startup options

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.

loading overlays

-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 "" [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

Joseph B. Mandeville, Athinoula A. Martinos Center for Biomedical Imaging at MGH/MIT/Harvard