Hi Kelly,

The Zilles CA atlas information is all in volume space. Those atlases are typically installed in the abin directory (try this command if you can't find them: apsearch -list_all_afni_dsets).

In terms of using the CA defined regions as ROIs, you could map them onto the MNI_N27 cortical surface of the same standard mesh density that you're using for your other subjects.

1- grab the MNI_N27 surfaces:
See instructions here (http://afni.nimh.nih.gov/pub/dist/doc/htmldoc/installations/TemplateSurfaces/TemplateSurfaces.html)

2- Find out if you have the CA atlases. The ones we distribute are in MNIa (MNI-anatomical) space that they come in. In AFNI, we handle space changes on the fly. But for this task we will need the atlases in question in MNI space. You can either get the MNI volumes from this link (http://afni.nimh.nih.gov/pub/dist/atlases/MNIatlases.tgz), or transform the volumes manually with: @Shift_Volume . Here I will use @Shift_Volume to illustrate the process.

#I ran this from the directory containing the CA atlases
@Shift_Volume -MNI_Anat_to_MNI -prefix MNI_caez_mpm_18 \
-dset MNIa_caez_mpm_18+tlrc.


3- Now template surfaces and volumes should be in good alignment, verify with:

#Verify the alignment with something like:
suma -spec MNI_N27:ld60 -vol ~/abin/MNI_caez_mpm_18+tlrc.
afni -niml &

(You can replace the suma -spec MNI_N27:ld60 with more traditional:
suma -spec ~/.afni/data/suma_MNI_N27/std.60.MNI_N27_both.spec -sv ~/.afni/data/suma_MNI_N27/MNI_N27_SurfVol.nii
You will need to supply the same -spec and -sv options for 3dVol2Surf later on.

#Have SUMA talk to AFNI and overlay in AFNI the MNI_caez_mpm_18 dataset. It should sit nicely on top of the surfaces. You can also see the volume in SUMA.

4- Map whatever you want from the Zilles MNI atlases to the surfaces with 3dVol2Surf for example.

5- As usual, make sure the results look good.

cheers,
Ziad