Hello Jennine,

The standard mesh surfaces have an almost identical geometry to the original surfaces. If they seem out of alignment, it is probably because of different transforms in the surface volume.

You can visually check to see if the surfaces have indeed the same geometry this way (as usual, if these options are not available in your current suma, then it is time to update):

suma -i_ply STANDARD_MESH.ply -i_fs ORIGINAL_MESH.asc &
(use suma -help to learn about the new options above)

If you don't want to update now, you can also create your own spec file with quickspec and use suma -spec YOUR_SPEC.spec &.

Once you've loaded both surfaces into SUMA, open two views, one showing the original mesh, the other showing the standard mesh then set the cross hairs to link by coordinate instead of node index:
View-->Suma Controller
under the All column, click on c and v

Click around on one surface and see if the cross hair jumps to the same location in the other. If that is the case, then you know the surfaces are OK. If not then something went wrong while creating the standard mesh surfaces.

Another way to verify that the two surfaces have an identical geometry (almost) is though the use of CompareSurfaces. This program is for quantitative comparisons, I doubt you'll need to use it.

Now that you know the surfaces are identical, you will need to use the same surface volume (-sv option) for both the 3dSurf2Vol and 3dVol2Surf.

One way to check that you are using the correct surface volume is to start suma with the original mesh and the surface volume in question and send the surface to AFNI. Verify that the surface overlaps properly with your volume ROI. Then restart suma with the standard mesh and the same surface volume used above and again send the surface to AFNI. You should also have an excellent alignment between the standard-mesh surface and the volume ROI.

If you find no trouble up to this point then package all the necessary data and send them to us.

cheers,
ziad