Content-type: text/html Manpage of tractstatimage

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. 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

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