DiffeoRegister performs diffeomorphic (non-linear) image registration from the command-line.
Running the program with option --help produces the following output:
Usage: DiffeoRegister [options] fixedImage movingImage1 [movingImage2
movingImage3 ... ]
-?,--help Displays this help message.
-a,--affine <txrtp> Apply the affine transform <txrtp>
calculated using the Register
tool, rather than performing an
initial affine registration.
-b,--bias-correct Turns on bias field correction.
-be,--bending-energy <energy-param> Set the bending energy
regularisation parameter. Default:
0.5
-C,--cost <func> Registers using the specified cost
function <func> (default:
Normalised correlation). <func>
must be one of: "rmsdiff" (RMS
difference) "normcorr" (Normalised
correlation).
-det,--determinant Specifies that an image of the
Jacobian determinant is to be
written to disk, with file name
suffix _Det.
-div,--divergence <divergence-param> Set the divergence regularisation
parameter. Default: 0.5
-f,--movie-frames <n> Set the number of movie frames in
the output image that shows the
transition betweeen the moving
image(s) and the fixed image. By
default, a movie will not be
created.
-h,--half-way Specifies that 'half-way'
co-registered images should be
created for both the fixed and
moving images (with prefix hw).
-intra,--intra-subject Specifies that this is
intra-subject registration, rather
than inter-subject.
-l,--ftol <tol> Set the fractional tolerance for
convergence (default: 0.001).
-le,--linear-elasticity <elasticity-param> Set the linear elasticity
regularisation parameter. Default:
0.5
-M,--roi-mask <roi-file> Mask the fixed image using an ROI
mask.
-m,--mask <image> Mask the fixed image using an
image mask.
-me,--membrane-energy <energy-param> Set the membrane energy
regularisation parameter. Default:
0.5
-n,--n-time-steps <n> Set the number of integration time
steps. Default: 16; min=2, max=64.
-na,--no-affine Do not estimate an initial affine
transform before performing
non-linear registration.
-nr,--no-rescale Do not rescale the intensities of
the moving image(s) to match those
of the fixed image.
-p,--interpolation <type> Sets the type of interPolation
used to create the final
transformed image (default:
Linear). <type> must be one of:
"nn" (Nearest neighbour) "linear"
(Linear) "sinc" (Sinc).
-r,--read <image> Specifies that deforming vector
fields are to be read from an
image on disk, and applied to the
moving image.
-ri,--read-invert <image> Specifies that deforming vector
fields are to be read from an
image on disk, and their inverse
applied to the moving image.
-s,--single Performs single-resolution
registration (not
multi-resolution, which is the
default).
-t,--threshold <number> Mask the fixed image using an
intensity threshold.
-v,--verbose Turns on verbose reporting to
System.out.
-ver,--version Prints the software build version,
and exits.
-w,--write Specifies that deforming vector
fields are to be written to an
image on disk, with file name
suffix _V.
-X,--max-samples <n> Set the maximum number of samples
for any image dimension. Images
with a number of samples greater
than this will be downsampled
before registration. Default: 256;
min=32, max=256. Must be a power
of 2.
-x,--max-iter <integer> Set the maximum number of
iterations at each resolution
(default: 100).