Usage tips

  • The space bar toggles between colors shown or not shown. On the image window when an activation overlay is present, hitting the space bar will remove the color overlay and also reveal the grayscale bar for adjusting the grayscale image. On the graph window, the color bar will toggle GLM display colors on/off.
  • The tab key toggles between the default pixelated images or smoother-appearing images that are created by linear interpolation across the zoom factor. When smoothing is used, the images, color activation maps, overlays, and pixelated crosshairs all are interpolated. For zoom=1, there is no effect.
  • When default windowing of intensity levels is poor due to non-uniform coils or to outliers (especially in maps), draw a rectangular overlay over the region of interest (top left to bottom right while holding down the right mouse key) and hit "i".
  • A good way to inspect motion is to select two different time points (anywhere in the series) on the graph window (left mouse button click) and then hit "l" to toggle back and forth to the last time point.
  • Although fMRI data files usually have the spatial resolution values correct, the time resolution often is wrong. To change the time resolution to 3 seconds in a NIFTI file, do this in jip: set time-step 3 [return] read input.nii [return] write output.nii [return] bye [return]. Alternatively, you can change the time resolution using a text editor on a jip-formatted header file, which is ASCII, and then write the file into NIFTI using jip.
  • Use z/Z to decrease/increase zoom factors. If the program balks at increasing the zoom factor again due to limitation on the screen size, it will instead zoom in on the images using integer factors. Pan across images using the crosshairs.
  • Window sizes can also be changed by using the mouse to drag the bottom corner and manually resize the window. However, window sizes are restricted to values consistent with integer “zoom” factors. The size of the screen used for the display window is assumed to be somewhat smaller than the actual screen size, because the actual screen typically uses some space for menus on panels associated with unix/Linux. If you think that a larger application window might fit onto your screen, and you find that “Z” will not increase the size more, try dragging the window corners.
Joseph B. Mandeville, Athinoula A. Martinos Center for Biomedical Imaging at MGH/MIT/Harvard