Brain Imaging & Analysis Center

Version1:
Specify surface data options. The meaning of the arguments depends on the MODE. The MODE can be entered as a number or (more commonly) as a text word. When entering the mode as a text word the quotation marks are optional. The default MODE value is -1 (no MODE specified). The meaning of the MODE is as follows:

• <default> - SURFFILE is a filename specifying a surface data file in 3D coordinates (see Format note below). Each new surfaces specified with the default MODE will appear in the same window.
  • FLG - Used to specify display options:
    • 1 - Display fast surface only (if available)
    • 2 - Display vertices as dots, don't draw triangles
    • 4 - Display triangles as wire frame (edges only, don't fill)

Note: if INFILE (fScan's first argument) is a SURFACE file a -surface option with no SURFFILE can be used to specify display flags for INFILE (e.g. fscan surf1 -surface 1).

• new - A new window will be created for this surface; otherwise the surface is drawn in the same window as the previous surface. NEW is assumed for the first surface drawn. This is the first -surface option; in this case the option is used to specify the remaining arguments for the first surface. (Entering 0 for the MODE is the same as 'new'.) FLAG has the same meaning as for the default mode (see above).
• paint - The SURFFILE argument is a PAINT file (see below) rather than a new surface. The paint file is added as a coloring overlay to the most recently specified surface.
• paintall - Like 'paint' MODE, except that the PAINT parameters can be applied to any surface, not just the previous surface.
• window - This can be used to set global parameters for a surface window. If WINNUM is specified it is the number of the surface window of interest (0 is first), otherwise the most recent window of the most recently spefifed surface will be assumed. The NAME parameter will be used as the window title. The FLAG parameter sets global flags for the window, as:
  • 1 - Display fast surface only (if available)
• newpaint - The SURFFILE argument is the name of a PAINT file to be created during this session.
• create - Create a new surface and save it in NEWFILE. The input data set (INFILE – see 'fscan help') is a 3-D image volume and the output data will be a 3-D surface file.
  • COLOR - The COLOR argument can be used to specify the color of the surface data. It can be entered as a 24-bit RGB value explicitly, or by using one of the following color names:
    • black
    • white
    • gray
    • red
    • green
    • blue
    • yellow
    • orange
    • purple
    • cyan
    • pink
    • brown
  • IMIN, IMAX - IMIN and IMAX are intensity thresholds; each input voxel with intensity >= IMIN and <= IMAX will be included in the surface.
  • FLAG - The FLAG argument is a bit flag used to specify options:
    • 010 - draw one side of surface only (no back)
    • 020 - set vertex colors from voxel intensities)
    • 040 - vertex height (Zvalue) is based on voxel intensity
    • 0100 - no triangles (save vertices only, don't create triangles)
    • 0200 - no smoothing (don't smooth voxel surface cubes)
    • 0400 - no border (includes all voxels, not just border voxels)
• output - Allows for rendered views to be saved to disk. In this case FILESPEC is a filename prefix for creating TIFF files (e.g. “output view” would produce view001.tif, view002.tif …). Actually writing views to files requires toggling the window's save flag interactively using 'T' (e.g. “1T” to start, “0T” to stop).
• PAINTFILE - File(s) containing surface parameter data, 1 value per vertex, to paint on the surface. Multiple files can be listed.

In each surface window there is a separate transformation matrix for each surface, as well as a global tranformation matrix for the window as a whole. These can be manipulated interactively.