Converting vertex locations from MNE STC-files to MNI coordinates
1. Obtain the label of the vertex you are interested in. For instance, if you have an .stc file made by MNE with the information about the sources you are interested in, open it up in matlab using STCFILE = MNE_read_stc_file(), and look in STCFILE.data for the source of interest, and then take a note of the corresponding label for that vertex in STCFILE.vertices. This label will be a number.
2. Armed with this label number, open up Freesurfer and load the surface file for your corresponding STC data (e.g. typing "tksurfer average lh inflated"). Then type, in ‘vertex label’, in the bottom left hand corner of the GUI, the label number you are interested in. The vertex will be selected, in blue, on the cortical surface display in the Freesurfer GUI. Be sure to eyeball the selected vertex to check it looks in the right place. On the MNE mailing list, the point often comes up that if you are using the ‘fs-average brain surface’, you need to subtract/add 1 to the label number (I can’t remember which). On averages/surfaces you have created yourself you don’t have to do this, but do check: it is easy to tell if the vertex you expected is selected, because successive vertex label numbers aren’t next to each other (ie vertex label 543 is several centimetres away from 544, and so will be obviously correct or incorrect)
3. Now look in the bottom left hand corner of the GUI – there are two sets of coordinates. RAS is the MNE/Freesurfer native coordinate. Ignore this. ‘Talairach’ is underneath. In fact, Freesurfer records the MNI coordinates internally, and then (for the purposes of displaying the data in the GUI) transforms the MNI coordinates to Talairach coordinates using Matthew Brett’s transform. Although the GUI shows these ‘Talairach’ coordinates, this isn’t what you want, because MNI is the accepted standard now.
4. So, to covert them back again to their true MNI form, use Brett’s inverse tal2MNI.m function.
5. You have the MNI coordinates, which you can now use in FMRIcron and other display packages.
This link describes coordinate systems in Freesurfer.