TractTool documentation

About TractTool

TractTool is a command line utility for identifying, from an input set of fibers, a subset that either intersects or avoids specified regions-of-interest (ROIs).

Basic usage pattern

Specify :

• an input tractography volume using the flag "-in", which takes the file name of the .vtk fiber volume as its argument

Output:

• number of fibers in this volume

TractTool -in tracts.vtk

Example of Output

Reading the input tract ... Done in 0.58s
Number of input fibers = 52615

-roi is used to define a specific region of interest (a binary image called ROI.nii.gz), through which a set of fibers go The output file name is set using the flag "-filter.
The value of the ROI can be specified using -label''', the default value being 1. ROI.nii.gz can then contain several ROIs corresponding to different labels.
In the following case, we are just interested in the fibers that intersect the region with the value equal to 10.

TractTool -in tracts.vtk -filter output.vtk -roi ROI.nii.gz -label 10

-inclusion is to be used to find the fibers that do NOT go through a specific ROI. In this case, set this flag to 0.
The following example outputs a tractography volume output.vtk that contains all the fibers from tracts.vtk, except the ones intersecting the ROI with value 10.

TractTool -in tracts.vtk -filter output.vtk -roi ROI.nii.gz -label 10 -inclusion 0

-nifti is used to transform a .vtk tractography volume into a nifti binary image.
The specifics of the nifti image output.nii.gz can be defined using -target followed by an exisiting nifti image, here called target.nii.gz.

TractTool -in tracts.vtk -nifti output.nii.gz -target target.nii.gz

List of options

⚠ (:table border=3 cellpadding=5 cellspacing=3 align=center:) ⚠ (:head:) specification ⚠ (:head:) type ⚠ (:head:) required ⚠ (:head:) default ⚠ (:cellnr align=center:) -in ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) Y ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -filter ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -roi ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -label ⚠ (:cell align=center:) integer(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 1 ⚠ (:cellnr align=center:) -inclusion ⚠ (:cell align=center:) integer(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 1 ⚠ (:cellnr align=center:) -nifti ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -target ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -view ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -overlay optional overlay volume for tract viewing ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -mode tract rendering mode: 0 for non-interactive and 1 for interactive (default) ⚠ (:cell align=center:) integer(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 1 ⚠ (:cellnr align=center:) -useTube tract rendering option: 0 for curve-based and fast (default) and 1 for tube-based and slow ⚠ (:cell align=center:) integer(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 0 ⚠ (:cellnr align=center:) -zoom tract rendering zoom factor ⚠ (:cell align=center:) double(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 1.5 ⚠ (:cellnr align=center:) -png number of screenshots to save in non-interactive viewing mode ⚠ (:cell align=center:) integer(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 20 ⚠ (:cellnr align=center:) -prefix prefix for screenshots ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -annotate ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -source DTI volume to retrieve diffusion features for tract annotation ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:tableend:)