AimsRegisterQNEstimate
    ----------------------

Affine registration by index minimization.

Options :

--test | -i | -t <string>
    Test image (to be registered).

--reference | -r <string>
    Reference image

--output | -o <string>
    Output motion.

[ --motion-init | -m <string> ]
    Input init motion.

[ --channel-reference | -cr <string> ]
    Channel to use if color image: r[ed], g[reen], b[lue], n[orm] (default)

[ --channel-test | -ct <string> ]
    Channel to use if color image: r[ed], g[reen], b[lue], n[orm] (default)

[ --points <string> ]
    Estimation points (in the reference image referential. (default: use all
    voxels. see also --stride)

[ --transformation | -tr <string> ]
    Transformation type: t[ranslation], r[igid], s[imilitude], a[ffine]
    (default: tra)

[ --optimizer | -op <string> ]
    Optimizer: p[owell], b[fgs], l[bfgs], n[ewton], t[rust-newton] (default :t)

[ --function | -f <string> ]
    Function to minimize: c[r] {correlation ratio}, m[i] {mutual information}
    (default: mi)

[ --regularize | -reg <string> ]
    Regularization term: 0 {none} (default), 1 {l1 norm}, 2 {l2 norm}

[ --pyramid <string> ]
    Pyramid mode: l[east square] {more precise} (default), m[oving average]
    {faster}

[ --stop <FLOAT> ]
    Stop criterion (default: 1E-5)

[ --trust <FLOAT> ]
    Trust radius (for newton mode) (default: 1.)

[ --stride <S32> ]
    Stride used to select reference points (only if --points is not used).
    (default: 1)

[ --exact-hessian | -eh <boolean> ]
    Do not approximate the Hessian matrix with Newton optimizer (default:
    false)

[ --level-start | -lb <S32> ]
    Pyramid level at which to start the registration (default: auto)

[ --level-stop | -le <S32> ]
    Pyramid level at which to end the registration (default: auto)

[ --level-incr | -li <S32> ]
    Increment between pyramid levels (default: auto)

[ --gc-init <string> ]
    Gravity center initialization w[eighted] (default), u[nweighted], n[one]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel | -d <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)