reorient

• purpose
• usage
• examples
• comments
• error messages

Purpose:

Rotates image files (.img files) 90 or 180 degrees and/or mirrors them along the major axes. This allows gross prealignment of images so that automated registration has a reasonable chance of success.

This program can also be used as a null operation that converts an input file into the output format used to compile AIR

A .air file describing the transformation can be saved

Usage:

reorient input output [options]

options (note unusual syntax, optional arguments do not start with '-'):

[o]

grants permission to overwrite output

[f output-air-file-name]

saves a .air file describing the transformation with input as the reslice file and output as the standard file

[x]

mirror along x axis

[y]

mirror along y axis

[z]

mirror along z axis

[xy]

rotate +90 degrees to interchange x and y axes

[yx]

rotate -90 degrees to interchange y and x axes

[xz]

rotate +90 degrees to interchange x and z axes

[zx]

rotate -90 degrees to interchange z and x axes

[yz]

rotate +90 degrees to interchange y and z axes

[zy]

rotate -90 degrees to interchange z and y axes

[xx]

rotate 180 degrees around x axis

[yy]

rotate 180 degrees around y axis

[zz]

rotate 180 degrees around z axis

where the following definitions apply:

input

the name of the input file

output

the name of the output file

output-air-file-name

the name of the .air file to save

Examples:

• This will load the file mri.img, rotate it 180 degrees around the x axis, rotate it 90 degrees to interchange the y and z axes, mirror it along the z axis and then overwrite the input files mri.img and mri.hdr with the result.

• If the AIR package is compiled to generate 16 bit images, the 8 bit file 8bitmri will be loaded as saved as a 16 bit file called 16bitmri.

• If foreign16bitmri is generated on another platform that requires byte swapping to use on the current platform, this command will generate a byte swapped version called swapped16bitmri

Comments:

• There are 48 different ways a file can ultimately be oriented, and half of these are 3D mirror images of the other half. Many combinations of operations will generate the same results. Unless you have already worked it out with other files from the same source, you will probably want to use some guided trial and error combined with image display to sort out how the files should be oriented. Be careful that you don't end up with a file that is a mirror image of the file that you are trying to register to. Don't assume that there are any conventions for the 3D representation of images from different sources. Don't forget that reversing the order of the planes in a data set converts it to its 3D mirror image.

Error messages: (alphabetical by case)

A file name for saving the .air file must follow argument 'f'

• provide the required file name

Cannot parse argument ____

• check syntax

Don't use minus sign (-) with this program

• omit '-' from optional arguments

output file cannot be named ____

• choose a different file name