Overlays & Wire Frames

Overlay files are ASCII text files containing either 3 or 4 entries per line. The first 3 entries are the (x,y,z) indices that define one voxel in 3-dimensional space. The optional 4th entry is a weighting factor between 0 and 1, with a default value of 1. The weight provides a means to account for partial voluming; the weight is generated whenever a wire frame is filled in the display or alignment programs by down-sampling from high resolution to the lower resolution of the voxel space.

               26 57 21 0.886693
               27 57 21 0.993509
               28 57 21 0.998889                This is a portion of an example file.
               29 57 21
               30 57 21
               31 57 21
               32 57 21 0.623892
               40 57 21 0.0739146
               
41 57 21 0.872825
Overlays are associated with voxel indices, so they are specific to a given matrix size. The size of the matrix is not stored in the overlay files. Errors will be reported when voxel indices fall outside these limits whenever overlays are applied to images.

The default file name is .ovl for reading/writing overlays, but this file can be renamed and included in a list of pre-defined overlays (see "-o" option on startup).



Wire Frames

Wire frame files are ASCII text files containing 4 entries per line. The first 3 entries are the (x,y,z) coordinates define control points for Bezier curves.  The 4th entry is a "pen down" (1-n) or "pen up" (0) flag. The "pen down" flag encodes the color of the wire frame, and an entry of 0 in this column terminates a wire frame segment. If the last point of the wire frame matches the first point, it is a closed wire frame. Closed wire frames can be filled by the display programs and turned into overlays.

               -12.500000 23.900002 6.000000  1
               -14.299999 22.500000 6.000000  1
               -15.500000 21.700001 6.000000  1
               -16.500000 20.900002 6.000000  1
               -17.500000 20.099998 6.000000  1        This is a portion of an example file.
               -17.500000 19.099998 6.000000  1
               -16.500000 18.700001 6.000000  1
               -14.500000 20.099998 6.000000  1
               -13.099998 21.099998 6.000000  1
               -11.299999 22.099998 6.000000  1
               -11.500000 22.500000 6.000000  1
               -11.900002 22.900002 6.000000  1
               -12.500000 23.900002 6.000000  0

Wire frames are associated with voxel spatial coordinates, so they are independent of matrix size or resolution. This provides a nice way to span different spaces with a region of interest.

The default file name is .wire for reading/writing wire frames, but this file can be renamed and included in a list of pre-defined overlays (see "-w" option on startup).


Lists of overlays or wire frames

Overlays or wire frames can be grouped into lists that are specified in files and loaded from the unix/linux command line at run time.  Below is an example for overlays. Lists of wire frames follow the same format.

putamen /cluster/petmr/jbm/template-1x1x1/putamen.ovl          red
postput /cluster/petmr/jbm/template-1x1x1/post-putamen.ovl   yellow
antput  /cluster/petmr/jbm/template-1x1x1/ant-putamen.ovl      blue
caudate /cluster/petmr/jbm/template-1x1x1/caudate.ovl           green


Joseph B. Mandeville, Athinoula A. Martinos Center for Biomedical Imaging at MGH/MIT/Harvard