Content-type: text/html Manpage of rgbscalarimg

rgbscalarimg

Section: User Commands (1)
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NAME

rgbscalarimg - Create an RGB image from diffusion peak directions, modulated by a scalar image (eg, anisotropy).

 

SYNOPSIS

rgbscalarimg [options]

 

DESCRIPTION

This program provides a command line method to get an RGB color-coded image similar to the one displayed in pdview. The RGB color triplet for each pixel comes from the absolute value of the specified eigenvector (for tensor eigensystem or PICo data) or the spherical function peak direction (for PAS / QBall data), so:


    |x| = r
    |y| = g 
    |z| = b

Each color channel is scaled by a scalar value. For tensor data, the default scalar is fractional anisotropy, so the scaling is naturally between 0 and 1. If another scalar image is used, the intensities are normalized and then used to scale the RGB data. When reading the output of sfpeaks, the default scalar is the trace of the Hessian of the strongest peak. The user may pass any scalar image that has identical dimensions to the diffusion data. The scalar multiplication is applied after the RGB is calculated and RGB gamma correction is applied, thus if you pass -rgbgamma 0.0 the output is greyscale and the contrast is the same as the scalar image.

If the scalar file passed to the program is an Analyze header, the voxel and data dimensions are read from the Analyze header and the -voxeldims and -datadims arguments can be omitted.

The output is either in MetaImage (ITK) or VTK format. The output may be visualized in ITK SNAP.

 

EXAMPLES

Get the RGB map modulated by FA from tensor data.

dteig < tensors.Bdouble | rgbscalarimg -datadims 128 128 60 -voxeldims 1.7 1.7 2.3 -outputroot rgb

The same thing, but using precomputed scalar data.

rgbscalarimg -scalarfile fa.hdr -outputroot rgb -inputfile dt_eig_sys.Bdouble

The same thing, but output the RGB map for e2, the second eigenvector

rgbscalarimg -scalarfile fa.hdr -outputroot rgb_e2 -inputfile dt_eig_sys.Bdouble -e2

A greyscale FA image with integer values between 0 and 255.

rgbscalarimg -scalarfile fa.hdr -outputroot fa.Bchar -inputfile dt_eig_sys.Bdouble -rgbgamma 0.0

 

OPTIONS

-datadims <x> <y> <z> The dimensions of the image, in voxels.

-voxeldims <x> <y> <z>
The x, y, and z dimension of each voxel, in millimetres.

-inputmodel <model>
Either "dteig" (tensor eigen systems, default), "pds" (spherical function peaks) or "pico" (output of picopdfs).

-scalarfile <file>
Either an Analyze / ITK / NIFTI-1 header file or a binary file. If an image header is specified, the -datadims and -voxeldims arguments are not necessary and are ignored.

If a binary file is specified, then the data type should be the same as the input data, which is double unless otherwise specified with the (-inputdatatype) option.

Whichever kind of scalar file is used, it should be defined in the same space as the diffusion data.

If no scalar file is given, the default is fractional anisotropy (tensor eigen system data) or Hessian trace (spherical function peaks).

-scalarrange <min> <max>
The minimum and maximum range of scalar values to display as different grey levels. Any voxels below the min will be black, those above the max will be white. By default, this range is calculated from the data (the smallest and largest 0.5% of scalars are excluded from the calculation so that outliers do not reduce the contrast).

-maxcomponents <max tensors per voxel>
Maximum number of tensor components in each voxel, for dteig data. The default is 1.

-numpds <max PDs per voxel>
Maximum number of spherical function peaks in each voxel, for pd or PICo data. The default is 3 for pd data and 1 for PICo data.

-outputformat <meta (default) | vtk>
Output format, default is meta.

-outputroot <file>
Output will be to file.[mha | vtk].

-gsgamma <g>
Gamma correction for the scalar image. The scalars are mapped between 0 and 1. Then I(out) = I(in)^g. Default is 1.0.

-rgbgamma <g>
Gamma correction for the RGB image. [r|g|b](out) = [r|g|b](in)^g. Default is 1.0. Set this to 0.0 to get a greyscale image.

-pdf <bingham | watson | acg>
PDF type of PICo data. The default is "bingham".
                   
-e1
Used only for tensor or pico data. Uses the first eigenvector to construct the RGB image, corresponding to the largest eigenvalue of the tensor. This is the default.

-e2
Used only for tensor or pico data. Uses the second eigenvector to construct the RGB image.

-e3
Used only for tensor or pico data. Uses the third eigenvector to construct the RGB image, corresponding to the smallest eigenvalue of the tensor.

 

AUTHORS

Philip Cook <camino@cs.ucl.ac.uk>

 

SEE ALSO

dteig(1), sfpeaks(1), pdview(1)

 

BUGS

Analyze output is not supported; Matlab, ITK and MRIcro all fail to read Analyze RGB images correctly. Please notify the Camino team if you require Analyze RGB images, and what program you intend to use them with.

The MetaImage specification defines the anatomical orientation used by Camino as R[ight]A[nterior]S[uperior], since the origin is left posterior inferior. ITK SNAP defines the orientation as the point of origin; ie Camino data is LPI, because voxel (0,0,0) is the left posterior inferior point of the image. Camino uses LPI in Meta headers.


 

Index

NAME
SYNOPSIS
DESCRIPTION
EXAMPLES
OPTIONS
AUTHORS
SEE ALSO
BUGS

This document was created by man2html, using the manual pages.
Time: 02:06:54 GMT, December 10, 2011