resamplemod(1) General Commands Manual resamplemod(1)
NAME
resamplemod - Turn a model perpendicular to Z axis and resection
SYNOPSIS
resamplemod [options] input_file output_file
DESCRIPTION
Resamplemod can be used to resample or resection a model of fiber tra-
jectories after rotating it so that the fibers run parallel to the Z
axis. The program can find the mean trajectories of the fibers them-
selves and then rotate the model to bring the mean trajectory parallel
to the Z axis, or one can supply a special contour to indicate the axis
that should be rotated to the vertical. Contours will be resampled at
single pixel intervals so that the model will have the correct dimen-
sions when it has the same Z scale factor as the original model.
OPTIONS
Resamplemod uses the PIP package for input (see the manual page for
pip) The following options can be specified either as command line
arguments (with the -) or one per line in a command file or parameter
file (without the -). Options can be abbreviated to unique letters;
the currently valid abbreviations for short names are shown in paren-
theses.
-input (-i) OR -InputFile File name
Input model file.
-output (-o) OR -OutputFile File name
Output model file.
-exclude (-e) OR -ExcludeObjects List of integer ranges
Objects to exclude from resampling; for example, closed contour
objects.
-direction (-d) OR -DirectionObjects List of integer ranges
Objects to use to determine mean direction of fibers. The
default is to use all of the objects; enter a list to use a sub-
set of objects, or just a single object number if you have cre-
ated a special object with a contour to indicate the direction.
-main (-m) OR -MainAxis Integer
Dominant axis along which fibers run (1 = X, 2 = Y, or 3 = Z.)
The default is the Z axis (3), which is appropriate for serial
section models. A different axis is generally needed for a
model from a tomogram. If the model was built on a tomogram
loaded into 3dmod with flipping (-Y), enter a number that refers
to the axis that was seen in 3dmod.
-skip (-s) OR -SkipInversion Integer
Do not invert contours that go from high to low along the main
axis. The default is to reorder contours if necessary so that
they go from low Z to high Z in the output model. With an entry
of 1, it will not invert contours in the output model, but it
will still invert the ones being averaged when determining the
mean direction of fibers so that they go in the same direction
as the main axis. This means that the main axis will end up with
a positive Z component no matter what direction the contours
being averaged point. To retain the direction in the contours
being averaged and make the main axis end up with a negative Z
component, enter a -1 so that the contours will not be inverted
for averaging either. If this option is used, it is essential
that all the contours being averaged point in about the same
direction, since any pointing in the opposite direction will not
be fixed.
-param (-p) OR -ParameterFile Parameter file
Read parameter entries as keyword-value pairs from a parameter
file.
-help (-h) OR -usage
Print help output.
-StandardInput
Read parameter entries from standard input.
HISTORY
Written by David Mastronarde, 2000; incorporated in IMOD 9/5/03
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.11.0 resamplemod(1)