.TH XFM2DEF 1 "$Date: 2010-08-11 04:06:42 $" "" "MINC User's Guide"
.SH NAME
xfm2def \- convert a MNI transform file to a deformation volume

.SH SYNOPSIS
\fBxfm2def\fR\ [options] \fIinput.xfm\fR\ \fIdef_vol.mnc\fR

.SH DESCRIPTION
\fIxfm2def\fR takes an input transform \fIinput.xfm\fR 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 \fIdef_vol.mnc\fR. Note that the
output is not a tranform file itself, you can then make use of this volume in a
MINC tranform 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).


.SH OPTIONS
.TP
\fB\-help\fR
Print summary of command-line options and exit.
.TP
\fB\-version\fR
Print the program's version number and exit.
.TP
\fB\-verbose\fR
Print out extra progress information while running.
.TP
\fB\-clobber\fR
Overwrite any existing output file
.TP
\fB\-xnelements\fR\ \fInx\fR
Number of elements along the xspace dimension.
.TP
\fB\-ynelements\fR\ \fIny\fR
Number of elements along the yspace dimension.
.TP
\fB\-znelements\fR\ \fInz\fR
Number of elements along the zspace dimension.
.TP
\fB\-xstep\fR\ \fIxstep\fR
Step between voxels along the xspace dimension.
.TP
\fB\-ystep\fR\ \fIystep\fR
Step between voxels along the yspace dimension.
.TP
\fB\-zstep\fR\ \fIzstep\fR
Step between voxels along the zspace dimension.
.TP
\fB\-xstart\fR\ \fIxstart\fR
Position of centre of first voxel along the xspace dimension.
.TP
\fB\-ystart\fR\ \fIystart\fR
Position of centre of first voxel along the yspace dimension.
.TP
\fB\-zstart\fR\ \fIzstart\fR
Position of centre of first voxel along the zspace dimension.
.TP
\fB\-xdircos\fR\ \fIx1\ x2\ x3\fR
Direction cosines for the xspace dimension.
.TP
\fB\-ydircos\fR\ \fIy1\ y2\ y3\fR
Direction cosines for the yspace dimension.
.TP
\fB\-zdircos\fR\ \fIz1\ z2\ z3\fR
Direction cosines for the zspace dimension.

.SH AUTHOR
Andrew Janke

.SH COPYRIGHTS
Copyright \(co 2010 Andrew Janke - a.janke@gmail.com