startup options for jip-display

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. If no options are provided (“xd &”), then it will look for a file named “.display” on the current directory and use those options, so that you can return to the directory at any time and bring up the analysis without needing to enter a long command line (if you have created “.display”). As an example, each of the time model programs will create a default file that contains the simple line “jip-display -t [file name]”. You then can alter that file with an editor. E.g., 

                jip-display -t glm.dat -S -3 -Y -e /template/name.nii -o /template/overlay-list.dat

help options

-h or -H          Get help, either the short version (-h) or the long version (-H).

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, facilitating an alias (right panel).

-Y                      Swap the orientation of Y vs Z plane; use this for most primate templates

-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

-L [label file]      read an image volume containing integer labels at each voxel. There also must exist

                         a second file with an extension of “.txt” to associate each voxel index with a label.

________ 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

Time models (e.g., GLM)

-t  [file]             load time-model from a control file, where the first line specifies the model type

-g  [file]             read 1st-level fMRI GLM file (old method; preserved temporarily for compatibility)

-G  [file]            read 1st-level PET SRTM control file (old method)

-r [file]               read 2nd-level random effects model (old method)

-T or -S            display T or S files with options -t, -g, -G, -r

-e [file]              input file excluded from time series analysis model

-n                     don't include time information: just load time-model maps

-N                    don’t load maps, but include time data

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