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tend - Man Page

diffusion image processing and analysis

Synopsis

tend COMMAND [OPTION]...

Description

tend(1) is a command-line interface to much of the functionality in “ten”, a C library for diffusion image processing. Ten is one library in the “Teem” collection of libraries. More information about Teem is at http://teem.sf.net. A checkout of Teem source is available via:

svn co https://svn.code.sf.net/p/teem/code/teem/trunk teem

Long-term maintenance of this software depends on funding, and funding depends on being able to document who is using it for what. If tend(1) or Ten has helped in your research, including for simple one-off experiments or mundane data hacking, the developers of Teem would love to know. There are multiple ways of communicating this. In your publications, consider adding a line such as this in the Acknowledgments: Data processing performed with the tend tool, part of the Teem toolkit available at http://teem.sf.net. Alternatively, please email glk@uchicago.edu and briefly describe how Teem software has helped in your work. Please also consider joining the teem-users mailing list. This is the primary forum for feedback, questions, and feature requests.

Like unu(1), another Teem command-line binary, it is often useful to chain together invocations of tend(1) with pipes, as in the following, which estimates tensors from DWIs, takes a slice of the tensor volume, computes the standard RGB colormap of the principal eigenvector, and then quantizes it to an 8-bit PNG:

tend estim -i dwi.nhdr -B kvp -knownB0 true \
 | tend slice -a 2 -p 30 \
 | tend evecrgb -c 0 -a cl2 -gam 1.2 \
 | unu quantize -b 8 -min 0 -max 1 -o z30-rgb.png

Options

Commands

Each of the following has a corresponding man page: for example, tend-about(1) for “tend about”.

tend about

Information about this program and its use

tend grads

Calculate balanced gradient directions for DWI acquisition

tend epireg

Register diffusion-weighted echo-planar images

tend bmat

Calculate B-matrix given gradient directions

tend estim

Estimate tensors from a set of DW images

tend sim

Simulate DW images from a tensor field

tend mfit

Estimate models from a set of DW images

tend mconv

Convert from one model to another

tend msim

Simulate DW images from an image of models

tend make

Create DT volume from confidence and eigensystem

tend avg

Average across tensor volumes

tend helix

Generate twisting helical tensor field

tend sten

Calculate structure tensors from a scalar field

tend glyph

Generate postscript or ray-traced renderings of 3D glyphs

tend ellipse

Generate postscript renderings of 2D glyphs

tend anplot

Graph anisotropy metric in barycentric coords

tend anvol

Apply an anisotropy metric to a DT volume

tend anscale

Scale the anisotropic component of the tensors

tend anhist

Generate barycentric histograms of anisotropy

tend triple

Compute volume of shape triples

tend tconv

Convert between different shape triples

tend point

Describe everything about one sample in a DT volume

tend slice

Slice 3D tensors to get slab/image of 3D/2D tensors

tend norm

Normalize tensor size

tend fiber

Fiber tractography, from one or more seeds

tend eval

Calculate one or more eigenvalues in a DT volume

tend evalpow

Modify shape by raising eigenvalues to some power

tend evalclamp

Modify shape by clamping eigenvalues in some range

tend evaladd

Modify shape by adding a constant to all eigenvalues

tend evalmult

Modify shape by multiplying eigenvalues by a constant

tend log

Calculates logarithm of the tensor

tend exp

Calculates exp() of the tensor

tend evec

Calculate one or more eigenvectors in a DT volume

tend evecrgb

Make an RGB volume from an eigenvector and an anisotropy

tend evq

Quantize directions of diffusion

tend unmf

Applies and removes the measurement frame

tend expand

Converts masked non-redundant tensor images to redundant

tend shrink

Converts a 9-value DT volume to a 7-value DT volume

tend bfit

Non-linear least-squares fitting of b-value curves

tend satin

Generate a pretty synthetic DT volume

See Also

gprobe(1), ilk(1), mrender(1), miter(1), nrrdSanity(1), overrgb(1), puller(1), unu(1), vprobe(1), tend-about(1), tend-anhist(1), tend-anplot(1), tend-anscale(1), tend-anvol(1), tend-avg(1), tend-bfit(1), tend-bmat(1), tend-ellipse(1), tend-epireg(1), tend-estim(1), tend-eval(1), tend-evaladd(1), tend-evalclamp(1), tend-evalmult(1), tend-evalpow(1), tend-evec(1), tend-evecrgb(1), tend-evq(1), tend-exp(1), tend-expand(1), tend-fiber(1), tend-glyph(1), tend-grads(1), tend-helix(1), tend-log(1), tend-make(1), tend-mconv(1), tend-mfit(1), tend-msim(1), tend-norm(1), tend-point(1), tend-satin(1), tend-shrink(1), tend-sim(1), tend-slice(1), tend-sten(1), tend-tconv(1), tend-triple(1), tend-unmf(1)

Referenced By

gprobe(1), ilk(1), miter(1), mrender(1), nrrdSanity(1), overrgb(1), puller(1), tend-about(1), tend-anhist(1), tend-anplot(1), tend-anscale(1), tend-anvol(1), tend-avg(1), tend-bfit(1), tend-bmat(1), tend-ellipse(1), tend-epireg(1), tend-estim(1), tend-eval(1), tend-evaladd(1), tend-evalclamp(1), tend-evalmult(1), tend-evalpow(1), tend-evec(1), tend-evecrgb(1), tend-evq(1), tend-exp(1), tend-expand(1), tend-fiber(1), tend-glyph(1), tend-grads(1), tend-helix(1), tend-log(1), tend-make(1), tend-mconv(1), tend-mfit(1), tend-msim(1), tend-norm(1), tend-point(1), tend-satin(1), tend-shrink(1), tend-sim(1), tend-slice(1), tend-sten(1), tend-tconv(1), tend-triple(1), tend-unmf(1), unu(1), vprobe(1).

April 2021