Usage : ./JsonCompareCommand System tags: [ -v ] or [ -h ] = List options in short format [ -V ] or [ -H ] = List options in long format [ -vxml ] or [..."</p>
<hr />
<div>Usage : ./JsonCompareCommand<br />
System tags: <br />
[ -v ] or [ -h ]<br />
= List options in short format<br />
[ -V ] or [ -H ]<br />
= List options in long format<br />
[ -vxml ] or [ -hxml ] or [ -exportXML ]<br />
= List options in xml format for BatchMake<br />
[ --xml ]<br />
= List options in xml format for Slicer<br />
[ -vgad ] or [ -hgad ] or [ -exportGAD ]<br />
= List options in Grid Application Description format<br />
[ -version ]<br />
= return the version number<br />
[ -date ]<br />
= return the cvs checkout date<br />
Command tags: <br />
[ -d < value > ]<br />
= Acceptable differences in numeric values in the files<br />
-t < filename > <br />
= Filename of the JSON file to be tested against the baseline JSON files.<br />
[ -B < filename > ]<br />
= List of baseline JSON files <N> <JSON1> <JSON2>...<JSONN><br />
[ -b < filename > ]<br />
= Baseline JSON file filename<br />
You must provide a -BaselineFile or -BaselineFiles option</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ImageCompareCommand&diff=57305TubeTK/Documentation/ImageCompareCommand2015-01-07T18:50:09Z<p>Christopher.mullins: Created page with " Description: Short description. USAGE: ./ImageCompareCommand [--returnparameterfile <std::string>] [--processinformationaddress <std::strin..."</p>
<hr />
<div> Description: Short description.<br />
<br />
USAGE: <br />
<br />
./ImageCompareCommand [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>]<br />
[--xml] [--echo] [-c <double>] [-n <int>] [-r<br />
<int>] [-i <double>] [-o <std::string>] [-b<br />
<std::vector<std::string>>] ... [-t<br />
<std::string>] [--] [--version] [-h]<br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-c <double>, --toleranceCoordinates <double><br />
Acceptable differences image origin/spacing. (default: 1e-06)<br />
<br />
-n <int>, --toleranceNumberOfPixels <int><br />
Number of Pixels that are acceptable to have intensity differences.<br />
(default: 0)<br />
<br />
-r <int>, --toleranceRadius <int><br />
Neighbor pixels to look for similar values. (default: 0)<br />
<br />
-i <double>, --toleranceIntensity <double><br />
Acceptable differences in pixels intensity. (default: 0)<br />
<br />
-o <std::string>, --outputImage <std::string><br />
Output difference image filename.<br />
<br />
-b <std::vector<std::string>>, --baselineImages<br />
<std::vector<std::string>> (accepted multiple times)<br />
Baseline images filename<br />
<br />
-t <std::string>, --testImage <std::string><br />
Filename of the image to be tested against the baseline images<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
Author(s): Stephen R. Aylward, Roland Kwitt (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/EnhanceUsingNJetDiscriminantAnalysis&diff=57304TubeTK/Documentation/EnhanceUsingNJetDiscriminantAnalysis2015-01-07T18:49:29Z<p>Christopher.mullins: Created page with " Description: Given an image and foreground and background masks, computes multiscale Jet (0, 1, and 2 order) features at each pixel, performs a multivariate LDA or PC..."</p>
<hr />
<div> Description: Given an image and foreground and background masks,<br />
computes multiscale Jet (0, 1, and 2 order) features at each pixel,<br />
performs a multivariate LDA or PCA for separating the classes, and<br />
generates the LDA/PCA instances of the images.<br />
<br />
USAGE: <br />
<br />
./EnhanceUsingNJetDiscriminantAnalysis [--returnparameterfile<br />
<std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo]<br />
[--loadBasisInfo <std::string>]<br />
[--saveBasisInfo <std::string>]<br />
[--saveFeatureImages <std::string>]<br />
[--useNumberOfLDABasis <int>]<br />
[--useNumberOfPCABasis <int>]<br />
[--whitenStdDevs<br />
<std::vector<double>>]<br />
[--whitenMeans<br />
<std::vector<double>>]<br />
[--ridgeScales<br />
<std::vector<double>>]<br />
[--secondScales<br />
<std::vector<double>>]<br />
[--firstScales<br />
<std::vector<double>>]<br />
[--zeroScales<br />
<std::vector<double>>] [--objectId<br />
<std::vector<int>>] [--labelmap<br />
<std::string>] [--] [--version]<br />
[-h] <std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--loadBasisInfo <std::string><br />
Load basis from a file.<br />
<br />
--saveBasisInfo <std::string><br />
Save basis to a file.<br />
<br />
--saveFeatureImages <std::string><br />
Save intermediate feature images to a file.<br />
<br />
--useNumberOfLDABasis <int><br />
Maximum number of LDA basis to compute (-1=all). (default: -1)<br />
<br />
--useNumberOfPCABasis <int><br />
Maximum number of PCA basis to compute. (default: 0)<br />
<br />
--whitenStdDevs <std::vector<double>><br />
Whiten standard deviationss.<br />
<br />
--whitenMeans <std::vector<double>><br />
Whiten means.<br />
<br />
--ridgeScales <std::vector<double>><br />
Scales at which Ridge features are computed.<br />
<br />
--secondScales <std::vector<double>><br />
Scales at which 2nd-order features are computed.<br />
<br />
--firstScales <std::vector<double>><br />
Scales at which 1st-order features are computed.<br />
<br />
--zeroScales <std::vector<double>><br />
Scales at which 0th-order features are computed. (default: 1)<br />
<br />
--objectId <std::vector<int>><br />
List of values that represent the objects in the label map. (default:<br />
255)<br />
<br />
--labelmap <std::string><br />
Label map that designates the object of interest and 'other.'<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume list.<br />
<br />
<std::string><br />
(required) Base name for output basis images<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/EnhanceUsingDiscriminantAnalysis&diff=57303TubeTK/Documentation/EnhanceUsingDiscriminantAnalysis2015-01-07T18:48:54Z<p>Christopher.mullins: Created page with " Description: Given multiple, registered images and foreground and background masks, computes a LDA (nClasses-1) + PCA space for separating the classes, and generates..."</p>
<hr />
<div> Description: Given multiple, registered images and foreground and<br />
background masks, computes a LDA (nClasses-1) + PCA space for separating<br />
the classes, and generates the LDA and PCA instances of the<br />
images.<br />
<br />
USAGE: <br />
<br />
./EnhanceUsingDiscriminantAnalysis [--returnparameterfile<br />
<std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo]<br />
[--loadBasisInfo <std::string>]<br />
[--saveBasisInfo <std::string>]<br />
[--useNumberOfLDABasis <int>]<br />
[--useNumberOfPCABasis <int>]<br />
[--objectId <std::vector<int>>]<br />
[--labelmap <std::string>] [--]<br />
[--version] [-h] <std::string><br />
<std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--loadBasisInfo <std::string><br />
Load Basis information from a file<br />
<br />
--saveBasisInfo <std::string><br />
Save basis information to a file<br />
<br />
--useNumberOfLDABasis <int><br />
Maximum number of LDA basis discriminants to compute (-1=all).<br />
(default: -1)<br />
<br />
--useNumberOfPCABasis <int><br />
Maximum number of PCA basis discriminants to compute. (default: 0)<br />
<br />
--objectId <std::vector<int>><br />
List of values that represent the objects in the label map.<br />
<br />
--labelmap <std::string><br />
Label map that designates the object of interest and 'other.'<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume list.<br />
<br />
<std::string><br />
(required) Basename for output basis images.<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/EnhanceTubesUsingDiscriminantAnalysis&diff=57302TubeTK/Documentation/EnhanceTubesUsingDiscriminantAnalysis2015-01-07T18:48:13Z<p>Christopher.mullins: Created page with " Description: Given an image and foreground and background masks, computes multiscale Jet (0, 1, and 2 order) features at each pixel, performs a multivariate LDA or PC..."</p>
<hr />
<div> Description: Given an image and foreground and background masks,<br />
computes multiscale Jet (0, 1, and 2 order) features at each pixel,<br />
performs a multivariate LDA or PCA for separating the classes, and<br />
generates the LDA/PCA instances of the images.<br />
<br />
USAGE: <br />
<br />
./EnhanceTubesUsingDiscriminantAnalysis [--returnparameterfile<br />
<std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo]<br />
[--saveFeatureImages <std::string>]<br />
[--seedTolerance <double>]<br />
[--loadDiscriminantInfo<br />
<std::string>] [-i] [--tubeScales<br />
<std::vector<double>>]<br />
[--outputSeedScaleImage<br />
<std::string>]<br />
[--saveDiscriminantInfo<br />
<std::string>] [--unknownId <int>]<br />
[--backgroundId <int>] [--tubeId<br />
<int>] [--labelmap <std::string>]<br />
[--] [--version] [-h] <std::string><br />
<std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--saveFeatureImages <std::string><br />
Base filename for saving feature images.<br />
<br />
--seedTolerance <double><br />
Tradeoff between sensitivity and specificity (higher value = more<br />
seeds) (default: 1)<br />
<br />
--loadDiscriminantInfo <std::string><br />
Load learned enhancement parameters from a file.<br />
<br />
-i, --useIntensityOnly<br />
Use intensity information at each scale only (default: 0)<br />
<br />
--tubeScales <std::vector<double>><br />
Scales at which tube features are computed. (default: 1,2,4)<br />
<br />
--outputSeedScaleImage <std::string><br />
Image that contains the chosen seed scale at each voxel.<br />
<br />
--saveDiscriminantInfo <std::string><br />
Save learned enhancement parameters to a file.<br />
<br />
--unknownId <int><br />
Value for unlabeled points in the label map. (default: 0)<br />
<br />
--backgroundId <int><br />
Value for background points in the label map. (default: 127)<br />
<br />
--tubeId <int><br />
Value for tube points in the label map. (default: 255)<br />
<br />
--labelmap <std::string><br />
Label map for object of interest and 'other.'<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume list.<br />
<br />
<std::string><br />
(required) Output image having enhanced tubes<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/EnhanceTubesUsingDiffusion&diff=57301TubeTK/Documentation/EnhanceTubesUsingDiffusion2015-01-07T18:47:38Z<p>Christopher.mullins: Created page with " Description: Compute vesselness score of an image using Frangi's method. USAGE: ./EnhanceTubesUsingDiffusion [--returnparameterfile <std::string>]..."</p>
<hr />
<div> Description: Compute vesselness score of an image using Frangi's<br />
method.<br />
<br />
USAGE: <br />
<br />
./EnhanceTubesUsingDiffusion [--returnparameterfile <std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo] [-s<br />
<double>] [-w <double>] [-e <double>] [-g<br />
<double>] [-b <double>] [-r <int>]<br />
[--iterations <int>] [--steps <int>]<br />
[--max <double>] [--min <double>]<br />
[--timestep <double>] [--] [--version]<br />
[-h] <std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-s <double>, --sensitivity <double><br />
How sensitive the filter is. (default: 20)<br />
<br />
-w <double>, --omega <double><br />
Our omega value. (default: 25)<br />
<br />
-e <double>, --epsilon <double><br />
Our epsilon value. (default: 0.01)<br />
<br />
-g <double>, --gamma <double><br />
How sensitive the filter is to second order structureness. (default:<br />
5)<br />
<br />
-b <double>, --beta <double><br />
How sensitive the filter is to blobness. (default: 0.5)<br />
<br />
-r <int>, --recalculate <int><br />
How many iterations do we recalculate vesselness. (default: 11)<br />
<br />
--iterations <int><br />
Number of iterations. (default: 50)<br />
<br />
--steps <int><br />
Number of sigma steps. (default: 1)<br />
<br />
--max <double><br />
Maximum sigma scale. (default: 1)<br />
<br />
--min <double><br />
Minimum sigma scale. (default: 1)<br />
<br />
--timestep <double><br />
Time Step. (default: 0.05)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume.<br />
<br />
<std::string><br />
(required) Blurred volume.<br />
<br />
Author(s): Patrick Reynolds (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware. It<br />
was funded by USC:EXPOSE and is an adaptation of the work of Hua Yang.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/EnhanceEdgesUsingDiffusion&diff=57300TubeTK/Documentation/EnhanceEdgesUsingDiffusion2015-01-07T18:47:10Z<p>Christopher.mullins: Created page with " Description: Performs edge enhancing anisotropic diffusion: smooths strongly in the direction parallel to an edge, while smoothing normal to the edge is inversely pro..."</p>
<hr />
<div> Description: Performs edge enhancing anisotropic diffusion: smooths<br />
strongly in the direction parallel to an edge, while smoothing normal to<br />
the edge is inversely proportional to the gradient. Implemented as<br />
described in Mendrik et al., Noise reduction in computed tomography<br />
scans using 3-D anisotropic diffusion with continuous switch, IEEE<br />
Transactions on Medical Imaging, 28(10), pp. 1585-1594, 2009.<br />
<br />
USAGE: <br />
<br />
./EnhanceEdgesUsingDiffusion [--returnparameterfile <std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo] [-n <int>]<br />
[-t <double>] [-e <double>] [-s <double>]<br />
[--] [--version] [-h] <std::string><br />
<std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-n <int>, --numIterations <int><br />
Number of iterations used in optimization. (default: 1)<br />
<br />
-t <double>, --timeStep <double><br />
Time step used in optimization. (default: 0.11)<br />
<br />
-e <double>, --EEDContrast <double><br />
Contrast of edges, as opposed to noise. If set too low, noise will not<br />
be filtered. If set too high, plate-like structures will not be<br />
preserved. (default: 30)<br />
<br />
-s <double>, --scale <double><br />
Scale at which first derivatives are calculated when determining the<br />
structure tensor and gradient magnitude. If set too low, filter will<br />
be overly sensitive to noise. If set too high, small structures will<br />
not be well preserved. (default: 1)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume.<br />
<br />
<std::string><br />
(required) Output volume.<br />
<br />
Author(s): Danielle F. Pace, Andinet Enquobahrie, Hua Yang, Stephen R.<br />
Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/EnhanceContrastUsingPrior&diff=57299TubeTK/Documentation/EnhanceContrastUsingPrior2015-01-07T18:46:31Z<p>Christopher.mullins: Created page with " Description: Given an image and a mask, process the image to maximize the SNR between the classes indicated by the mask. USAGE: ./EnhanceContrastUsingPrior [--ret..."</p>
<hr />
<div> Description: Given an image and a mask, process the image to maximize<br />
the SNR between the classes indicated by the mask.<br />
<br />
USAGE: <br />
<br />
./EnhanceContrastUsingPrior [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>]<br />
[--xml] [--echo] [-S <int>] [-i <int>] [-n<br />
<int>] [-o <int>] [-b <float>] [-s <float>]<br />
[--] [--version] [-h] <std::string><br />
<std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-S <int>, --seed <int><br />
Random number seed (-1 = none). (default: -1)<br />
<br />
-i <int>, --iterations <int><br />
Number of iterations of optimization. (default: 100)<br />
<br />
-n <int>, --maskBackgroundValue <int><br />
Background label value in the mask. (default: 127)<br />
<br />
-o <int>, --maskObjectValue <int><br />
Object label value in the mask. (default: 255)<br />
<br />
-b <float>, --backgroundScale <float><br />
Scale of the background measure. (default: 20)<br />
<br />
-s <float>, --objectScale <float><br />
Scale of the image measure. (default: 1)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume.<br />
<br />
<std::string><br />
(required) Input mask.<br />
<br />
<std::string><br />
(required) Output, contrast-enhanced, image.<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware. It<br />
was funded in part by USC:EXPOSE.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/EnhanceCoherenceUsingDiffusion&diff=57298TubeTK/Documentation/EnhanceCoherenceUsingDiffusion2015-01-07T18:45:53Z<p>Christopher.mullins: Created page with " Description: Performs coherence enhancing anisotropic diffusion: smooths flow-like structures (ex. vessels/tubes). Strong smoothing is performed in the direction of l..."</p>
<hr />
<div> Description: Performs coherence enhancing anisotropic diffusion: smooths<br />
flow-like structures (ex. vessels/tubes). Strong smoothing is performed<br />
in the direction of least intensity contrast (i.e. parallel to the<br />
tube). Implemented as described in Mendrik et al., Noise reduction in<br />
computed tomography scans using 3-D anisotropic diffusion with<br />
continuous switch, IEEE Transactions on Medical Imaging, 28(10), pp.<br />
1585-1594, 2009.<br />
<br />
USAGE: <br />
<br />
./EnhanceCoherenceUsingDiffusion [--returnparameterfile <std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo] [-n<br />
<int>] [-t <double>] [-a <double>] [-c<br />
<double>] [-s <double>] [--]<br />
[--version] [-h] <std::string><br />
<std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-n <int>, --numIterations <int><br />
Number of iterations used in optimization. (default: 1)<br />
<br />
-t <double>, --timeStep <double><br />
Time step used in optimization. (default: 0.11)<br />
<br />
-a <double>, --alpha <double><br />
Regularization parameter to ensure that the diffusion tensor matrix is<br />
positive definite and to prevent division by zero. Should be set to<br />
something very small. (default: 0.001)<br />
<br />
-c <double>, --CEDContrast <double><br />
Ratio between the second and third eigenvalues that indicates a<br />
tube-like structure. If set too low, small spherical structures will<br />
not be preserved. If set too high, tubular structures will not be<br />
filtered. (default: 15)<br />
<br />
-s <double>, --scale <double><br />
Scale at which first derivatives are calculated when determining the<br />
structure tensor and gradient magnitude. If set too low, filter will<br />
be overly sensitive to noise. If set too high, small structures will<br />
not be well preserved. (default: 1)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume.<br />
<br />
<std::string><br />
(required) Output volume.<br />
<br />
Author(s): Danielle F. Pace, Andinet Enquobahrie, Hua Yang, Stephen R.<br />
Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/EnhanceCoherenceAndEdgesUsingDiffusion&diff=57297TubeTK/Documentation/EnhanceCoherenceAndEdgesUsingDiffusion2015-01-07T18:45:10Z<p>Christopher.mullins: Created page with " Description: Continuous switch between edge enhancing anisotropic diffusion (for homogeneous regions and plate-like structures) and coherence enhancing anisotropic di..."</p>
<hr />
<div> Description: Continuous switch between edge enhancing anisotropic<br />
diffusion (for homogeneous regions and plate-like structures) and<br />
coherence enhancing anisotropic diffusion (for tube-like structures and<br />
small spherical structures). Implemented as described in Mendrik et al.,<br />
Noise reduction in computed tomography scans using 3-D anisotropic<br />
diffusion with continuous switch, IEEE Transactions on Medical Imaging,<br />
28(10), pp. 1585-1594, 2009.<br />
<br />
USAGE: <br />
<br />
./EnhanceCoherenceAndEdgesUsingDiffusion [--returnparameterfile<br />
<std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo] [-n<br />
<int>] [-t <double>] [-y <double>]<br />
[-a <double>] [-c <double>] [-e<br />
<double>] [-s <double>] [--]<br />
[--version] [-h] <std::string><br />
<std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-n <int>, --numIterations <int><br />
Number of iterations used in optimization. (default: 1)<br />
<br />
-t <double>, --timeStep <double><br />
Time step used in optimization. (default: 0.11)<br />
<br />
-y <double>, --hybridContrast <double><br />
Contrast of small structures and tubes to be filtered with coherence<br />
enhancing diffusion (CED). If set too low, noise in homogeneous<br />
regions will look like valid contrast and may be filtered with CED,<br />
instead of edge enhancing diffusion (EED). If set too high, only small<br />
structures and tubes with high contrast will be filtered with CED,<br />
while lower-contrast small structures and tubes will be filtered with<br />
EED. (default: 30)<br />
<br />
-a <double>, --alpha <double><br />
Regularization parameter to ensure that the diffusion tensor matrix is<br />
positive definite and to prevent division by zero (used by both the<br />
coherence enhancing diffusion and the continuous switch). Should be<br />
set to something very small. (default: 0.001)<br />
<br />
-c <double>, --CEDContrast <double><br />
Ratio between the second and third eigenvalues that indicates a<br />
tube-like structure (used by the coherence enhancing diffusion). If<br />
set too low, small spherical structures will not be preserved. If set<br />
too high, tubular structures will not be filtered. (default: 30)<br />
<br />
-e <double>, --EEDContrast <double><br />
Contrast of edges, as opposed to noise (used by the edge enhancing<br />
diffusion). If set too low, noise will not be filtered. If set too<br />
high, plate-like structures will not be preserved. (default: 20)<br />
<br />
-s <double>, --scale <double><br />
Scale at which first derivatives are calculated when determining the<br />
structure tensor and gradient magnitude. If set too low, filter will<br />
be overly sensitive to noise. If set too high, small structures will<br />
not be well preserved. (default: 1)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume.<br />
<br />
<std::string><br />
(required) Output volume.<br />
<br />
Author(s): Danielle F. Pace, Andinet Enquobahrie, Hua Yang, Stephen R.<br />
Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/DeblendTomosynthesisSlicesUsingPrior&diff=57296TubeTK/Documentation/DeblendTomosynthesisSlicesUsingPrior2015-01-07T18:44:21Z<p>Christopher.mullins: Created page with " Description: Deblends images. USAGE: ./DeblendTomosynthesisSlicesUsingPrior [--returnparameterfile <std::string>]..."</p>
<hr />
<div> Description: Deblends images.<br />
<br />
USAGE: <br />
<br />
./DeblendTomosynthesisSlicesUsingPrior [--returnparameterfile<br />
<std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo] [-S<br />
<int>] [-i <int>] [-m<br />
<std::string>] [-s <float>] [-o<br />
<float>] [-g <float>] [-b <float>]<br />
[-a <float>] [--] [--version] [-h]<br />
<std::string> <std::string><br />
<std::string> <std::string><br />
<std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-S <int>, --seed <int><br />
Random number seed (0 = none). (default: 0)<br />
<br />
-i <int>, --iterations <int><br />
Number of iterations of optimization. (default: 100)<br />
<br />
-m <std::string>, --metricMask <std::string><br />
Points with non-zero values in this mask are used in match<br />
computations.<br />
<br />
-s <float>, --sigma <float><br />
Amount to blur top and bottom layers. (default: 5)<br />
<br />
-o <float>, --offset <float><br />
Offset such that v = a * bot + b * top + offset. (default: 0)<br />
<br />
-g <float>, --gamma <float><br />
Weighting for top volume. (default: -0.05)<br />
<br />
-b <float>, --beta <float><br />
Weighting for middle volume. (default: 1)<br />
<br />
-a <float>, --alpha <float><br />
Weighting for bottom volume. (default: -0.05)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input volume on one side of the middle.<br />
<br />
<std::string><br />
(required) Input volume in the middle.<br />
<br />
<std::string><br />
(required) Input volume on one side of the middle.<br />
<br />
<std::string><br />
(required) Input mask.<br />
<br />
<std::string><br />
(required) Output middle layer corrected for blending.<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware. It<br />
was funded in part by USC:EXPOSE.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ConvertTubeToTubeGraph&diff=57295TubeTK/Documentation/ConvertTubeToTubeGraph2015-01-07T18:43:44Z<p>Christopher.mullins: Created page with " Description: Maps tubes into a graph structure using an central Voronoi tessellation. USAGE: ./ConvertTubeToTubeGraph [--returnparameterfile <std::string>]..."</p>
<hr />
<div> Description: Maps tubes into a graph structure using an central Voronoi<br />
tessellation.<br />
<br />
USAGE: <br />
<br />
./ConvertTubeToTubeGraph [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>]<br />
[--xml] [--echo] [--] [--version] [-h]<br />
<std::string> <std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input tubes that are supposed to be converted.<br />
<br />
<std::string><br />
(required) Central Voronoi tesselation upon which the mapping is<br />
based.<br />
<br />
<std::string><br />
(required) Graph file that is about to be written.<br />
<br />
Author(s): Stephen R. Aylward, Roland Kwitt (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ConvertTubesToSurface&diff=57294TubeTK/Documentation/ConvertTubesToSurface2015-01-07T18:43:10Z<p>Christopher.mullins: Created page with " Description: Renders ITK tube SpatialObject data structures into polygons representing the wall of the tubes. The .vtk and .stl file formats are supported. USAGE:..."</p>
<hr />
<div> Description: Renders ITK tube SpatialObject data structures into<br />
polygons representing the wall of the tubes. The .vtk and .stl file<br />
formats are supported.<br />
<br />
USAGE: <br />
<br />
./ConvertTubesToSurface [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>]<br />
[--xml] [--echo] [--] [--version] [-h]<br />
<std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) File containing the input tubes.<br />
<br />
<std::string><br />
(required) File to place the rendered tube wall.<br />
<br />
Author(s): Matthew McCormick (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ConvertTubesToImage&diff=57293TubeTK/Documentation/ConvertTubesToImage2015-01-07T18:42:28Z<p>Christopher.mullins: Created page with " Description: Computes a binary image from tubes USAGE: ./ConvertTubesToImage [--returnparameterfile <std::string>] [--processinformationadd..."</p>
<hr />
<div> Description: Computes a binary image from tubes<br />
<br />
USAGE: <br />
<br />
./ConvertTubesToImage [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>]<br />
[--xml] [--echo] [-r] [--] [--version] [-h]<br />
<std::string> <std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-r, --<br />
Fill-in the radius of the vessels, not just centerlines. (default: 0)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Template image for determining space constraints.<br />
<br />
<std::string><br />
(required) File containing the input tubes.<br />
<br />
<std::string><br />
(required) Binary output image that is being generated.<br />
<br />
Author(s): Stephen R. Aylward, Roland Kwitt, Kitware<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ConvertTubesToDensityImage&diff=57292TubeTK/Documentation/ConvertTubesToDensityImage2015-01-07T18:41:55Z<p>Christopher.mullins: Created page with " Description: Computes an Euclidean distance map from tubes. USAGE: ./ConvertTubesToDensityImage [--returnparameterfile <std::string>]..."</p>
<hr />
<div> Description: Computes an Euclidean distance map from tubes.<br />
<br />
USAGE: <br />
<br />
./ConvertTubesToDensityImage [--returnparameterfile <std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo]<br />
[--useSquareDistance] [--outputSize<br />
<std::vector<int>>] [--outputSpacing<br />
<std::vector<double>>]<br />
[--inputTemplateImage <std::string>] [--]<br />
[--version] [-h] <std::string><br />
<std::string> <std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--useSquareDistance<br />
Use squared distance instead of linear. (default: 0)<br />
<br />
--outputSize <std::vector<int>><br />
Sets the output image dimension (in case of no template image).<br />
<br />
--outputSpacing <std::vector<double>><br />
Sets the output element spacing (in case of no template image).<br />
<br />
--inputTemplateImage <std::string><br />
Template image for determining space constraints.<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) File containing the input tubes.<br />
<br />
<std::string><br />
(required) Density image that is being generated.<br />
<br />
<std::string><br />
(required) Radius image that is being generated.<br />
<br />
<std::string><br />
(required) Tangent image that is being generated.<br />
<br />
Author(s): Stephen R. Aylward, Roland Kwitt (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ConvertTubeGraphToImage&diff=57291TubeTK/Documentation/ConvertTubeGraphToImage2015-01-07T18:41:08Z<p>Christopher.mullins: Created page with " Description: Computes an image from a graph representation and the CVT centroids. USAGE: ./ConvertTubeGraphToImage [--returnparameterfile <std::string>]..."</p>
<hr />
<div> Description: Computes an image from a graph representation and the CVT<br />
centroids.<br />
<br />
USAGE: <br />
<br />
./ConvertTubeGraphToImage [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>]<br />
[--xml] [--echo] [--] [--version] [-h]<br />
<std::string> <std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) File with CVT centroids.<br />
<br />
<std::string><br />
(required) Input graph.<br />
<br />
<std::string><br />
(required) Output image filename (will be used as base name for more<br />
image output).<br />
<br />
Author(s): Stephen R. Aylward, Roland Kwitt (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ConvertTRE&diff=57290TubeTK/Documentation/ConvertTRE2015-01-07T18:40:20Z<p>Christopher.mullins: Created page with " Description: Convert a TubeX file from to a TubeTK file. USAGE: ./ConvertTRE [--returnparameterfile <std::string>] [--processinformationaddress <std..."</p>
<hr />
<div> Description: Convert a TubeX file from to a TubeTK file.<br />
<br />
USAGE: <br />
<br />
./ConvertTRE [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>] [--xml]<br />
[--echo] [-i <std::string>] [-r] [--] [--version] [-h]<br />
<std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-i <std::string>, --image <std::string><br />
(Optional) Input image used when converting from TubeTK to TubeX.<br />
Ignored in normal mode.<br />
<br />
-r, --reverse<br />
Convert tre files from TubeTK to TubeX. (default: 0)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input TRE<br />
<br />
<std::string><br />
(required) Output TRE<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation&diff=57289TubeTK/Documentation2015-01-07T18:39:43Z<p>Christopher.mullins: /* Applications */</p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
<br />
{| border="1" cellpadding="10" cellspacing="0"<br />
|+ [[image:TubeTK_Header.jpg|1000px]]<br />
|-<br />
| style="background:#efefef;" align="left" valign="top" width="150px" | <br />
<br />
'''[[TubeTK|Home]]'''<br />
*[[TubeTK/About|About]]<br />
*[[TubeTK/Images|Image Gallery]]<br />
*[[TubeTK/Data|Data and Publications]]<br />
<br><br />
----<br />
<br><br />
'''For Users'''<br />
* [[TubeTK/Installation|Installation]]<br />
* [[TubeTK/Documentation|Methods & Apps]]<br />
* [[TubeTK/Slicer|TubeTK with 3D Slicer]]<br />
* [[TubeTK/OsiriX|TubeTK with OsiriX]]<br />
<br><br />
----<br />
<br><br />
'''For Developers'''<br />
* [[TubeTK/Development|Development Docs]]<br />
<br><br />
----<br />
<br><br />
'''[https://github.com/TubeTK/TubeTK/issues Report Bugs<br>Request Features]'''<br />
<br><br />
<br><br />
----<br />
<br><br />
'''[[TubeTK/Contact|Contact Us]]'''<br />
<br />
| width="800px" align="left" | <br />
= Applications =<br />
# '''GUI Applications'''<br />
# '''Command-line (CLI) Applications'''<br />
#* Command-line applications can be run directly from the command line, or graphically using 3D Slicer<br />
#* [[TubeTK/Documentation/AtlasBuilderUsingIntensity | AtlasBuilderUsingIntensity]]<br />
#* [[TubeTK/Documentation/ComputeBinaryImageSimilarityMetrics | ComputeBinaryImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageSimilarityMetrics | ComputeImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageStatisticsUsingMask | ComputeImageStatisticsUsingMask]]<br />
#* [[TubeTK/Documentation/ComputeSegmentTubesParameters | ComputeSegmentTubesParameters]]<br />
#* [[TubeTK/Documentation/ComputeTubeGraphProbability | ComputeTubeGraphProbability]]<br />
#* [[TubeTK/Documentation/ComputeTubeMeasures | ComputeTubeMeasures]]<br />
#* [[TubeTK/Documentation/ComputeTubeProbability | ComputeTubeProbability]]<br />
#* [[TubeTK/Documentation/ConvertInnerOpticToPlus | ConvertInnerOpticToPlus]]<br />
#* [[TubeTK/Documentation/ConvertShrunkenSeedImageToList | ConvertShrunkenSeedImageToList]]<br />
#* [[TubeTK/Documentation/ConvertTRE | ConvertTRE]]<br />
#* [[TubeTK/Documentation/ConvertTubeGraphToImage | ConvertTubeGraphToImage]]<br />
#* [[TubeTK/Documentation/ConvertTubesToDensityImage | ConvertTubesToDensityImage]]<br />
#* [[TubeTK/Documentation/ConvertTubesToImage | ConvertTubesToImage]]<br />
#* [[TubeTK/Documentation/ConvertTubesToSurface | ConvertTubesToSurface]]<br />
#* [[TubeTK/Documentation/ConvertTubeToTubeGraph | ConvertTubeToTubeGraph]]<br />
#* [[TubeTK/Documentation/CropImage | CropImage]]<br />
#* [[TubeTK/Documentation/DeblendTomosynthesisSlicesUsingPrior | DeblendTomosynthesisSlicesUsingPrior]]<br />
#* [[TubeTK/Documentation/EnhanceCoherenceAndEdgesUsingDiffusion | EnhanceCoherenceAndEdgesUsingDiffusion]]<br />
#* [[TubeTK/Documentation/EnhanceCoherenceUsingDiffusion | EnhanceCoherenceUsingDiffusion]]<br />
#* [[TubeTK/Documentation/EnhanceContrastUsingPrior | EnhanceContrastUsingPrior]]<br />
#* [[TubeTK/Documentation/EnhanceEdgesUsingDiffusion | EnhanceEdgesUsingDiffusion]]<br />
#* [[TubeTK/Documentation/EnhanceTubesUsingDiffusion | EnhanceTubesUsingDiffusion]]<br />
#* [[TubeTK/Documentation/EnhanceTubesUsingDiscriminantAnalysis | EnhanceTubesUsingDiscriminantAnalysis]]<br />
#* [[TubeTK/Documentation/EnhanceUsingDiscriminantAnalysis | EnhanceUsingDiscriminantAnalysis]]<br />
#* [[TubeTK/Documentation/EnhanceUsingNJetDiscriminantAnalysis | EnhanceUsingNJetDiscriminantAnalysis]]<br />
#* [[TubeTK/Documentation/ImageCompareCommand | ImageCompareCommand]]<br />
#* [[TubeTK/Documentation/JsonCompareCommand | JsonCompareCommand]]<br />
#* [[TubeTK/Documentation/MergeAdjacentImages | MergeAdjacentImages]]<br />
#* [[TubeTK/Documentation/MergeTubeGraphs | MergeTubeGraphs]]<br />
#* [[TubeTK/Documentation/RegisterImages | RegisterImages]]<br />
#* [[TubeTK/Documentation/RegisterUsingImageCenters | RegisterUsingImageCenters]]<br />
#* [[TubeTK/Documentation/RegisterUsingSlidingGeometries | RegisterUsingSlidingGeometries]]<br />
#* [[TubeTK/Documentation/ResampleImage | ResampleImage]]<br />
#* [[TubeTK/Documentation/SampleCLIApplication | SampleCLIApplication]]<br />
#* [[TubeTK/Documentation/SegmentBinaryImageSkeleton | SegmentBinaryImageSkeleton]]<br />
#* [[TubeTK/Documentation/SegmentConnectedComponents | SegmentConnectedComponents]]<br />
#* [[TubeTK/Documentation/SegmentConnectedComponentsUsingParzenPDFs | SegmentConnectedComponentsUsingParzenPDFs]]<br />
#* [[TubeTK/Documentation/SegmentTubes | SegmentTubes]]<br />
#* [[TubeTK/Documentation/SegmentUsingOtsuThreshold | SegmentUsingOtsuThreshold]]<br />
#* [[TubeTK/Documentation/ShrinkImage | ShrinkImage]]<br />
#* [[TubeTK/Documentation/SimulateAcquisitionArtifactsUsingPrior | SimulateAcquisitionArtifactsUsingPrior]]<br />
#* [[TubeTK/Documentation/SubSampleTubes | SubSampleTubes]]<br />
#* [[TubeTK/Documentation/TextCompareCommand | TextCompareCommand]]<br />
#* [[TubeTK/Documentation/TransformTubes | TransformTubes]]<br />
#* [[TubeTK/Documentation/HessianVesselness2D | Hessian Vesselness 2D]]<br />
#* [[TubeTK/Documentation/ExtractCurves2D | Extract Curves 2D]]<br />
#* [[TubeTK/Documentation/ComputeTortuosity | Compute Tortuosity]]<br />
#* [[TubeTK/Documentation/Sliding_Organ_Registration | Sliding Geometries Registration]]<br />
# '''3D Slicer Python Applications'''<br />
#* [[TubeTK/Documentation/InteractivePDFSegmenter | Interactive PDF Segmenter]]<br />
<br />
= Modules =<br />
# Pre-processing<br />
#* [[TubeTK/Anisotropic Hybrid Diffusion with Continuous Switch|Anisotropic Hybrid Diffusion with Continuous Switch]]<br />
# Object segmentation<br />
# Tube extraction<br />
# Data structures<br />
# Topology analysis<br />
# Editing<br />
# Export<br />
# [[TubeTK/OpenIGTLink|OpenIGTLink]]<br />
# Python<br />
#* [http://nbviewer.ipython.org/5925084 Tube NumPy Array]<br />
<br />
= Related Efforts =<br />
<br />
* [[TubeTK/Related Work|Related Work]]<br />
* [https://musiic.lcsr.jhu.edu Medical Ultrasound Imaging and Intervention Collaboration (MUSIIC)]<br />
* [http://www.vmtk.org Vascular Modeling Toolkit (VMTK)]<br />
<br />
|}<br />
<br />
[[Category:TubeTK|Documentation]]</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation&diff=57288TubeTK/Documentation2015-01-07T18:38:43Z<p>Christopher.mullins: /* Applications */</p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
<br />
{| border="1" cellpadding="10" cellspacing="0"<br />
|+ [[image:TubeTK_Header.jpg|1000px]]<br />
|-<br />
| style="background:#efefef;" align="left" valign="top" width="150px" | <br />
<br />
'''[[TubeTK|Home]]'''<br />
*[[TubeTK/About|About]]<br />
*[[TubeTK/Images|Image Gallery]]<br />
*[[TubeTK/Data|Data and Publications]]<br />
<br><br />
----<br />
<br><br />
'''For Users'''<br />
* [[TubeTK/Installation|Installation]]<br />
* [[TubeTK/Documentation|Methods & Apps]]<br />
* [[TubeTK/Slicer|TubeTK with 3D Slicer]]<br />
* [[TubeTK/OsiriX|TubeTK with OsiriX]]<br />
<br><br />
----<br />
<br><br />
'''For Developers'''<br />
* [[TubeTK/Development|Development Docs]]<br />
<br><br />
----<br />
<br><br />
'''[https://github.com/TubeTK/TubeTK/issues Report Bugs<br>Request Features]'''<br />
<br><br />
<br><br />
----<br />
<br><br />
'''[[TubeTK/Contact|Contact Us]]'''<br />
<br />
| width="800px" align="left" | <br />
= Applications =<br />
# '''GUI Applications'''<br />
# '''Command-line (CLI) Applications'''<br />
#* Command-line applications can be run directly from the command line, or graphically using 3D Slicer<br />
#* [[TubeTK/Documentation/AtlasBuilderUsingIntensity | AtlasBuilderUsingIntensity]]<br />
#* [[TubeTK/Documentation/ComputeBinaryImageSimilarityMetrics | ComputeBinaryImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageSimilarityMetrics | ComputeImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageStatisticsUsingMask | ComputeImageStatisticsUsingMask]]<br />
#* [[TubeTK/Documentation/ComputeSegmentTubesParameters | ComputeSegmentTubesParameters]]<br />
#* [[TubeTK/Documentation/ComputeTubeGraphProbability | ComputeTubeGraphProbability]]<br />
#* [[TubeTK/Documentation/ComputeTubeMeasures | ComputeTubeMeasures]]<br />
#* [[TubeTK/Documentation/ComputeTubeProbability | ComputeTubeProbability]]<br />
#* [[TubeTK/Documentation/ConvertInnerOpticToPlus | ConvertInnerOpticToPlus]]<br />
#* [[TubeTK/Documentation/ConvertShrunkenSeedImageToList | ConvertShrunkenSeedImageToList]]<br />
#* [[TubeTK/Documentation/ConvertToMetaImage | ConvertToMetaImage]]<br />
#* [[TubeTK/Documentation/ConvertToMetaImageCLI | ConvertToMetaImageCLI]]<br />
#* [[TubeTK/Documentation/ConvertTRE | ConvertTRE]]<br />
#* [[TubeTK/Documentation/ConvertTubeGraphToImage | ConvertTubeGraphToImage]]<br />
#* [[TubeTK/Documentation/ConvertTubesToDensityImage | ConvertTubesToDensityImage]]<br />
#* [[TubeTK/Documentation/ConvertTubesToImage | ConvertTubesToImage]]<br />
#* [[TubeTK/Documentation/ConvertTubesToSurface | ConvertTubesToSurface]]<br />
#* [[TubeTK/Documentation/ConvertTubeToTubeGraph | ConvertTubeToTubeGraph]]<br />
#* [[TubeTK/Documentation/CropImage | CropImage]]<br />
#* [[TubeTK/Documentation/DeblendTomosynthesisSlicesUsingPrior | DeblendTomosynthesisSlicesUsingPrior]]<br />
#* [[TubeTK/Documentation/EnhanceCoherenceAndEdgesUsingDiffusion | EnhanceCoherenceAndEdgesUsingDiffusion]]<br />
#* [[TubeTK/Documentation/EnhanceCoherenceUsingDiffusion | EnhanceCoherenceUsingDiffusion]]<br />
#* [[TubeTK/Documentation/EnhanceContrastUsingPrior | EnhanceContrastUsingPrior]]<br />
#* [[TubeTK/Documentation/EnhanceEdgesUsingDiffusion | EnhanceEdgesUsingDiffusion]]<br />
#* [[TubeTK/Documentation/EnhanceTubesUsingDiffusion | EnhanceTubesUsingDiffusion]]<br />
#* [[TubeTK/Documentation/EnhanceTubesUsingDiscriminantAnalysis | EnhanceTubesUsingDiscriminantAnalysis]]<br />
#* [[TubeTK/Documentation/EnhanceUsingDiscriminantAnalysis | EnhanceUsingDiscriminantAnalysis]]<br />
#* [[TubeTK/Documentation/EnhanceUsingNJetDiscriminantAnalysis | EnhanceUsingNJetDiscriminantAnalysis]]<br />
#* [[TubeTK/Documentation/ImageCompareCommand | ImageCompareCommand]]<br />
#* [[TubeTK/Documentation/JsonCompareCommand | JsonCompareCommand]]<br />
#* [[TubeTK/Documentation/MergeAdjacentImages | MergeAdjacentImages]]<br />
#* [[TubeTK/Documentation/MergeTubeGraphs | MergeTubeGraphs]]<br />
#* [[TubeTK/Documentation/RegisterImages | RegisterImages]]<br />
#* [[TubeTK/Documentation/RegisterUsingImageCenters | RegisterUsingImageCenters]]<br />
#* [[TubeTK/Documentation/RegisterUsingSlidingGeometries | RegisterUsingSlidingGeometries]]<br />
#* [[TubeTK/Documentation/ResampleImage | ResampleImage]]<br />
#* [[TubeTK/Documentation/SampleCLIApplication | SampleCLIApplication]]<br />
#* [[TubeTK/Documentation/SegmentBinaryImageSkeleton | SegmentBinaryImageSkeleton]]<br />
#* [[TubeTK/Documentation/SegmentConnectedComponents | SegmentConnectedComponents]]<br />
#* [[TubeTK/Documentation/SegmentConnectedComponentsUsingParzenPDFs | SegmentConnectedComponentsUsingParzenPDFs]]<br />
#* [[TubeTK/Documentation/SegmentTubes | SegmentTubes]]<br />
#* [[TubeTK/Documentation/SegmentUsingOtsuThreshold | SegmentUsingOtsuThreshold]]<br />
#* [[TubeTK/Documentation/ShrinkImage | ShrinkImage]]<br />
#* [[TubeTK/Documentation/SimulateAcquisitionArtifactsUsingPrior | SimulateAcquisitionArtifactsUsingPrior]]<br />
#* [[TubeTK/Documentation/SubSampleTubes | SubSampleTubes]]<br />
#* [[TubeTK/Documentation/TextCompareCommand | TextCompareCommand]]<br />
#* [[TubeTK/Documentation/TransformTubes | TransformTubes]]<br />
#* [[TubeTK/Documentation/HessianVesselness2D | Hessian Vesselness 2D]]<br />
#* [[TubeTK/Documentation/ExtractCurves2D | Extract Curves 2D]]<br />
#* [[TubeTK/Documentation/ComputeTortuosity | Compute Tortuosity]]<br />
#* [[TubeTK/Documentation/Sliding_Organ_Registration | Sliding Geometries Registration]]<br />
# '''3D Slicer Python Applications'''<br />
#* [[TubeTK/Documentation/InteractivePDFSegmenter | Interactive PDF Segmenter]]<br />
<br />
= Modules =<br />
# Pre-processing<br />
#* [[TubeTK/Anisotropic Hybrid Diffusion with Continuous Switch|Anisotropic Hybrid Diffusion with Continuous Switch]]<br />
# Object segmentation<br />
# Tube extraction<br />
# Data structures<br />
# Topology analysis<br />
# Editing<br />
# Export<br />
# [[TubeTK/OpenIGTLink|OpenIGTLink]]<br />
# Python<br />
#* [http://nbviewer.ipython.org/5925084 Tube NumPy Array]<br />
<br />
= Related Efforts =<br />
<br />
* [[TubeTK/Related Work|Related Work]]<br />
* [https://musiic.lcsr.jhu.edu Medical Ultrasound Imaging and Intervention Collaboration (MUSIIC)]<br />
* [http://www.vmtk.org Vascular Modeling Toolkit (VMTK)]<br />
<br />
|}<br />
<br />
[[Category:TubeTK|Documentation]]</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ConvertShrunkenSeedImageToList&diff=57287TubeTK/Documentation/ConvertShrunkenSeedImageToList2015-01-07T18:32:19Z<p>Christopher.mullins: Created page with " Description: Given a shrunken mask image and the original pixel coordinate image, generate a list of non-zero pixels. USAGE: ./ConvertShrunkenSeedImageToList [--..."</p>
<hr />
<div> Description: Given a shrunken mask image and the original pixel<br />
coordinate image, generate a list of non-zero pixels.<br />
<br />
<br />
USAGE: <br />
<br />
./ConvertShrunkenSeedImageToList [--returnparameterfile <std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo] [-t<br />
<double>] [--] [--version] [-h]<br />
<std::string> <std::string><br />
<std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-t <double>, -- <double><br />
Shrunken image pixels with values above this threshold are added as<br />
points to the seed list (default: 0)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input image<br />
<br />
<std::string><br />
(required) Input scale image<br />
<br />
<std::string><br />
(required) Input points file from shrinking the image<br />
<br />
<std::string><br />
(required) Output list<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation&diff=57286TubeTK/Documentation2015-01-07T18:31:52Z<p>Christopher.mullins: /* Applications */</p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
<br />
{| border="1" cellpadding="10" cellspacing="0"<br />
|+ [[image:TubeTK_Header.jpg|1000px]]<br />
|-<br />
| style="background:#efefef;" align="left" valign="top" width="150px" | <br />
<br />
'''[[TubeTK|Home]]'''<br />
*[[TubeTK/About|About]]<br />
*[[TubeTK/Images|Image Gallery]]<br />
*[[TubeTK/Data|Data and Publications]]<br />
<br><br />
----<br />
<br><br />
'''For Users'''<br />
* [[TubeTK/Installation|Installation]]<br />
* [[TubeTK/Documentation|Methods & Apps]]<br />
* [[TubeTK/Slicer|TubeTK with 3D Slicer]]<br />
* [[TubeTK/OsiriX|TubeTK with OsiriX]]<br />
<br><br />
----<br />
<br><br />
'''For Developers'''<br />
* [[TubeTK/Development|Development Docs]]<br />
<br><br />
----<br />
<br><br />
'''[https://github.com/TubeTK/TubeTK/issues Report Bugs<br>Request Features]'''<br />
<br><br />
<br><br />
----<br />
<br><br />
'''[[TubeTK/Contact|Contact Us]]'''<br />
<br />
| width="800px" align="left" | <br />
= Applications =<br />
# '''GUI Applications'''<br />
# '''Command-line (CLI) Applications'''<br />
#* Command-line applications can be run directly from the command line, or graphically using 3D Slicer<br />
#* [[TubeTK/Documentation/AtlasBuilderUsingIntensity | AtlasBuilderUsingIntensity]]<br />
#* [[TubeTK/Documentation/ComputeBinaryImageSimilarityMetrics | ComputeBinaryImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageSimilarityMetrics | ComputeImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageStatisticsUsingMask | ComputeImageStatisticsUsingMask]]<br />
#* [[TubeTK/Documentation/ComputeSegmentTubesParameters | ComputeSegmentTubesParameters]]<br />
#* [[TubeTK/Documentation/ComputeTubeGraphProbability | ComputeTubeGraphProbability]]<br />
#* [[TubeTK/Documentation/ComputeTubeMeasures | ComputeTubeMeasures]]<br />
#* [[TubeTK/Documentation/ComputeTubeProbability | ComputeTubeProbability]]<br />
#* [[TubeTK/Documentation/ConvertInnerOpticToPlus | ConvertInnerOpticToPlus]]<br />
#* [[TubeTK/Documentation/ConvertShrunkenSeedImageToList | ConvertShrunkenSeedImageToList]]<br />
#* [[TubeTK/Documentation/CropImage | CropImage]]<br />
#* [[TubeTK/Documentation/HessianVesselness2D | Hessian Vesselness 2D]]<br />
#* [[TubeTK/Documentation/ExtractCurves2D | Extract Curves 2D]]<br />
#* [[TubeTK/Documentation/ComputeTortuosity | Compute Tortuosity]]<br />
#* [[TubeTK/Documentation/Sliding_Organ_Registration | Sliding Geometries Registration]]<br />
# '''3D Slicer Python Applications'''<br />
#* [[TubeTK/Documentation/InteractivePDFSegmenter | Interactive PDF Segmenter]]<br />
<br />
= Modules =<br />
# Pre-processing<br />
#* [[TubeTK/Anisotropic Hybrid Diffusion with Continuous Switch|Anisotropic Hybrid Diffusion with Continuous Switch]]<br />
# Object segmentation<br />
# Tube extraction<br />
# Data structures<br />
# Topology analysis<br />
# Editing<br />
# Export<br />
# [[TubeTK/OpenIGTLink|OpenIGTLink]]<br />
# Python<br />
#* [http://nbviewer.ipython.org/5925084 Tube NumPy Array]<br />
<br />
= Related Efforts =<br />
<br />
* [[TubeTK/Related Work|Related Work]]<br />
* [https://musiic.lcsr.jhu.edu Medical Ultrasound Imaging and Intervention Collaboration (MUSIIC)]<br />
* [http://www.vmtk.org Vascular Modeling Toolkit (VMTK)]<br />
<br />
|}<br />
<br />
[[Category:TubeTK|Documentation]]</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ConvertInnerOpticToPlus&diff=57285TubeTK/Documentation/ConvertInnerOpticToPlus2015-01-07T18:31:01Z<p>Christopher.mullins: Created page with " Description: Convert a sequence of ultrasound screen capture images and tracker data in InnerOptic's format to the format used by the Plus ultrasound library. The Pl..."</p>
<hr />
<div> Description: Convert a sequence of ultrasound screen capture images and<br />
tracker data in InnerOptic's format to the format used by the Plus<br />
ultrasound library. The Plus library uses the MetaImage file format<br />
where the third dimension is time. Tracker information is stored as<br />
additional metadata fields in the MetaImage header.<br />
<br />
USAGE: <br />
<br />
./ConvertInnerOpticToPlus [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>]<br />
[--xml] [--echo] [-f <double>] [-t <int>]<br />
[-d] [-i <int>] [-e <int>] [-s <int>] [--]<br />
[--version] [-h] <std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-f <double>, --duplicateFractionalThreshold <double><br />
Fractional threshold of pixels that are the same before a frame is<br />
considered a duplicate. (default: 0.7)<br />
<br />
-t <int>, --duplicateTolerance <int><br />
Tolerance for considering pixels the same. (default: 3)<br />
<br />
-d, --duplicatesNotInvalid<br />
Do not mark duplicate frames INVALID.<br />
<br />
-i <int>, --incrementIndex <int><br />
Frame index increment. (default: 1)<br />
<br />
-e <int>, --endIndex <int><br />
Index of the last frame to extract (inclusive). (default: 9999)<br />
<br />
-s <int>, --startIndex <int><br />
Index of the first frame to extract (starts from zero). (default: 0)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) InnerOptic metadata file. This file contain tracker<br />
information and references the ultrasound screenshot .ppm files, which<br />
should be in the same directory.<br />
<br />
<std::string><br />
(required) Output MetaImage FileName. The .mha or .mhd filename<br />
extension is recommended.<br />
<br />
<br />
Author(s): Matthew M. McCormick (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation&diff=57284TubeTK/Documentation2015-01-07T18:30:16Z<p>Christopher.mullins: /* Applications */</p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
<br />
{| border="1" cellpadding="10" cellspacing="0"<br />
|+ [[image:TubeTK_Header.jpg|1000px]]<br />
|-<br />
| style="background:#efefef;" align="left" valign="top" width="150px" | <br />
<br />
'''[[TubeTK|Home]]'''<br />
*[[TubeTK/About|About]]<br />
*[[TubeTK/Images|Image Gallery]]<br />
*[[TubeTK/Data|Data and Publications]]<br />
<br><br />
----<br />
<br><br />
'''For Users'''<br />
* [[TubeTK/Installation|Installation]]<br />
* [[TubeTK/Documentation|Methods & Apps]]<br />
* [[TubeTK/Slicer|TubeTK with 3D Slicer]]<br />
* [[TubeTK/OsiriX|TubeTK with OsiriX]]<br />
<br><br />
----<br />
<br><br />
'''For Developers'''<br />
* [[TubeTK/Development|Development Docs]]<br />
<br><br />
----<br />
<br><br />
'''[https://github.com/TubeTK/TubeTK/issues Report Bugs<br>Request Features]'''<br />
<br><br />
<br><br />
----<br />
<br><br />
'''[[TubeTK/Contact|Contact Us]]'''<br />
<br />
| width="800px" align="left" | <br />
= Applications =<br />
# '''GUI Applications'''<br />
# '''Command-line (CLI) Applications'''<br />
#* Command-line applications can be run directly from the command line, or graphically using 3D Slicer<br />
#* [[TubeTK/Documentation/AtlasBuilderUsingIntensity | AtlasBuilderUsingIntensity]]<br />
#* [[TubeTK/Documentation/ComputeBinaryImageSimilarityMetrics | ComputeBinaryImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageSimilarityMetrics | ComputeImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageStatisticsUsingMask | ComputeImageStatisticsUsingMask]]<br />
#* [[TubeTK/Documentation/ComputeSegmentTubesParameters | ComputeSegmentTubesParameters]]<br />
#* [[TubeTK/Documentation/ComputeTubeGraphProbability | ComputeTubeGraphProbability]]<br />
#* [[TubeTK/Documentation/ComputeTubeMeasures | ComputeTubeMeasures]]<br />
#* [[TubeTK/Documentation/ComputeTubeProbability | ComputeTubeProbability]]<br />
#* [[TubeTK/Documentation/ConvertInnerOpticToPlus | ConvertInnerOpticToPlus]]<br />
#* [[TubeTK/Documentation/CropImage | CropImage]]<br />
#* [[TubeTK/Documentation/HessianVesselness2D | Hessian Vesselness 2D]]<br />
#* [[TubeTK/Documentation/ExtractCurves2D | Extract Curves 2D]]<br />
#* [[TubeTK/Documentation/ComputeTortuosity | Compute Tortuosity]]<br />
#* [[TubeTK/Documentation/Sliding_Organ_Registration | Sliding Geometries Registration]]<br />
# '''3D Slicer Python Applications'''<br />
#* [[TubeTK/Documentation/InteractivePDFSegmenter | Interactive PDF Segmenter]]<br />
<br />
= Modules =<br />
# Pre-processing<br />
#* [[TubeTK/Anisotropic Hybrid Diffusion with Continuous Switch|Anisotropic Hybrid Diffusion with Continuous Switch]]<br />
# Object segmentation<br />
# Tube extraction<br />
# Data structures<br />
# Topology analysis<br />
# Editing<br />
# Export<br />
# [[TubeTK/OpenIGTLink|OpenIGTLink]]<br />
# Python<br />
#* [http://nbviewer.ipython.org/5925084 Tube NumPy Array]<br />
<br />
= Related Efforts =<br />
<br />
* [[TubeTK/Related Work|Related Work]]<br />
* [https://musiic.lcsr.jhu.edu Medical Ultrasound Imaging and Intervention Collaboration (MUSIIC)]<br />
* [http://www.vmtk.org Vascular Modeling Toolkit (VMTK)]<br />
<br />
|}<br />
<br />
[[Category:TubeTK|Documentation]]</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTubeProbability&diff=57283TubeTK/Documentation/ComputeTubeProbability2015-01-07T17:04:18Z<p>Christopher.mullins: Created page with "Description: Takes all points of the input tubes, maps them into the space of the mean Euclidean distance image, and outputs the distance values at those points. USAGE:..."</p>
<hr />
<div>Description: Takes all points of the input tubes, maps them into the space of the mean Euclidean distance image, and outputs the distance values at those points.<br />
<br />
USAGE: <br />
<br />
./ComputeTubeProbability [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>]<br />
[--xml] [--echo] [--] [--version] [-h]<br />
<std::string> <std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input tube file.<br />
<br />
<std::string><br />
(required) Mean Euclidean distance map.<br />
<br />
<std::string><br />
(required) Output file with point 'probabilities.'<br />
<br />
<br />
Author(s): Stephen R. Aylward, Roland Kwitt (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation&diff=57282TubeTK/Documentation2015-01-07T17:03:43Z<p>Christopher.mullins: /* Applications */</p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
<br />
{| border="1" cellpadding="10" cellspacing="0"<br />
|+ [[image:TubeTK_Header.jpg|1000px]]<br />
|-<br />
| style="background:#efefef;" align="left" valign="top" width="150px" | <br />
<br />
'''[[TubeTK|Home]]'''<br />
*[[TubeTK/About|About]]<br />
*[[TubeTK/Images|Image Gallery]]<br />
*[[TubeTK/Data|Data and Publications]]<br />
<br><br />
----<br />
<br><br />
'''For Users'''<br />
* [[TubeTK/Installation|Installation]]<br />
* [[TubeTK/Documentation|Methods & Apps]]<br />
* [[TubeTK/Slicer|TubeTK with 3D Slicer]]<br />
* [[TubeTK/OsiriX|TubeTK with OsiriX]]<br />
<br><br />
----<br />
<br><br />
'''For Developers'''<br />
* [[TubeTK/Development|Development Docs]]<br />
<br><br />
----<br />
<br><br />
'''[https://github.com/TubeTK/TubeTK/issues Report Bugs<br>Request Features]'''<br />
<br><br />
<br><br />
----<br />
<br><br />
'''[[TubeTK/Contact|Contact Us]]'''<br />
<br />
| width="800px" align="left" | <br />
= Applications =<br />
# '''GUI Applications'''<br />
# '''Command-line (CLI) Applications'''<br />
#* Command-line applications can be run directly from the command line, or graphically using 3D Slicer<br />
#* [[TubeTK/Documentation/AtlasBuilderUsingIntensity | AtlasBuilderUsingIntensity]]<br />
#* [[TubeTK/Documentation/ComputeBinaryImageSimilarityMetrics | ComputeBinaryImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageSimilarityMetrics | ComputeImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageStatisticsUsingMask | ComputeImageStatisticsUsingMask]]<br />
#* [[TubeTK/Documentation/ComputeSegmentTubesParameters | ComputeSegmentTubesParameters]]<br />
#* [[TubeTK/Documentation/ComputeTubeGraphProbability | ComputeTubeGraphProbability]]<br />
#* [[TubeTK/Documentation/ComputeTubeMeasures | ComputeTubeMeasures]]<br />
#* [[TubeTK/Documentation/ComputeTubeProbability | ComputeTubeProbability]]<br />
#* [[TubeTK/Documentation/CropImage | CropImage]]<br />
#* [[TubeTK/Documentation/HessianVesselness2D | Hessian Vesselness 2D]]<br />
#* [[TubeTK/Documentation/ExtractCurves2D | Extract Curves 2D]]<br />
#* [[TubeTK/Documentation/ComputeTortuosity | Compute Tortuosity]]<br />
#* [[TubeTK/Documentation/Sliding_Organ_Registration | Sliding Geometries Registration]]<br />
# '''3D Slicer Python Applications'''<br />
#* [[TubeTK/Documentation/InteractivePDFSegmenter | Interactive PDF Segmenter]]<br />
<br />
= Modules =<br />
# Pre-processing<br />
#* [[TubeTK/Anisotropic Hybrid Diffusion with Continuous Switch|Anisotropic Hybrid Diffusion with Continuous Switch]]<br />
# Object segmentation<br />
# Tube extraction<br />
# Data structures<br />
# Topology analysis<br />
# Editing<br />
# Export<br />
# [[TubeTK/OpenIGTLink|OpenIGTLink]]<br />
# Python<br />
#* [http://nbviewer.ipython.org/5925084 Tube NumPy Array]<br />
<br />
= Related Efforts =<br />
<br />
* [[TubeTK/Related Work|Related Work]]<br />
* [https://musiic.lcsr.jhu.edu Medical Ultrasound Imaging and Intervention Collaboration (MUSIIC)]<br />
* [http://www.vmtk.org Vascular Modeling Toolkit (VMTK)]<br />
<br />
|}<br />
<br />
[[Category:TubeTK|Documentation]]</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTubeMeasures&diff=57281TubeTK/Documentation/ComputeTubeMeasures2015-01-07T17:02:43Z<p>Christopher.mullins: Created page with "Description: Returns the ridgeness, roundness, curvature, and levelness measures. USAGE: ./ComputeTubeMeasures [--returnparameterfile <std::string>]..."</p>
<hr />
<div>Description: Returns the ridgeness, roundness, curvature, and levelness measures.<br />
<br />
USAGE: <br />
<br />
./ComputeTubeMeasures [--returnparameterfile <std::string>]<br />
[--processinformationaddress <std::string>]<br />
[--xml] [--echo] [-g <double>] [--] [--version]<br />
[-h] <std::string> <std::string> <std::string><br />
<std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-g <double>, --scale <double><br />
Standard deviation of the ridge. (default: 4)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input image.<br />
<br />
<std::string><br />
(required) Output image.<br />
<br />
<std::string><br />
(required) Output image.<br />
<br />
<std::string><br />
(required) Output image.<br />
<br />
<std::string><br />
(required) Output image.<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation&diff=57280TubeTK/Documentation2015-01-07T17:02:20Z<p>Christopher.mullins: /* Applications */</p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
<br />
{| border="1" cellpadding="10" cellspacing="0"<br />
|+ [[image:TubeTK_Header.jpg|1000px]]<br />
|-<br />
| style="background:#efefef;" align="left" valign="top" width="150px" | <br />
<br />
'''[[TubeTK|Home]]'''<br />
*[[TubeTK/About|About]]<br />
*[[TubeTK/Images|Image Gallery]]<br />
*[[TubeTK/Data|Data and Publications]]<br />
<br><br />
----<br />
<br><br />
'''For Users'''<br />
* [[TubeTK/Installation|Installation]]<br />
* [[TubeTK/Documentation|Methods & Apps]]<br />
* [[TubeTK/Slicer|TubeTK with 3D Slicer]]<br />
* [[TubeTK/OsiriX|TubeTK with OsiriX]]<br />
<br><br />
----<br />
<br><br />
'''For Developers'''<br />
* [[TubeTK/Development|Development Docs]]<br />
<br><br />
----<br />
<br><br />
'''[https://github.com/TubeTK/TubeTK/issues Report Bugs<br>Request Features]'''<br />
<br><br />
<br><br />
----<br />
<br><br />
'''[[TubeTK/Contact|Contact Us]]'''<br />
<br />
| width="800px" align="left" | <br />
= Applications =<br />
# '''GUI Applications'''<br />
# '''Command-line (CLI) Applications'''<br />
#* Command-line applications can be run directly from the command line, or graphically using 3D Slicer<br />
#* [[TubeTK/Documentation/AtlasBuilderUsingIntensity | AtlasBuilderUsingIntensity]]<br />
#* [[TubeTK/Documentation/ComputeBinaryImageSimilarityMetrics | ComputeBinaryImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageSimilarityMetrics | ComputeImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageStatisticsUsingMask | ComputeImageStatisticsUsingMask]]<br />
#* [[TubeTK/Documentation/ComputeSegmentTubesParameters | ComputeSegmentTubesParameters]]<br />
#* [[TubeTK/Documentation/ComputeTubeGraphProbability | ComputeTubeGraphProbability]]<br />
#* [[TubeTK/Documentation/ComputeTubeMeasures | ComputeTubeMeasures]]<br />
#* [[TubeTK/Documentation/CropImage | CropImage]]<br />
#* [[TubeTK/Documentation/HessianVesselness2D | Hessian Vesselness 2D]]<br />
#* [[TubeTK/Documentation/ExtractCurves2D | Extract Curves 2D]]<br />
#* [[TubeTK/Documentation/ComputeTortuosity | Compute Tortuosity]]<br />
#* [[TubeTK/Documentation/Sliding_Organ_Registration | Sliding Geometries Registration]]<br />
# '''3D Slicer Python Applications'''<br />
#* [[TubeTK/Documentation/InteractivePDFSegmenter | Interactive PDF Segmenter]]<br />
<br />
= Modules =<br />
# Pre-processing<br />
#* [[TubeTK/Anisotropic Hybrid Diffusion with Continuous Switch|Anisotropic Hybrid Diffusion with Continuous Switch]]<br />
# Object segmentation<br />
# Tube extraction<br />
# Data structures<br />
# Topology analysis<br />
# Editing<br />
# Export<br />
# [[TubeTK/OpenIGTLink|OpenIGTLink]]<br />
# Python<br />
#* [http://nbviewer.ipython.org/5925084 Tube NumPy Array]<br />
<br />
= Related Efforts =<br />
<br />
* [[TubeTK/Related Work|Related Work]]<br />
* [https://musiic.lcsr.jhu.edu Medical Ultrasound Imaging and Intervention Collaboration (MUSIIC)]<br />
* [http://www.vmtk.org Vascular Modeling Toolkit (VMTK)]<br />
<br />
|}<br />
<br />
[[Category:TubeTK|Documentation]]</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTubeGraphProbability&diff=57279TubeTK/Documentation/ComputeTubeGraphProbability2015-01-07T17:01:38Z<p>Christopher.mullins: Created page with "Description: Propagates averaged information of a (mean) graph to the current graph based on connectivity information. USAGE: ./ComputeTubeGraphProbability [--returnpar..."</p>
<hr />
<div>Description: Propagates averaged information of a (mean) graph to the current graph based on connectivity information.<br />
<br />
USAGE: <br />
<br />
./ComputeTubeGraphProbability [--returnparameterfile <std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo] [--]<br />
[--version] [-h] <std::string><br />
<std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input graph file. Filename serves as base for output files<br />
, .matProb.txt, .cntProb.txt, .brcProb.txt.<br />
<br />
<std::string><br />
(required) Mean input graph.<br />
<br />
<std::string><br />
(required) Output graph file (base name).<br />
<br />
<br />
Author(s): Stephen R. Aylward, Roland Kwitt (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation&diff=57278TubeTK/Documentation2015-01-07T17:01:05Z<p>Christopher.mullins: /* Applications */</p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
<br />
{| border="1" cellpadding="10" cellspacing="0"<br />
|+ [[image:TubeTK_Header.jpg|1000px]]<br />
|-<br />
| style="background:#efefef;" align="left" valign="top" width="150px" | <br />
<br />
'''[[TubeTK|Home]]'''<br />
*[[TubeTK/About|About]]<br />
*[[TubeTK/Images|Image Gallery]]<br />
*[[TubeTK/Data|Data and Publications]]<br />
<br><br />
----<br />
<br><br />
'''For Users'''<br />
* [[TubeTK/Installation|Installation]]<br />
* [[TubeTK/Documentation|Methods & Apps]]<br />
* [[TubeTK/Slicer|TubeTK with 3D Slicer]]<br />
* [[TubeTK/OsiriX|TubeTK with OsiriX]]<br />
<br><br />
----<br />
<br><br />
'''For Developers'''<br />
* [[TubeTK/Development|Development Docs]]<br />
<br><br />
----<br />
<br><br />
'''[https://github.com/TubeTK/TubeTK/issues Report Bugs<br>Request Features]'''<br />
<br><br />
<br><br />
----<br />
<br><br />
'''[[TubeTK/Contact|Contact Us]]'''<br />
<br />
| width="800px" align="left" | <br />
= Applications =<br />
# '''GUI Applications'''<br />
# '''Command-line (CLI) Applications'''<br />
#* Command-line applications can be run directly from the command line, or graphically using 3D Slicer<br />
#* [[TubeTK/Documentation/AtlasBuilderUsingIntensity | AtlasBuilderUsingIntensity]]<br />
#* [[TubeTK/Documentation/ComputeBinaryImageSimilarityMetrics | ComputeBinaryImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageSimilarityMetrics | ComputeImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageStatisticsUsingMask | ComputeImageStatisticsUsingMask]]<br />
#* [[TubeTK/Documentation/ComputeSegmentTubesParameters | ComputeSegmentTubesParameters]]<br />
#* [[TubeTK/Documentation/ComputeTubeGraphProbability | ComputeTubeGraphProbability]]<br />
#* [[TubeTK/Documentation/CropImage | CropImage]]<br />
#* [[TubeTK/Documentation/HessianVesselness2D | Hessian Vesselness 2D]]<br />
#* [[TubeTK/Documentation/ExtractCurves2D | Extract Curves 2D]]<br />
#* [[TubeTK/Documentation/ComputeTortuosity | Compute Tortuosity]]<br />
#* [[TubeTK/Documentation/Sliding_Organ_Registration | Sliding Geometries Registration]]<br />
# '''3D Slicer Python Applications'''<br />
#* [[TubeTK/Documentation/InteractivePDFSegmenter | Interactive PDF Segmenter]]<br />
<br />
= Modules =<br />
# Pre-processing<br />
#* [[TubeTK/Anisotropic Hybrid Diffusion with Continuous Switch|Anisotropic Hybrid Diffusion with Continuous Switch]]<br />
# Object segmentation<br />
# Tube extraction<br />
# Data structures<br />
# Topology analysis<br />
# Editing<br />
# Export<br />
# [[TubeTK/OpenIGTLink|OpenIGTLink]]<br />
# Python<br />
#* [http://nbviewer.ipython.org/5925084 Tube NumPy Array]<br />
<br />
= Related Efforts =<br />
<br />
* [[TubeTK/Related Work|Related Work]]<br />
* [https://musiic.lcsr.jhu.edu Medical Ultrasound Imaging and Intervention Collaboration (MUSIIC)]<br />
* [http://www.vmtk.org Vascular Modeling Toolkit (VMTK)]<br />
<br />
|}<br />
<br />
[[Category:TubeTK|Documentation]]</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeSegmentTubesParameters&diff=57277TubeTK/Documentation/ComputeSegmentTubesParameters2015-01-07T17:00:16Z<p>Christopher.mullins: Created page with "Description: Demonstration of how to write a CLI application. Performs blurring. USAGE: ./ComputeSegmentTubesParameters [--returnparameterfile <std::string>]..."</p>
<hr />
<div>Description: Demonstration of how to write a CLI application. Performs blurring.<br />
<br />
USAGE: <br />
<br />
./ComputeSegmentTubesParameters [--returnparameterfile <std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo] [-v<br />
<int>] [-b <int>] [--] [--version] [-h]<br />
<std::string> <std::string><br />
<std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
-v <int>, --maskTubeId <int><br />
Value used to indicate vessel pixels in the mask. (default: 255)<br />
<br />
-b <int>, --maskBackgroundId <int><br />
Value used to indicate background pixels in the mask. (default: 127)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Mask indicates vessel and background labels<br />
<br />
<std::string><br />
(required) Scale of potential vessel at every point.<br />
<br />
<std::string><br />
(required) Input image.<br />
<br />
<std::string><br />
(required) Parameters for SegmentTubes are written to this file.<br />
<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation&diff=57276TubeTK/Documentation2015-01-07T16:59:52Z<p>Christopher.mullins: /* Applications */</p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
<br />
{| border="1" cellpadding="10" cellspacing="0"<br />
|+ [[image:TubeTK_Header.jpg|1000px]]<br />
|-<br />
| style="background:#efefef;" align="left" valign="top" width="150px" | <br />
<br />
'''[[TubeTK|Home]]'''<br />
*[[TubeTK/About|About]]<br />
*[[TubeTK/Images|Image Gallery]]<br />
*[[TubeTK/Data|Data and Publications]]<br />
<br><br />
----<br />
<br><br />
'''For Users'''<br />
* [[TubeTK/Installation|Installation]]<br />
* [[TubeTK/Documentation|Methods & Apps]]<br />
* [[TubeTK/Slicer|TubeTK with 3D Slicer]]<br />
* [[TubeTK/OsiriX|TubeTK with OsiriX]]<br />
<br><br />
----<br />
<br><br />
'''For Developers'''<br />
* [[TubeTK/Development|Development Docs]]<br />
<br><br />
----<br />
<br><br />
'''[https://github.com/TubeTK/TubeTK/issues Report Bugs<br>Request Features]'''<br />
<br><br />
<br><br />
----<br />
<br><br />
'''[[TubeTK/Contact|Contact Us]]'''<br />
<br />
| width="800px" align="left" | <br />
= Applications =<br />
# '''GUI Applications'''<br />
# '''Command-line (CLI) Applications'''<br />
#* Command-line applications can be run directly from the command line, or graphically using 3D Slicer<br />
#* [[TubeTK/Documentation/AtlasBuilderUsingIntensity | AtlasBuilderUsingIntensity]]<br />
#* [[TubeTK/Documentation/ComputeBinaryImageSimilarityMetrics | ComputeBinaryImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageSimilarityMetrics | ComputeImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageStatisticsUsingMask | ComputeImageStatisticsUsingMask]]<br />
#* [[TubeTK/Documentation/ComputeSegmentTubesParameters | ComputeSegmentTubesParameters]]<br />
#* [[TubeTK/Documentation/CropImage | CropImage]]<br />
#* [[TubeTK/Documentation/HessianVesselness2D | Hessian Vesselness 2D]]<br />
#* [[TubeTK/Documentation/ExtractCurves2D | Extract Curves 2D]]<br />
#* [[TubeTK/Documentation/ComputeTortuosity | Compute Tortuosity]]<br />
#* [[TubeTK/Documentation/Sliding_Organ_Registration | Sliding Geometries Registration]]<br />
# '''3D Slicer Python Applications'''<br />
#* [[TubeTK/Documentation/InteractivePDFSegmenter | Interactive PDF Segmenter]]<br />
<br />
= Modules =<br />
# Pre-processing<br />
#* [[TubeTK/Anisotropic Hybrid Diffusion with Continuous Switch|Anisotropic Hybrid Diffusion with Continuous Switch]]<br />
# Object segmentation<br />
# Tube extraction<br />
# Data structures<br />
# Topology analysis<br />
# Editing<br />
# Export<br />
# [[TubeTK/OpenIGTLink|OpenIGTLink]]<br />
# Python<br />
#* [http://nbviewer.ipython.org/5925084 Tube NumPy Array]<br />
<br />
= Related Efforts =<br />
<br />
* [[TubeTK/Related Work|Related Work]]<br />
* [https://musiic.lcsr.jhu.edu Medical Ultrasound Imaging and Intervention Collaboration (MUSIIC)]<br />
* [http://www.vmtk.org Vascular Modeling Toolkit (VMTK)]<br />
<br />
|}<br />
<br />
[[Category:TubeTK|Documentation]]</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeImageStatisticsUsingMask&diff=57275TubeTK/Documentation/ComputeImageStatisticsUsingMask2015-01-07T16:59:02Z<p>Christopher.mullins: Created page with "Description: Compute image statistics for each region indicated in a mask file. USAGE: ./ComputeImageStatisticsUsingMask [--returnparameterfile <std::string>]..."</p>
<hr />
<div>Description: Compute image statistics for each region indicated in a mask file.<br />
<br />
USAGE: <br />
<br />
./ComputeImageStatisticsUsingMask [--returnparameterfile <std::string>]<br />
[--processinformationaddress<br />
<std::string>] [--xml] [--echo] [--]<br />
[--version] [-h] <std::string><br />
<std::string> <std::string><br />
<br />
<br />
Where: <br />
<br />
--returnparameterfile <std::string><br />
Filename in which to write simple return parameters (int, float,<br />
int-vector, etc.) as opposed to bulk return parameters (image,<br />
geometry, transform, measurement, table).<br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<std::string><br />
(required) Input mask.<br />
<br />
<std::string><br />
(required) Input volume.<br />
<br />
<std::string><br />
(required) Output statistics volume.<br />
<br />
<br />
Author(s): Stephen R. Aylward (Kitware)<br />
<br />
Acknowledgements: This work is part of the TubeTK project at Kitware.</div>Christopher.mullinshttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation&diff=57274TubeTK/Documentation2015-01-07T16:58:19Z<p>Christopher.mullins: /* Applications */</p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
<br />
{| border="1" cellpadding="10" cellspacing="0"<br />
|+ [[image:TubeTK_Header.jpg|1000px]]<br />
|-<br />
| style="background:#efefef;" align="left" valign="top" width="150px" | <br />
<br />
'''[[TubeTK|Home]]'''<br />
*[[TubeTK/About|About]]<br />
*[[TubeTK/Images|Image Gallery]]<br />
*[[TubeTK/Data|Data and Publications]]<br />
<br><br />
----<br />
<br><br />
'''For Users'''<br />
* [[TubeTK/Installation|Installation]]<br />
* [[TubeTK/Documentation|Methods & Apps]]<br />
* [[TubeTK/Slicer|TubeTK with 3D Slicer]]<br />
* [[TubeTK/OsiriX|TubeTK with OsiriX]]<br />
<br><br />
----<br />
<br><br />
'''For Developers'''<br />
* [[TubeTK/Development|Development Docs]]<br />
<br><br />
----<br />
<br><br />
'''[https://github.com/TubeTK/TubeTK/issues Report Bugs<br>Request Features]'''<br />
<br><br />
<br><br />
----<br />
<br><br />
'''[[TubeTK/Contact|Contact Us]]'''<br />
<br />
| width="800px" align="left" | <br />
= Applications =<br />
# '''GUI Applications'''<br />
# '''Command-line (CLI) Applications'''<br />
#* Command-line applications can be run directly from the command line, or graphically using 3D Slicer<br />
#* [[TubeTK/Documentation/AtlasBuilderUsingIntensity | AtlasBuilderUsingIntensity]]<br />
#* [[TubeTK/Documentation/ComputeBinaryImageSimilarityMetrics | ComputeBinaryImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageSimilarityMetrics | ComputeImageSimilarityMetrics]]<br />
#* [[TubeTK/Documentation/ComputeImageStatisticsUsingMask | ComputeImageStatisticsUsingMask]]<br />
#* [[TubeTK/Documentation/CropImage | CropImage]]<br />
#* [[TubeTK/Documentation/HessianVesselness2D | Hessian Vesselness 2D]]<br />
#* [[TubeTK/Documentation/ExtractCurves2D | Extract Curves 2D]]<br />
#* [[TubeTK/Documentation/ComputeTortuosity | Compute Tortuosity]]<br />
#* [[TubeTK/Documentation/Sliding_Organ_Registration | Sliding Geometries Registration]]<br />
# '''3D Slicer Python Applications'''<br />
#* [[TubeTK/Documentation/InteractivePDFSegmenter | Interactive PDF Segmenter]]<br />
<br />
= Modules =<br />
# Pre-processing<br />
#* [[TubeTK/Anisotropic Hybrid Diffusion with Continuous Switch|Anisotropic Hybrid Diffusion with Continuous Switch]]<br />
# Object segmentation<br />
# Tube extraction<br />
# Data structures<br />
# Topology analysis<br />
# Editing<br />
# Export<br />
# [[TubeTK/OpenIGTLink|OpenIGTLink]]<br />
# Python<br />
#* [http://nbviewer.ipython.org/5925084 Tube NumPy Array]<br />
<br />
= Related Efforts =<br />
<br />
* [[TubeTK/Related Work|Related Work]]<br />
* [https://musiic.lcsr.jhu.edu Medical Ultrasound Imaging and Intervention Collaboration (MUSIIC)]<br />
* [http://www.vmtk.org Vascular Modeling Toolkit (VMTK)]<br />
<br />
|}<br />
<br />
[[Category:TubeTK|Documentation]]</div>Christopher.mullins