jip-display (a.k.a. xd) is a general 4-D display package with integrated GLM options. Navigation of the GUI uses arrows and mouse buttons with function dependent upon the location of the cursor.

Startup example

Load multiple files with identical voxel dimensions (but potentially multiple time points). Load 3 gray-scale files, one P-value map, 2 linear activation files (e.g., signal change, fractional anistropy, …), and a list of “overlays” that define regions of interest:

                                          xd [gray1] [gray2] [gray3] -P [PValue1] -a [activation1] -a [activation2] -o [overlay-list.dat]


There are 4 dimensions (x, y, z, time), so there are 8 arrows: up, down, left, right, in (<), out (>), future (+), past (-).

Use these arrows to navigator through the data set while the cursor is located on the image data.  Note that standard keyboards have some of these arrows in cap positions, but you can these keys without caps: <>-+ ,.-=

Arrows are used contextually in the GUI based upon cursor location. When the cursor is on an image, they move the crosshairs.  When crosshairs are removed but an overlay (region of interest) exists, they move the overlay. On the colorbar or graph, they adjust the range.  On a text field, they might toggle through options. Use the "?" help function to interrogate a region of the window for more information.


There are 2 active buttons: left and right. On a 3-button mouse, buttons 2 and 3 are equivalent. If there is a scroll wheel, it moves in/out of the screen in 3-plane mode, and it also can adjust colorbar or graph ranges. When the cursor is on text buttons, refer to the information area on the bottom of the window for a guide as to the meaning of the buttons. Mouse button selection on text fields generally have single-stroke keyboard alternatives. Position the mouse cursor on a text field and look to the information area (lower left) for help.

display modes

There are 2 basic display modes: mosaic and tri-planar display. Two switch between these displays, either use the text field on the right side above the image window, or hit "3".

In 3-plane mode, the Y-Z display orientation can be switched to accommodate rodent (x-y coronal) or primate (x-y axial) data.

In mosaic mode, the configuration of panels can be changed (top right text field), the number of slices in the mosaic can be set or selected (use "#" text on top right), and three different orientations can be selected (coronal, sagital, axial).

overlays & wire frames

There are two ways to define regions of interest. "Overlays" are associated with voxel indices and are the basis for averages across image regions (e.g., for time series analysis). "Wire frames" are based upon spatial coordinates and are useful for defining defining overlays (from a closed wire frame) and for visualization. Wire frames translate across different resolutions; overlays do not. Overlays and wire frames can be pre-loaded in lists on start-up using "-o" and "-w" options, or they can be defined interactively. Closed wire frames can be turned into overlays by filling them. Overlays cannot be turned into wire frames. Currently, wire frames can only be defined on x-y image planes.

time models

One of the best features of this display package is the integrated time models for neuro-imaging data. Models include a first-level general linear model (GLM) analysis for fMRI data, a GLM implementation of the simplified reference tissue model (SRTM) with time-varying changes in "binding potentials”, a second-level random-effects of mixed-effects model for summarizing first-level GLM analyses, and fitting functions for performing common fits of MRI data (e.g., T1, T2, ADC, DTI, …).

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