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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


  T - a streamline containing points T(1)...T(N).


  l - the length of the streamline.


  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. By default, raw streamlines are resampled to a resolution of 0.1 mm, which will reduce the bias. Voxel lists are not resampled by default; the image intensity is sampled once at the centre of each voxel intersected by the streamline.

 

NON IMAGE-BASED STATISTICS

Non image-based statistics use information embedded in the streamlines themselves. Currently, the only statistic of this kind is the streamline length, l.

 

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 SubjectA.oneDT.Bdouble | track -inputmodel dt -seedfile subAROI.hdr 
  -interpolate vectors -stepsize 0.5 -anisthresh 0.1 | tractstats -tractstat mean 
   -interpolate -scalarfile fa.hdr > tractMeanFA.Bdouble

Get the minimum mean diffusivity along the tracts


  cat SubjectA.oneDT.Bdouble | track -inputmodel dt -seedfile subAROI.hdr 
  -interpolate vectors -stepsize 0.5 -anisthresh 0.1 | tractstats -tractstat min
   -interpolate -scalarfile md.hdr > tractMinMD.Bdouble

 

OPTIONS

-inputmodel <model>
The input model for the tracts, either "raw" or "voxels". Default is "raw".

-scalarfile <file>
Path to an image containing the scalar values. The image should be defined in the same space as the streamlines. The image dimensions are taken from the header.

-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". 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.

-resamplestepsize <size>
Resamples interpolated streamlines such that the maximum length between successive points is size mm. The default is to resample to 0.1 mm. Smaller resampling sizes sample the scalar image at a finer resolution, but increase computation time. Note that procstreamlines will also do this, so you can save some time by disabling resampling if you have passed the tracts through procstreamlines.

-noresample
Disables resampling of input streamlines. This is the default for voxel lists.

-voxeldims <x> <y> <z>
The x, y, and z dimension of each voxel, in millimetres. Not required if a scalar file is used, since the voxel dimensions are contained in the header. If a scalar file is not used, then this argument is required to convert streamlines in voxel format to physical space.

 

AUTHORS

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

 

SEE ALSO

tractstatimage(1), analyzedti(1), track(1), procstreamlines(1)

 

BUGS

This is new code, the implementation / interface may change.


 

Index

NAME
SYNOPSIS
DESCRIPTION
TRACT SCALAR STATISTICS
NON IMAGE-BASED STATISTICS
OUTPUT
EXAMPLES
OPTIONS
AUTHORS
SEE ALSO
BUGS

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Time: 02:06:54 GMT, December 10, 2011