Class | Description |
---|---|
AddNoise |
app for adding rician noise to noiseless synthetic noiseless
measurements given SNR and scheme file
|
BallSticksOrientationViewer |
Simple tool to visualize principal directions of ball and stick data.
|
BinaryToText |
Purpose:
Converts binary data to text.
|
ChunkStats |
Purpose:
Computes statistics of chunks of data.
|
ClassifiedModelFit |
Purpose:
Classified model fitting program.
|
CombineTwoFibreLUTs |
Combines LUTs with different crossing angles into one.
|
CompartmentModelOrientationViewer |
Simple tool to visualize principal directions of compartment model data.
|
ConnectivityMapping | |
ConsistencyFraction |
Purpose:
Computes the consistency fraction from multiple-fibre reconstruction
outputs.
|
CountSeeds |
Counts the number of seed voxels (voxels with values > 0).
|
CP_Stats |
Reads PICo probability maps and computes a voxel-based statistic of them.
|
DataStats |
Purpose:
Computes simple statistics of data files.
|
DeconvToCamenoFormat |
Purpose:
Converts the output of Donald Tournier's sig2fod program to the format
expected in the Cameno suite.
|
DT_EigenSystem |
Purpose:
Computes the eigensystem of each diffusion tensor.
|
DT_FitMatrix |
Purpose:
Creates a matrix for fitting the diffusion tensor via a linear
transform.
|
DT_ShapeStatistics |
Computes indices of tensor shape.
|
DT_ToCamino |
Converts a NIFTI, ITK or Analyze tensor volume to Camino format.
|
DT_ToNii |
Converts Camino dts to Nifti format.
|
ElectrostaticSubsets |
Orders electrostatic points into subsets following the method in Cook et al (ISMRM 2005, p.
|
EntryPoint |
Unified entrypoint for all camino commands,
incorporating generic main method structure
and command checking.
|
EstimateSNR |
Estimates SNR using different methods explained in the paper "Measurement of signal-to-noise ratios in MR
images: Influence of multichannel coils, parallel imaging, and reconstruction filters" by Olaf Dietrich
et al, JMRI 26:376-385 (2007).
|
Executable |
first stab at a base-level executable class.
|
F_TestThresholdSelector |
Purpose:
Loads F-test data for interactive threshold selection.
|
FanningGrid |
Outputs a ball and stick model fanning structure
|
FracAnis |
Purpose:
Computes the fractional anisotropy of each diffusion tensor.
|
FSL_ToScheme |
Converts FSL b-vectors and b-values to Camino scheme file format.
|
GatherStats | |
GenerateDTLUT |
Makes lookup tables for PICo from diffusion tensor data.
|
GenerateMFR_LUT |
Purpose:
Generates a LUT that is indexed using the Hessian of the peaks of
multi-fibre methods.
|
ImageToVoxel |
Converts Analyze / NIFTI / MHA files to voxel order.
|
ImportSH_Coeffs |
Purpose:
Converts the spherical harmonic (SH) output of several third party programs to the format
expected in Camino.
|
InversionStats |
Purpose:
Computes statistics of properties of the inversion outputs.
|
LinearRecon |
Purpose:
Performs a linear reconstruction in each voxel.
|
MeanDiff |
Purpose:
Computes the mean diffusivity (trace/3) of each diffusion tensor.
|
MESD |
Purpose:
Runs maximum entropy spherical deconvolution on each voxel's worth of
data on the input stream.
|
ModelFit |
Purpose:
Diffusion data inversion application using model fitting.
|
MultiFibreReconStats |
Purpose:
Computes statistics of properties of the multiple-fibre
reconstruction outputs.
|
OrderElectrostaticPoints |
Orders electrostatic points according to the method in Cook et al (ISMRM 2006, p.
|
OrientationBiasMap |
Iterates over the hemisphere, fitting synthetic data at each point and evaluating its error statistics.
|
PD_OrientationViewer |
Simple tool to visualize principal directions of tensor data.
|
PICoPDF_OrientationViewer |
Simple tool to visualize principal directions of PICo data.
|
PICoPDFs |
Calculate PICo PDFs in each voxel.
|
PointSetToScheme |
Converts point sets to scheme files, given additional imaging parameters.
|
ProcessStreamlines |
Processes streamline output from StreamlineTractography or from a previous invocation of this
program.
|
QBallMX |
Purpose:
Generates the transition matrix for QBall
Description: The default option uses the method
descibed by Tuch (MRM, 2004) to generate
the transition matrix for QBall.
|
Reorient |
Purpose:
Does diffusion tensor reorientation to accompany an image
transformation.
|
RGB_ScalarImage |
Produces a scalar-modulated RGB image, colored by the tensor eigenvector or ODF peak direction.
|
ScannerToVoxel |
Purpose:
Converts scanner order data to the voxel order format used by the Camino
suite.
|
SchemeToFSL |
Converts Camino scheme files to FSL b-vectors and b-values.
|
SequenceStats |
Purpose:
Computes statistics of a number of similar results from different random
rotations.
|
Shredder |
Extracts periodic chunks from binary data.
|
SphFuncAnisotropy |
Purpose:
Computes the anisotropy of an input stream of spherical functions.
|
SphFuncBitMap |
Purpose:
Generates a bitmap showing the spherical function in each voxel
of a region of the input data.
|
SphFuncKurtosis |
Purpose:
Computes the kurtosis (fourth root of normalized fourth moment:
\sqrt[4]{\int (f(x) - m)^4/\int f^4(x) dx) normalized by the
anisotropy (see SphFuncAnisotropy) of an input stream of spherical
functions.
|
SphFuncPD_Stats |
Purpose:
Computes the peak directions of spherical functions.
|
SphFuncPeaksOrientationViewer |
Simple tool to visualize principal directions of spherical function data.
|
SphFuncPICoCalibrationData |
Generates data for Hessian-based PICo calibration.
|
SphFuncSkewness |
Purpose:
Computes the skewness (cube root of normalized third moment:
\sqrt[3]{\int (f(x) - m)^3/\int f^3(x) dx) of an input stream of
spherical functions.
|
SphHarmFitter |
Purpose:
Computes the anisotropy based on the spherical harmonic fit.
|
SphPDF_Fit |
Fits a spherical PDF to a collection of axes, and outputs a result in the same format
as PICoPDFs (number of PDs is assumed to be 1).
|
Split4D_NiiImage |
Splits a 4D Nifti image into 3D component volumes.
|
StreamlineTractography |
Does tractography.
|
SubsetScheme |
Produces information about the quality of electrostatic subsets, and produces scheme
files for those subsets given the scheme file for the full set.
|
SyntheticData |
Purpose:
Creates a stream of synthetic data
Description:
Outputs a specified number of voxels worth of data synthesized from the
specified test function with the specified imaging parameters and noise
level.
|
TargetProbsToASCII |
Converts the results of tracking with target volumes to a text file.
|
TensorOrientationViewer |
Simple tool to visualize principal directions of tensor data.
|
ThresholdB0 |
Purpose:
Creates a background mask.
|
TraceD |
Purpose:
Computes the trace of each diffusion tensor.
|
TractCounter |
Counts the number of streamlines in a file.
|
TractShredder |
Like shredder, but used to sample periodically from a set of streamlines
|
TractStatistics |
Generates statistics of streamline tracts, either of the tracts themselves or of scalar values
along the tracts.
|
VoxelClassify |
Purpose:
Classifies each voxel as background, isotropic, anisotropic Gaussian or
non-Gaussian.
|
VoxelMean |
module that takes several voxels of data and generates the mean
in each direction.
|
VoxelToScanner |
Purpose:
Converts voxel order data to scanner order.
|
VTK_Streamlines |
Converts streamlines from raw format to VTK polylines (in binary form).
|
WriteZeros |
Purpose:
Write binary zeros (or any other number) to the standard
output.
|
Enum | Description |
---|---|
StreamlineTractography.ImageType |