Brain Imaging & Analysis Center

usage: 'NAME',mode,value,param,flag T

The surface objects commands ('T') allow you to select and manipulate 3D objects (e.g. fiber tracks).

NAME: the meaning of this argument varies depending on the MODE

• modes 0-2: ROI mask image (default is previous window)
• mode 5: object param subset name
• mode 7: new data set name

The MODE argument controls what type of object command to perform.
MODE:

• 0 - turn off PARAM bit(s) for objects in ROI
  • NAME - ROI mask image (default is previous window)
  • VALUE - index of ROI region (see FLAG)
  • PARAM - bit value in object parameter (default=1)
  • FLAG:
    • 0 - set all objects
    • 1 - VALUE is ROI num if ROIs, else intensity (default)
    • 2 - VALUE is intensity value
    • 4 - include only objects with endpoint in ROI (default includes objects intersecting ROI)
• 1 - turn on PARAM bit(s) for objects in ROI
  • NAME, VALUE, PARAM, and FLAG same as mode 0.
• 2 - turn off PARAM for active objects not passing through ROI
  • NAME, VALUE, PARAM, and FLAG same as mode 0.
• 3 - in/activate objects based on parameter value (ObjectParam) stored with each
  • PARAM - mask flag
    • 0 - in/activate where (ObjectParam & VALUE) is non-zero.
    • >0 - in/activate where (ObjectParam & VALUE) == PARAM.
  • FLAG - If 0 inactivate, else activate
• 4 - in/activate objects based on number of data points
  • PARAM - Control flag
    • 0 - objects with at least VALUE points
    • 1 - objects with less than VALUE points
    • FLAG - If 0 inactivate, else activate
• 5 - set/clear param for objects where ??
  • NAME - object param subset name
• 7 - save active objects as new data set
  • NAME - new data set name
• 8 - set OBJFLAG to VALUE
  • If VALUE is omitted this displays current OBJFLAG value
• 9 - set OBJMASK to VALUE
  • If VALUE is omitted this displays current OBJMASK value
• 10 - set NUMFASTOBJECTS to VALUE
  • If VALUE is omitted this displays current NUMFASTOBJECTS value
  • If NUMFASTOBJECTS is positive, that many fibers will be displayed in Fast mode
• 11 - generate object parameter values by sampling associated images at each object vertex
  • NAME: reference image (default is prev window)
  • VALUE:
    • 1 - FA values (1/vtx)
    • 2 - ADC values (1/vtx)
    • 3 - track length values (mm), 1/track
    • 4 - length (npts) histogram of active objects
• 12 - generate new data set with objects as avg of all active objects connected to each ROI (1/ROI). This assumes active objects already seed selected.
  • NAME: ROI image (default is all active objects)
  • VALUE: Averaged values (bitmask)
    • 1 - # of source objects (1/obj)
    • 2 - length of tracks mm (1/obj) + StDev
    • 4 - total average param values (1/obj) + SD
    • 8 - average param 1/mm (1/vtx)
    • 16 - stdev for each 1/vtx param avgs
    • 32 - # objects along path (1/vtx)
  • PARAM: Selection options:
    • 1 - selected tracks connected to each ROI
    • 2 - selected tracks connecting all pairs of ROI's (default)
    • 4 - include tracks passing through target ROI (default is endpt in ROI)
• 20 - set NOBJECTS to VALUE
• 21 - set NCOORDS to VALUE

Notes:
Track param bit 1 means track is active
ROIVALUE - index value in ROI mask

• 0 - all voxels
• >0 - voxels with value ROIVALUE

Examples:

Turn off all objects:
  0,0,1,0T
Turn on only objects with at least 50 points:
  4,50,0T
Turn off objects with less than 100 points:
  4,100,1,0T
Turn on only objects with at least 20 points that pass through ROI in data set "seed"
  4,20,0T
  0,0,1,0T
  "seed"1,1T
  

See Also:
fScan Home, fScan Manual, KeyCmds, SurfKeys, Manual Help