jip-display (aka xd) is designed as a unix/linux program that requires that all necessary files are specified on the unix line at startup. The general syntax
xd [file1] [file2] ... [options]
When multiple image files are specified, they must match in (x,y,z) dimensions.
options that affect the display format
-y flip the y orientation of images up/down (X11 versus openGL standard, DICOM vs.
NIFTI); each instance of -y flips the images again, enabling incorporation of this option
into an alias.
-z [integer] set the beginning zoom factor
-x [integer] set the beginning number of panels in x
-m [integer] start in mosaic format with this many panels (<= # of slices)
-3 start in tri-plane display mode
overlays & wire frames
-o [file] read a file containing a list of overlays
-w [file] read a file containing a list of wireframes
________ options above this point also can be used in "jip-align" _________
loading colormaps
-a [file] load color map file using linear scale
-P or -p [file] load color map file using log scale; assumes -log_10(p) in file
-A [file] load color map using log scale; assumes -ln(p) in file
General Linear Model (GLM)
-g [file] read 1st-level fMRI GLM control file
-G [file] read 1st-level fMRI PET SRTM control file
-r [file] read 2nd-level (random effects model) GLM
-T or -S display T or S files with -G option
-e [file] input file excluded from GLM
-t don't include time information: just load GLM maps