Example commands are shown for Windows but can also be used on OS X or linux. The 'fgbl' or 'fg3' executables can be used instead of 'fgrt'.
Build your hair (or accessory) mesh to match the base head mesh of the model set (tri and quad facets only). For the FaceGen 'Animate' model set the base head mesh is:
~/Animate/Head/HeadHires.tri
(Where ~ is your model set directory). And its base texture image is:
HeadHires.png
Convert to a mesh format you can work with, for example:
> fgbl mesh convert HeadHires.tri HeadHires.obj
And use this as a guide for your hair. Do not move/scale/rotate it. If you'll be using FaceGen for rendering, it does support texture image transparency, however to avoid rendering artifacts avoid intersecting polys.
Once finished, export to Wavefront OBJ and convert your hair mesh to FaceGen TRI format:
> fgbl mesh convert hairBig.obj hairBig.tri
If you've defined morph targets (aka blendshapes) for your hair you can add them too:
> fgrt morph create hairBig.tri hairBig_morph.obj d "Even Bigger"
Create an EGM (shape statistics) file for it:
> cd ~/Animate
> fg3t ssm InternalBaseFace.tri -fv HeadHires_neck_seam.tri hairBig.tri
Save the texture image for your hair in a recognized format (PNG, JPG, BMP, GIF, TIF, TGA), for example:
hairBig.png
If you want it to appear in Modeller or 3D Print you must also create label for it:
> echo "Big Hair" > hairBig.txt
Now copy your hair files to the parts directory you want them to appear in, for example:
~/Animate/Hair/hairBig.tri
~/Animate/Hair/hairBig.egm
~/Animate/Hair/hairBig.png
~/Animate/Hair/hairBig.txt