Hello Tara,

It is not quite clear to me what you mean by taking the FreeSurfer mask to AFNI/SUMA.

I think the first thing you want to do is map that region to standard mesh surfaces. To do so, you will need to run on the fsaverage directory in FreeSurfer:
@SUMA_Make_Spec_FS -sid fsaverage -GIFTI
This will create a SUMA directory with fsaverage surfaces in orignal and standard-mesh forms.

Convert the cluster from FreeSurfer to GIFTI (.gii) format with something like: mris_convert

At this stage the cluster is readable by SUMA and can be displayed on the fsaverage surfaces. Check that this is the case and that all is well aligned.

Next we map that cluster onto standard mesh surfaces so that this cluster can be mapped to any of your subjects' surfaces.

Map the cluster.gii dataset onto standard mesh surfaces with SUMA's SurfToSurf. The standard-mesh surfaces are created for you by @SUMA_Make_Spec_FS

The resultant standard-mesh cluster, call it std.cluster.gii, can be used on any of your subject's standard mesh surfaces, as long as they are of the same mesh density.

You can also take the surface cluster from standard meshes to volume masks for use in AFNI using 3dSurfToVol.

I hope this helps get you going.

cheers,
Ziad