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Documentation: DTI-TK::TVtool

TVtool documentation

About TVtool

• TVtool is a command line utility for basic processing of tensor volumes, including
  • computing maps of tensor-derived scalar indices, such as fractional anisotropy (FA)
  • computing maps of tensor-derived vectors, such as the eigenvectors
  • computing maps of related tensors, such as the deviatoric tensors
  • computing arithmetic of two tensor volumes, such as addition

Basic Usage Pattern

• Specify an input tensor volume using the flag "-in" which takes the file name of the tensor volume as its argument

TVtool -in tensor.nii.gz

• Specify a processing task using additional flag(s), e.g. the flag "-fa" without any arguments is used to compute the FA map

TVtool -in tensor.nii.gz -fa

• Output file name is set to some default value based on the input file name (like the example above) but can be customized using the flag "-out" with an argument

List of Usages

To compute the map of fractional anisotropy (FA)

TVtool -in tensor.nii.gz -fa

To compute the map of trace (TR) (equal to 3 times the mean diffusivity)

TVtool -in tensor.nii.gz -tr

To compute the map of axial diffusivity (AD)

TVtool -in tensor.nii.gz -ad

To compute the map of radial diffusivity (RD)

TVtool -in tensor.nii.gz -rd

To compute the principal diffusion direction image

 TVtool -in tensor.nii.gz -pd

To compute the principal diffusion direction mapped into an RGB image

 TVtool -in tensor.nii.gz -rgb

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:) -out ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -ad ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -rd ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -tr ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -fa ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -norm ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -dnorm ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -tsp ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -dtsp ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -dydisp ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -dycoh ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -lps ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -eigs ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -pdmp ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -faThreshold ⚠ (:cell align=center:) double(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 0.2 ⚠ (:cellnr align=center:) -pd ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -rgb ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -faWeighting ⚠ (:cell align=center:) integer(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 1 ⚠ (:cellnr align=center:) -spd ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -reorient ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -trans ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -euler ⚠ (:cell align=center:) double(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -dev ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -dyadic ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -index ⚠ (:cell align=center:) integer(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 0 ⚠ (:cellnr align=center:) -scale ⚠ (:cell align=center:) double(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -add ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -subtract ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -mosaic ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -piece ⚠ (:cell align=center:) integer(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) 16 ⚠ (:cellnr align=center:) -aop ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -mask ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -nan ⚠ (:cell align=center:) flag ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -print ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -vsm ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -sm ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:cellnr align=center:) -SMOption ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) EDS, ED, DDS, EDS or GDS ⚠ (:cellnr align=center:) -replacement ⚠ (:cell align=center:) string(s) ⚠ (:cell align=center:) N ⚠ (:cell align=center:) ⚠ (:tableend:)