Hi, Veronica-

Re. Q1: Well, I am not aware of a method for changing the meshes in that way. I guess BrainStorm has some specific meshes that it produces, then? I don't know if MapIcosahedron would translate that to a standard mesh; I have never used that program.

Re. Q2: Yes, you can convert your ROI points into a surface dataset, and then apply that as a mask.
In the AFNI Bootcamp data set, there is a demo of doing part of this. If you don't have a copy of the Bootcamp demo dataset, then you can download it as described here (and under any setup instructions):
[afni.nimh.nih.gov]

curl -O [afni.nimh.nih.gov]
tar xvzf CD.tgz
cd CD
tcsh s2.cp.files . ~
cd ..

There is a relevant script/example in the subdirectory: AFNI_data6/FT_analysis/FT/SUMA/, called "run.roi2dset". That provides an example of converting an ROI that was drawn using SUMA into a surface dset (*.niml.dset), which can be applied to a mask; the command is:

ROI2dataset -prefix $prefix.lh.niml.dset -input $prefix.lh.niml.roi

where "$prefix" is a variable that could be whatever you have chosen (in the script, the default is "tuna", charmingly enough); you could also specify either of the hemisphere meshes equivalently ("rh" as well as the chosen "lh").
The script goes on to demonstrated creating a volume from that new surface dset; but your question is about using that dset as a mask. You can apply it as a mask to another dset DSET2.lh.niml.dset via:

3dcalc -a $prefix.lh.niml.dset -b DSET2.lh.niml.dset -expr 'step(a)*b' -prefix OUTPUT.lh.niml.dset

--pt