Hi Rick,
Here is a 3dVol2Surf cludge that I tried but it does not seem to work, any idea why?:
3dVol2Surf -spec lh.mesh160.white.dup.spec -sv SurfVol_Alnd_Exp+orig -grid_parent functional+orig\[3,6,9] -map_func ave -f_keep_surf_order -f_pn_mm 2 -oob_index -1 -oob_value 0 -no_headers -out_1D 3dVol2Surf.functional.1D
where -spec mesh160.white.dup.spec is:
# SUMA_MapIcosahedron-main spec file for lh.mesh160
#define the group
Group = lh.mesh160
#define various States
StateDef = mappedWhite
StateDef = mappedWhite2
NewSurface
SurfaceFormat = ASCII
SurfaceType = FreeSurfer
FreeSurferSurface = lh.mesh160_mappedWhite.asc
MappingRef = SAME
SurfaceState = mappedWhite
EmbedDimension = 3
NewSurface
SurfaceFormat = ASCII
SurfaceType = FreeSurfer
FreeSurferSurface = lh.mesh160_mappedWhite2.asc
MappingRef = SAME
SurfaceState = mappedWhite2
EmbedDimension = 3
and lh.mesh160_mappedWhite2.asc and lh.mesh160_mappedWhite2.asc are the same file. This seems like it should have worked by "growing" lh.mesh160_mappedWhite2.asc 2 mm. However, the output does not seem to differ from using only one surface:
3dVol2Surf -spec lh.mesh160.white.spec -sv SurfVol_Alnd_Exp+orig -grid_parent functional+orig\[3,6,9] -map_func mask -oob_index -1 -oob_value 0 -no_headers -out_1D 3dVol2Surf.functional.1D
I think anyone with bad gray/csf contrast either from not so great scans or from studies where this isn't enough time to collect multiple volumes would benifit from being able to apply nomals...
Many thanks,
Jeremy
