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tractstatimage

Section: User Commands (1)
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NAME

tractstatimage - Computes images based on statistics from streamline tracts.

SYNOPSIS

tractstatimage [options]

DESCRIPTION

This program is an extension to tractstats that combines statistics from streamline tracts into an image.

The tract statistic is computed for each tract using the methods described in tractstats(1). The statistic from each tract is combined into a single value according to the image statistic, which is specified by the -imagestat option. The image statistic in each voxel in the image is computed from the tract statistics of either all tracts seeded in that voxel (default behaviour) or all tracts that intersect the voxel.

IMAGE STATISTICS

The image statistic is either the mean, minimum, maximum, median, or variance of the tract statistics in each voxel. By default, each voxel of the image only contains the values from tracts that are seeded in that voxel. This option can be changed with the -countintersect option.

COUNT INTERSECT

With the -countintersect option, the value from each tract is added to all voxels intersected by the tract.

EXAMPLES

Output the maximum of the mean FA values (one value per input tract) in each voxel.

cat tracts.Bfloat | tractstatimage -scalarfile fa.nii.gz -outputroot tract_meanFA_max \
-tractstat mean -imagestat max

OPTIONS

-scalarfile <file>: Path to an image containing the scalars. 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 "mean", "min", "max", "median", "var", "sum", "length", "endpointsep". This is the statistic computed for each tract. All options except "length" and "endpointsep" refer to image statistics, and should be accompanied by a scalar file.
-header <hdr>: Used to define image space when a scalar file is not used, eg when the tractstat is "length".
-imagestat <stat>: One of "mean", "min", "max", "median", "var". This is the statistic computed on the tract statistics in each voxel.
-countintersect: Each tract statistic is placed in all voxels intersected by the tract, rather than just in the seed voxel.
-outputroot <root>: Output of the image statistic is to root.[ext], which is defined by the input header.

AUTHORS

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

BUGS

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

Tractstatimage