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tractstats

Section: User Commands (1)
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NAME

tractstats - Computes statistics from streamline tracts.

SYNOPSIS

tractstats [options]

DESCRIPTION

This program computes statistics from streamline tracts, either using the tracts themselves or using the values of a scalar image along the streamline.

TRACT SCALAR STATISTICS

Tract scalar statistics are computed by evaluating a scalar image along the length of the streamline, and returning some function of the scalar values. The scalar image should be defined in the same space as the streamlines.

Some definitions

l - the length of the streamline.

S(T) - a vector of scalar values computed by evaluating the scalar image at each point
in T.

S(T) - a vector of scalar values computed by evaluating the scalar image at each point in T.

The tract statistic may be either the mean, sum, minimum, maximum, median, or variance of S(T), the values at each point along the streamline. The option "meanvar" returns both the mean and variance.

Interpolation in the context of this program means linearly interpolating the image data. The image intensity is evaluated at each point in T.

The assumption here is that the points on T are approximately evenly sampled. If T was defined using a fixed step size algorithm (-interpolated passed to track) then the distance between points will be equal, which is optimum for estimating the mean image value along T. If the step size is variable, for example in FACT, then the points on T are not evenly sampled, which introduces a bias. Resampling to a smaller step size in procstreamlines will reduce this bias (which may be small to begin with).

NON IMAGE-BASED STATISTICS

Non image-based statistics use information embedded in the streamlines themselves. Currently, this includes "length", the path length along the streamline, and "enspointsep", the euclidean distance between the streamline end points.

OUTPUT

The output is the tract statistic for each streamline sent to the image, in the order in which they are read from the input.

EXAMPLES

Track in an ROI and get the mean FA along each tract.

cat tracts.Bfloat | tractstats -tractstat mean -interpolate -scalarfile fa.hdr > tractMeanFA.Bdouble

Get the minimum mean diffusivity along the tracts

cat tracts.Bfloat | tractstats -tractstat min -interpolate -scalarfile md.hdr > tractMinMD.Bdouble

OPTIONS

-scalarfile <file>

Path to an image containing the scalar values. The image should be defined in the same physical space as the streamlines.

-header <hdr>

Used to define image space when a scalar file is not used, eg when the tractstat is "length".

-interpolate Use tri-linear interpolation to find the image value at each point on the streamline. If this is not specified, the default behaviour is to use nearest-neighbour interpolation.

-tractstat <stat>

One of "none", "mean", "min", "max", "sum", "median", "var", "meanvar", "length", "endpointsep". All statistics except "meanvar" and "none" produce one value per
streamline. "meanvar" produces [mean, var] for each streamline, and "none" outputs the value of the scalar image at each point along the streamline.

AUTHORS

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

BUGS

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Time: 02:07:11 GMT, December 04, 2017

Tractstats