Program name: 3dwarper

Function: Nonlinear registration between 3D high-resolution T1-weighted MR images of the brain.

Author: Babak A. Ardekani, Ph.D.

Reference: Ardekani BA, Guckemus S, Bachman A, Hoptman MJ, Wojtaszek M, Nierenberg J.

Usage:

3dwarper –sub subject –trg target [–iter N] [–R] [–u filename]

[–o filename] [–cubicspline] [–c] [–T filename] [–sd N] [–w N] [–s N] [-A]

Required arguments:

–sub subject

Specifies the image to be registered to the target image. subject is expected to be an image of type ‘short’ in ANALYZE format.

–trg target

Specifies the image to which the subject image is to be registered. target is expected to be an image of type ‘short’ in ANALYZE format.

Optional arguments:

–iter N

Specifies the number of multi-resolution levels. N must be an integer between 1 and 4. Default N=4.

–R

Performs an initial 6-parameter linear rigid-body registration before starting the non-linear registration process.

–u filename

Stores the displacement vector field in the specified filename. Default filename=object.wrp

–o filename

Stores the transformed (registered) object image in the specified filename. Default filename=Cobject.img

–cubicspline

The output transformed (registered) object image is generated using the cubic spline interpolation (default is trilinear interpolation).

–c

Approximates the displacement vector field as a truncated Fourier-Legendre series.

–T filename

Applies the linear transformation (4×4 matrix) specified in filename to the object image before starting the registration process.

–sd N

Specifies the degree of smoothing applied to the displacement vector field. Typically ranges between 4.0 to 12.0 mm (default = search window size minus 1 mm).

–w N

Correlation window size in voxels (default=5; minimum=3).

–s N

Search window size in voxels (default=5; minimum=3).

–A

When this option is specified, the program first goes through three resolution levels. It then computes an initial affine transformation based on the results and restarts the optimization process. Slightly more accurate registrations may be expected with this option.