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. The first line contains the dimensions of the space; overlays will be loaded into the time series space, the anatomical space, or both depending upon whether dimensions match the spaces.
dimensions 80 64 32
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
The default file name is “.ovl" for reading/writing overlays, but menu entries enable overlays to be written with user-specified names as voxel lists like above or as bitmaps using the NIFTI format.
Lists of overlays or wire frames
Overlays can be grouped into lists that are specified in files and loaded from the command line, from menus, or as part of an anatomical template directory. Below is an example overlay list. The first two entries (short name and file specification) are required, whereas the color is optional; generally, it’s simpler to let the program choose the color.
putamen /cluster/petmr/jbm/template-1x1x1/putamen.ovl
postput /cluster/petmr/jbm/template-1x1x1/post-putamen.ovl
antput /cluster/petmr/jbm/template-1x1x1/ant-putamen.ovl
caudate /cluster/petmr/jbm/template-1x1x1/caudate.ovl green