AFNI program: Vecwarp
Output of -help
Usage: Vecwarp [options]
Transforms (warps) a list of 3-vectors into another list of 3-vectors
according to the options. Error messages, warnings, and informational
messages are written to stderr. If a fatal error occurs, the program
exits with status 1; otherwise, it exits with status 0.
-apar aaa = Use the AFNI dataset 'aaa' as the source of the
transformation; this dataset must be in +acpc
or +tlrc coordinates, and must contain the
attributes WARP_TYPE and WARP_DATA which describe
the forward transformation from +orig coordinates
to the 'aaa' coordinate system.
N.B.: The +orig version of this dataset must also be
readable, since it is also needed when translating
vectors between SureFit and AFNI coordinates.
Only the .HEAD files are actually used.
-matvec mmm = Read an affine transformation matrix-vector from file
'mmm', which must be in the format
u11 u12 u13 v1
u21 u22 u23 v2
u31 u32 u33 v3
where each 'uij' and 'vi' is a number. The forward
transformation is defined as
[ xout ] [ u11 u12 u13 ] [ xin ] [ v1 ]
[ yout ] = [ u21 u22 u23 ] [ yin ] + [ v2 ]
[ zout ] [ u31 u32 u33 ] [ zin ] [ v3 ]
Exactly one of -apar or -matvec must be used to specify the
-forward = -forward means to apply the forward transformation;
*OR* -backward means to apply the backward transformation
-backward * For example, if the transformation is specified by
'-apar fred+tlrc', then the forward transformation
is from +orig to +tlrc coordinates, and the backward
transformation is from +tlrc to +orig coordinates.
* If the transformation is specified by -matvec, then
the matrix-vector read in defines the forward
transform as above, and the backward transformation
is defined as the inverse.
* If neither -forward nor -backward is given, then
-forward is the default.
-input iii = Read input 3-vectors from file 'iii' (from stdin if
'iii' is '-' or the -input option is missing). Input
data may be in one of the following ASCII formats:
* SureFit .coord files:
lines of text ...
int x y z
int x y z
In this case, everything up to and including the
count is simply passed through to the output. Each
(x,y,z) triple is transformed, and output with the
int label that precedes it. Lines that cannot be
scanned as 1 int and 3 floats are treated as comments
and are passed to through to the output unchanged.
N.B.-1: For those using SureFit surfaces created after
the SureFit/Caret merger (post. 2005), you need
to use the flag -new_surefit. Talk to Donna about
N.B.-2: SureFit coordinates are
x = distance Right of Left-most dataset corner
y = distance Anterior to Posterior-most dataset corner
z = distance Superior to Inferior-most dataset corner
For example, if the transformation is specified by
-forward -apar fred+tlrc
then the input (x,y,z) are relative to fred+orig and the
output (x,y,z) are relative to fred+tlrc. If instead
-backward -apar fred+tlrc
is used, then the input (x,y,z) are relative to fred+tlrc
and the output (x,y,z) are relative to fred+orig.
For this to work properly, not only fred+tlrc must be
readable by Vecwarp, but fred+orig must be as well.
If the transformation is specified by -matvec, then
the matrix-vector transformation is applied to the
(x,y,z) vectors directly, with no coordinate shifting.
* AFNI .1D files with 3 columns
x y z
x y z
In this case, each (x,y,z) triple is transformed and
written to the output. Lines that cannot be scanned
as 3 floats are treated as comments and are passed
through to the output unchanged.
N.B.: AFNI (x,y,z) coordinates are in DICOM order:
-x = Right +x = Left
-y = Anterior +y = Posterior
-z = Inferior +z = Superior
-output ooo = Write the output to file 'ooo' (to stdout if 'ooo'
is '-', or if the -output option is missing). If the
file already exists, it will not be overwritten unless
the -force option is also used.
-force = If the output file already exists, -force can be
used to overwrite it. If you want to use -force,
it must come before -output on the command line.
Vecwarp -apar fred+tlrc -input fred.orig.coord > fred.tlrc.coord
This transforms the vectors defined in original coordinates to
Talairach coordinates, using the transformation previously defined
by AFNI markers.
Vecwarp -apar fred+tlrc -input fred.tlrc.coord -backward > fred.test.coord
This does the reverse transformation; fred.test.coord should differ from
fred.orig.coord only by roundoff error.
Author: RWCox - October 2001
++ Compile date = May 22 2013
This page auto-generated on
Thu May 23 09:55:13 EDT 2013