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analyzedti

Section: User Commands (1)
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NAME

analyzedti - Takes Analyze format raw data and outputs DT data in Analyze format

SYNOPSIS

analyzedti <4dimageroot | imagelist> <output root> <schemefile> [-bgmask <file> -bgthresh <value> -inversion <value> -outputdatatype <type>]

DESCRIPTION

This script is a wrapper that takes Analyze input and outputs the following Analyze images:

excode.hdr (exit codes for the reconstruction)

lns0.hdr   (log of the mean S(0) in each voxel)
dxx.hdr    (component dxx of diffusion tensor)
dxy.hdr    (component dxy of diffusion tensor)
dxz.hdr    (component dxz of diffusion tensor)
dyy.hdr    (component dyy of diffusion tensor)
dyz.hdr    (component dyz of diffusion tensor)
dzz.hdr    (component dzz of diffusion tensor)
dl1.hdr    (Largest  eigenvalue of the tensor)
dl2.hdr    (Middle   eigenvalue of the tensor)
dl3.hdr    (Smallest eigenvalue of the tensor)
fa.hdr     (Fractional anisotropy)
tr.hdr     (Trace of the diffusion tensor)
rd.hdr     (Radial diffusion: average of the two smallest eigenvalues)

Other statistics may be computed in addition to the above output. See OPTIONS. As well as the Analyze output, the tensors and the eigen decompositions are also stored in Camino format.

The output root is prepended onto the above file names. If the output root is a directory (for example, "./"), then include a trailing directory separator.

The default data type of each output image is 64-bit big-endian double. This may be changed with the -outputdatatype option.

The input can either be a 4D Analyze file or a text file containing a list of 3D Analyze images, in the format described in analyze2voxel(1). The 3D images are assumed to be be in the same directory as the text file, unless the -imageprefix option is used.

The script expects a scheme file in SI units, see camino(1).

In addition to the Analyze images, two Camino files are produced:

dt.B${type} (diffusion tensors)
dt_eig_sys.B${type} (diffusion tensor eigen systems)

These files can be used as input to other Camino programs.

SPM SCALING

For input: the data is scaled according to the SPM scale fields in the Analyze header. Scaling is not applied if the scale slope is 0 (which would result in a zero image).

For output: The SPM "scale" field in the Analyze header is set to 1E12 by default in the headers d??.hdr and tr.hdr. This allows easy visualization of the tensor elements, eigenvalues, and trace in units of 10^6 mm^2 / s in MRICro (and other programs that use SPM's scale field). The associated values in the .img files are NOT scaled, and remain in the units of the scheme file. The header scale factor can be manually set by using the -hdrscale option.

EXAMPLES

Read the 4D Analyze DWI file DW.hdr, scheme file EPI.scheme, and output images to the dtimg directory:

analyzedti DW.hdr ./dtimg/ EPI.scheme

Do the same thing, but run a nonlinear tensor fit and set all voxels with S(0) < 100 to background:

analyzedti DW.hdr ./dtimg/ EPI.scheme -bgthresh 100 -inversion 2

OPTIONS

The first three arguments are required. Additional options include

-bgmask <file>: A brain / background binary mask. See modelfit(1). The associated option -maskdatatype is also allowed.
-bgthresh <value>: Threshold on the unweighted signal, voxels below value will be marked as background. See modelfit(1).
-inversion: The type of diffusion tensor calculation. The default is a linear fit, the same as the default for modelfit. Any diffusion-tensor reconstruction is allowed, including RESTORE and its associated options. See modelfit(1). Multi-tensor reconstruction is not supported by this script.
-imageprefix <prefix>: If the imagelist is not in the same directory as the data files it describes, then specify the directory with this option, including a trailing directory separator char.
-outputdatatype: Sets the output data type of the images. Must be one of: char, short, int, float, long, double.
-vodata: Outputs the raw data, arranged in voxel order, as big-endian floats. This is the default input data type for Camino programs that expect raw data.
-gzip: Compresses output of Camino data files and .img files.
-hdrscale <scale>: Sets SPM scale field in the Analyze header to scale. Default is 1E12.
-md: Computes the mean diffusivity (md = tr / 3).
-rd: Computes the radial diffusivity (rd = [l2 + l3] / 2).
-ra: Computes the relative anisotropy.
-2dfa: Computes the fractional anisotropy of the 2D cross section of the tensor, which has eigenvalues l2 and l3.
-cl: Computes the linearity statistic, see dtshape(1).
-cp: Computes the planarity statistic, see dtshape(1).
-cs: Computes the spherical statistic, see dtshape(1).

AUTHORS

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

This document was created by man2html, using the manual pages.
Time: 02:07:11 GMT, December 04, 2017

Analyzedti