xfm2def

xfm2def [options] input.xfm def_vol.mnc

xfm2def takes an input transform input.xfm that can consist of a series of concatenated transforms in a single xfm file and converts this into a single deformation volume that is output as def_vol.mnc. Note that the output is not a transform file itself, you can then make use of this volume in a MINC transform by creating an .xfm file as such:

MNI Transform File

Transform_Type = Grid_Transform;
Displacement_Volume = def_vol.mnc;

The output resolution and sampling of the deformation grid must be specified or a default size will be used. (100x100x100 1mm steps centred around the origin).

-help

Print summary of command-line options and exit.

-version

Print the program's version number and exit.

-verbose

Print out extra progress information while running.

-clobber

Overwrite any existing output file

-xnelements nx

Number of elements along the xspace dimension.

-ynelements ny

Number of elements along the yspace dimension.

-znelements nz

Number of elements along the zspace dimension.

-xstep xstep

Step between voxels along the xspace dimension.

-ystep ystep

Step between voxels along the yspace dimension.

-zstep zstep

Step between voxels along the zspace dimension.

-xstart xstart

Position of centre of first voxel along the xspace dimension.

-ystart ystart

Position of centre of first voxel along the yspace dimension.

-zstart zstart

Position of centre of first voxel along the zspace dimension.

-xdircos x1 x2 x3

Direction cosines for the xspace dimension.

-ydircos y1 y2 y3

Direction cosines for the yspace dimension.

-zdircos z1 z2 z3

Direction cosines for the zspace dimension.

Andrew Janke

Copyright © 2010 Andrew Janke - a.janke@gmail.com