Content-type: text/html
Manpage of tractstatimage
tractstatimage
Section: User Commands (1)
Index
Return to Main Contents
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. If the image statistic is mean or variance, each tract statistic
is weighted by the length of the streamline segment that traverses the voxel.
EXAMPLES
Mask all voxels in the image that are not background or CSF.
mask -bgthresh 50 -csfthresh 400 -inputfile voxelOrder.Bfloat
-schemefile A.scheme -outputdatatype short > nocsf.img
analyzeheader -initfromheader rawData.hdr -datatype short > nocsf.hdr
Track from each voxel in the brain, and compute an image of the mean tract FA.
track -seedfile nocsf.hdr -inputmodel dt -inputfile tensors.Bdouble
-anisthresh 0.1 | tractstatimage -scalarfile fa.hdr -outputroot tract_meanFA
Use the wild bootstrap to generate 10 streamlines from each voxel, and output the maximum
of the 10 tract mean FA values in each voxel.
track -inputfile voxelOrder.Bfloat -inputmodel bootstrap -schemefile A.scheme -bgmask nocsf.hdr -anisthresh 0.1 -iterations 10 -seedfile nocsf.hdr -wildbsmodel dt | tractstatimage -scalarfile fa.hdr -outputroot tract_meanFA_max -imagestat max
OPTIONS
- -inputmodel <model>
-
The input model for the tracts, either "raw" or "voxels". Default is "raw".
- -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". This is the statistic
computed for each tract. All options except "length" refer to image statistics.
- -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.
- -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. If the streamlines have been processed by
procstreamlines, they will already be resampled to 0.1 mm unless otherwise specified.
- -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.
- -outputroot <root>
-
Output of the image statistic is to root.[hdr,img].
AUTHORS
Philip Cook <camino@cs.ucl.ac.uk>
SEE ALSO
tractstats(1), track(1), procstreamlines(1)
BUGS
This is new code, the implementation / interface may change.
Index
- NAME
-
- SYNOPSIS
-
- DESCRIPTION
-
- IMAGE STATISTICS
-
- COUNT INTERSECT
-
- EXAMPLES
-
- OPTIONS
-
- AUTHORS
-
- SEE ALSO
-
- BUGS
-
This document was created by
man2html,
using the manual pages.
Time: 02:06:54 GMT, December 10, 2011