jip-align (aka align) is designed as a unix/linux program that requires that all necessary files are specified on the unix line at startup. The general syntax is
align [file for individual] -t [file for template] ... [options]
options that affect the display format
The alignment and display package share many startup options.
Refer to the jip-display startup page.
-o file read a file containing a list of overlays
wrapping of images in x,y,z during alignment
-w or -W 110 means wrap in x & y but not z (this is DEFAULT)
-I [file] read Initializations from file using same syntax as output
file type "align.com" [e.g., shifts, rotatations, ...]
-l or -L [string] Each character in the string corresponds to one of the 12 Linear
affine parameters; any character but "0" means the parameter
will be adjusted. Use this in scripts to turn off alignment of some parameters when a
prior alignment step has been performed (e.g., the 1st stage uses good anatomical
images, and the 2nd stage uses images with matched slices and no slice adjustment).
-r or -R [value] Set the rolloff filter to "value", which is an integer specifying the fraction of the field of
view (1/value) for a smoothing kernel