ortho

PURPOSE

ortho takes a set of images representing a 3-D volume, and generates a set of images that are orthogonally oriented to the original slicing direction.

TYPICAL USAGE

ortho -images images.lst    \
-input xy_images/ \
-xz_images \
-output xz_images/

COMMAND LINE OPTIONS

-every integer_stride

the number of pixels between successive output images; for example, a stride of 100 would request that only every 100th plane be output

-format scanf_style_format_string

the format for extracting the z coordinate from an image name;  this should contain a %d conversion specifier that will place the image's z coordinate into an int

-image_list images.lst

specifies a file which contains the list of images to process; the format of this file is just a list of image names, one per line.  If additional text occurs on a line, the additional text will be ignored.  If the line is blank or it begins with a '#' character, the entire line will be ignored.

-input directory/

specifies the directory from which to read images

-memory  limit_in_megabytes

instructs the program to use at most the given number of megabytes for storing intermediate data structures

-output directory/

specifies the directory into which output image files will be placed

-x minX[-maxX]

specifies the range of x values to include in the cross-sectional output images

-xz_images

if this option is given, the cross-sectional output images will each be in the x-z plane.  Each output image will have a unique y value associated with it.

-y minY[-maxY]

specifies the range of y values to include in the cross-sectional output images

-yz_images

If this option is given, the cross-sectional output images wil each be in the y-z plane.  Each output image will have a unique x value associated with it.

-z minZ[-maxZ]

specifies the range of z values to include in the cross-sectional output images

 

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