SingleTensorFT documentation

About SingleTensorFT

SingleTensorFT is a command line utility for generating white matter tractography of the brain from a DTI volume.

Basic Usage Pattern:

Specify :

• an input tensor volume using the flag "-in", which takes the file name of the tensor volume as its argument
• a white matter mask using the "-seed", to which the tractography will be limited
• the name of the output file using "-out"

SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk

List of Usage

-label is an option to modify if the value of the binary nifti image is different from 1, in the following case, it is 10

SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -label 10 -out tensor.vtk

-minLength and -maxLength determine the minimum and maximum sizes of the fibers. In the following case, the tractography will only encompass the fibers that measure between 100 and 150mm

SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -minLength 100 -maxLength 150 -out tensor.vtk

-minFA and maxAngle are two stopping criteria. The following example will perform the tractography until very low FA values (0.05) and high angles (with the possibility of tracts turning at right angles)

SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -minFA 0.05 -maxAngle 90 -out tensor.vtk

-stepSize defines the length of a step through the diffusion tensor field. The default value is 0.5 but if one is interested in long tracts only, increasing this value increases the speed of the process.

SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -stepSize 2 -out tensor.vtk

-upsample can be modified if the initial resolution of the tensor image is very low and the user wants a denser tractography. In the following case, the fiber bundles are 3 times denser than what they would have been with the default value

SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -upsample 3 -out tensor.vtk

List of options

⚠ (:table border=3 cellpadding=5 cellspacing=3 align=center:) ⚠ (:head:) specification ⚠ (:head:) type ⚠ (:head:) required ⚠ (:head:) default ⚠ (:head:) unit ⚠ (:cellnr align=center:) -in ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) Y ⚠ (:cell align=center:) ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -seed ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) Y ⚠ (:cell align=center:) ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -label ⚠ (:cell align=center:) integer(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 1 ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -minLength ⚠ (:cell align=center:) double(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 10 ⚠ (:cell align=center:) mm ⚠ (:cellnr align=center:) -maxLength ⚠ (:cell align=center:) double(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 1000 ⚠ (:cell align=center:) mm ⚠ (:cellnr align=center:) -minFA ⚠ (:cell align=center:) double(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 0.15 ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -maxAngle ⚠ (:cell align=center:) double(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 45 ⚠ (:cell align=center:) degrees ⚠ (:cellnr align=center:) -stepSize ⚠ (:cell align=center:) double(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 0.5 ⚠ (:cell align=center:) mm ⚠ (:cellnr align=center:) -upsample ⚠ (:cell align=center:) integer(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 1 ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -out ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) Y ⚠ (:cell align=center:) ⚠ (:cell align=center:) ⚠ (:tableend:)