Brain Imaging & Analysis Center

-create surface SURFNAME COLOR IMIN IMAX FLAG DOTSIZE EDGEFLAG EDGEVAL
-create plane WIDTH NPIXS FLAG
-create corner
-create sphere
-create paint PAINTNAME SURFNAME FLAG IMIN IMAX THICKNESS SMOOTHFLG
-create paint FLAG IMIN IMAX THICKNESS SMOOTHFLG
-create paint PAINTNAME label SRCFILE LABELFILE CTABFILE
-create paint PAINTNAME annot SRCFILE

The CREATE command is used to create a new data set.

Create SURFACE
This will sample intensity values in the current image volume to create a new 3-D surface data.

• FLAG - The FLAG argument lets you specify sampling options:
  • 1 - binary: use low bit (maskbits) as voxel values for creating surface
  • 2 - fastsurf: flag this as a FAST surface (coarser 2nd surface version within data set)
  • 4 - ROI: only include image voxels within current active ROI
  • 010 - growonly: just set flag (bit=4) on image voxels that would be included on surface
  • 020 - colors: set surface color to image color (default if COLOR not specified)
  • 040 - height: set Z value to intensity
  • 0100 - notriangles: vertices only, don't create triangles
  • 0200 - nosmooth: don't smooth vertex locations across neighboring triangles (smooth is default)
  • 0400 - boundary: create surface at all image intensity boundaries
  • 01000 - objects: make different colors different objects
  • 02000 - gtdepth: reverse depth flag; show points with higher (usually lower) Z values
  • 010000 - noshow: create surface data but don't create surface display window
  • 040000 - append: append to existing data set
  • 0100000 - outside: include voxels ⇐ IMIN or >= IMAX (usually only >= IMIN and ⇐ IMAX)
• DOTSIZE -
• EDGEFLAG:
  • 0 - don't include edge of ROI as surface points
  • 1 - treate edge of ROI as part of surface
  • >=2 - process edges in EDGEFLAG/2 passes (not sure why)
• EDGEVAL - surface edge value flag (default=2)

Create PAINT
This will sample intensity values in the current image volume to create a 'paint' overlay for existing 3-D surface data. The inputs are the image volume (current data set) and surface (previous data set). Names for paint and surf can be omitted

 -create paint PAINTNAME SURFNAME FLAG IMIN IMAX THICKNESS
 	create PAINTNAME for SURFNAME from intensities in IO_IN volume
	SURF is previous window by default
 -create paint FLAG IMIN IMAX THICKNESS
 	names of paint and surf can be omitted
 -create paint PAINTNAME label SRCFILE LABELFILE CTABFILE
	create PAINTNAME by combining SRCFILE LABELFILE CTABFILE
 -create paint PAINTNAME annot SRCFILE
	??

FLAG:	1	MKPT_MAKEVTX
		2	MKPT_NMLOUT	
		4	MKPT_ZEROS
	  010	MKPT_FILTERED - paint filtered values from window			
	  020	MKPT_NMLFIRST
	  040	MKPT_NOFRAMELIMIT

Note: If the input voxel data set (io) has multiple time points (up to 50), a separate paint “frame” will be created for each time point. If NT > 50 you must specify the NOFRAMELIMIT flag to get multiple frames, otherwise it only generates 1 frame (assuming a movie is not really wanted).

See Also:
fScan Home, fScan Manual, CmdLineOptions, Manual Help