WIP s/M/EEG forward solutions

[maedoc]

This is a work in progress (WIP) on #26. I'll update the checklist as I go.

• 4D 248 MEG
• 10-20 EEG
• sEEG or ECoG defaults?
• [ ] dipole or surface file for the cortical surface sources (produced by FreeSurfer & scripts)
• [ ] squid file for MEG sensors (4D 248 by default, or provided by user)
• [ ] elec file for EEG sensors (10-20 by default, or provided by user)
• [ ] internal potential locations for sEEG if provided
• [ ] ECoG positions if provided
• [x] three BEM surfaces: outer skin, outer skull, inner skull (produced by mne_watershed_bem)
• [x] geometry description (autogenerate/template)
• [x] conductivities (defaults or provided by user)
• [ ] visual verification of BEM surfaces, cortex & sensors (check step, requires pyqtgraph or freeview..)
• [x] sequence of calls to OpenMEEG commands om_*
• [x] convert sensors & lead fields to TVB format (Python script)

Did I forget anything?

sEEG sensors are localized on a CT, which needs to be registered with FreeSurfer's T1. There we need the vox2ras-tkr xfm for the CT to obtain positions valid for the cortical and BEM surfaces.

[timpx]

Additional for SEEG: coregistration of T1 and CT (or MRI), creation of a nifti files with electrodes positions shown inside (e.g. with colorvalue = 256), creation of a text file indicating for each electrode contact the corresponding region in the parcellation

[maedoc]

Notes from last week

• put everything into FS's T1 space, including BEM surfaces
• electrodes will already be described in a text file as start point, exit point, number of contacts and name