tend-grads - Man Page
calculate balanced gradient directions for DWI acquisition
Synopsis
tend grads [-n <# dir>] [-i <grads>] [-seed <value>] [-step <step>] [-single] [-snap <interval>] [-jitter <jitter>] [-miniter <# iters>] [-maxiter <# iters>] [-minvelo <vel>] [-exp <exponent>] [-dp <potential change>] [-minimprov <delta>] [-minmean <len>] [-izv <insert>] [-o <filename>]
Description
Composites an RGBA nrrd over a background color (or image), after doing gamma correction, then quantizes to an 8-bit image. Actually, the input nrrd can have more than 4 values per pixel, but only the first four are used. If the RGBA nrrd s floating point, the values are taken at face value; if it is fixed point, the values interpreted as having been quantized (so that 8-bit RGBA images will act as you expect). When compositing with a background image, the given background image does not have to be the same size as the input image; it will be resampled (with linear interpolation) to fit.
Options
- -n <# dir>
desired number of diffusion gradient directions (int) default: “6”
- -i <grads>
initial gradient directions to start with, instead of default random initial directions (overrides “-n”); default: “”
- -seed <value>
seed value to used with airSrandMT() (unsigned int) default: “42”
- -step <step>
time increment in solver (double) default: “1.0”
- -single
instead of the default behavior of tracking a pair of antipodal points (appropriate for determining DWI gradients), use only single points (appropriate for who knows what).
- -snap <interval>
specifies an interval between which snapshots of the point positions should be saved out. By default (not using this option), there is no such snapshot behavior (int) default: “0”
- -jitter <jitter>
amount by which to perturb points when given an input nrrd (double) default: “0.1”
- -miniter <# iters>
min number of iterations for which to run the simulation (int) default: “0”
- -maxiter <# iters>
max number of iterations for which to run the simulation (int) default: “1000000”
- -minvelo <vel>
low threshold on mean velocity of repelling points, at which point repulsion phase of algorithm terminates. (double) default: “0.00001”
- -exp <exponent>
the exponent n that determines the potential energy 1/r^n. (double) default: “1”
- -dp <potential change>
low threshold on fractional change of potential at which point repulsion phase of algorithm terminates. (double) default: “0.000000001”
- -minimprov <delta>
in the second phase of the algorithm, when stochastically balancing the sign of the gradients, the (small) improvement in length of mean gradient which triggers termination (as further improvements are unlikely. (double) default: “0.00005”
- -minmean <len>
if length of mean gradient falls below this, finish the balancing phase (double) default: “0.0001”
- -izv <insert>
adding zero vector at beginning of grads (bool) default: “false”
- -o <filename>
file to write output nrrd to (string); default: “-”