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fScan Reference Manual, Chapter 2 (CmdLineOptions): addroi

ROI -- Create new Regions of Interest


  • -roi POINT [NAME] x y z
  • -roi BLOCK [NAME] x0 y0 z0 nx ny nz
  • -roi BLOCK [NAME] x0 y0 nx ny
  • -roi BLOCK [NAME] x0 nx
  • -roi CIRCLE [NAME] x0 y0 z0 rad
  • -roi CIRCLE [NAME] x0 y0 rad
  • -roi CIRCLE [NAME] x0 y0 z0 radx rady radz
  • -roi ARROW [NAME] x0 y0 z0 x1 y1 z1
  • -roi ARROW [NAME] x0 y0 x1 y1
  • -roi ARROW [NAME] x0
  • -roi CLUSTER refimage flag name

For adding new ROIs:

ROI's can be added to the current data set by explicitly specifying the ROI type, location, and size. The list above shows the various ROI types and how they are specified. The meaning of he arguments is:

  • NAME - specify a name for this ROI (no spaces or punctuation)
  • X0,Y0,Z0 - specify the starting location of the ROI as upper left corner of the first slice. The default origin is 0,0,0.
  • NX,NY,NZ - specify the size of the ROI. The default size is 1x1x1 (i.e. a point) if X0,Y0,Z0 are specified, otherwise it is the entire volume.
  • RAD,RADX,RADY,RADZ - specify radii for circular ROIs
  • COLOR - specify color for ROI (24-bit RGB value)

The RX type of ROI (when implemented) creates a slice prescription ROI on the current data set based on slice orientation in REFIMAGE.

The CLUSTER type ROI assumes that the current data set is an ROI mask image (in which regions are defined by voxels with the same intensity value). The CLUSTER command uses the input mask image to create an ROI list (name=NAME) of CLUSTER type ROIs where each cluster is defined by its mask value. For each CLUSTER, the center-of-mass location and the radius along the 3 principal axes are stored. By default, the new ROI list is attached to the input mask data set.

  • REFIMAGE, find peak intensity value and voxel location.
  • FLAG: (no values yet)
  • NAME: name of ROI list. If omitted, the list is linked to input mask images.

See Also:

fScan Home,
fScan Manual,
Manual Help

jvs/fscan/manual/chapter2/addroi.txt · Last modified: 2015/06/06 19:25 by voyvodic