AirReslicewarp

AirReslicewarp is a Java gui wrapper for the AIR 5.2.1 (Roger Woods, UCLA) reslice_warp program.
Reslice_warp takes .warp files and uses the information that they contain to load the corresponding image file and generate a new, realigned file. This program can also take alternate reslice image files and apply the same transformations to them.
For more information about the AIR package see the AIR 5 homepage.
AIR documentation for the reslice_warp program.

Invocation

java AirReslicewarp

This starts up the java interpreter and runs the AirReslicewarp application. You need to have set up your environment for java in order for this to work. AirReslicewarp is also available in the AirToolChest, GlobalWorkbench and GlobalDesktop computing environments.

java  AirToolChest

java  GlobalWorkbench

java  GlobalDesktop

AirReslicewarp window

The command line version of this program can apply one transformation to one alternate image file. Using this gui, you can apply N transformations (from a directory or file list) to 1 or N alternate images, or apply 1 transformation to N alternate images (from a directory or file list). Below is the matrix of possible uses of this program.

Input warp file(s)	Alternate reslice images(s)	Output image(s)	Description
1	0	1	apply one transformation to one original image
n	0	n	apply N transformations to N original images
1	1	1	apply one transformation to one alternate image
1	n	n	apply one transformation to N alternate images
n	1	n	apply N transformations to one alternate image
n	n	n	apply N transformations to N alternate images respectively

Information to be entered

Input Warp file(s)
Select the input .warp file(s)/directory/filelist.
Output Image directory/file
Output directory where the resliced images will be placed. The filenames will be the same as in .warp files.
Output File prefix
Optional file prefix that will be prepended to the output filenames.
Options...
Bring up advanced options.

Options... Use intensity scale factor
Specify the intensity scale factor.
Alternate reslice file(s)
Alternate reslice analyze (.hdr .img) image file(s)/directory/filelist. If checked, the number of reslice files must be N, where N is 1, or the same number as the number of selected .warp files, or any number if only 1 warp file was selected. All reslice file(s) must be spatially equivalent (same voxel sizes and dimensions) to the default reslice file specified in the .warp file.
Options... Interpolation model
Select the model that should be used when reslicing the image.
Options... half-window X width
Half-window X width
Options... half-window Y width
Half-window Y width.
Options... half-window Z width
Half-window Z width

Last updated Wed Jan 16 14:14:38 EST 2002