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 theseed voxel.
-outputroot <root>
Output of the image statistic is to root.[ext], which is defined by the input header.