document initial workflow for source localisation

[cjayb]

Many source localisation methods exist, each with their parameter choices and idiosyncrasies. However, some basic steps are common to all methods (more or less?). I'd like to see a Wiki-page (with a suitably descriptive name so it will pop up when people use the search function...) with a simple walk-through. Each step could link to a more detailed description of

• maxfilter, possibly with a little discussion about the fact that choices here may affect source analysis (but nothing too 'scary'!)
• artefacts and noise (link to recommendations, e.g., Miika's for EEG)
• baseline and epoching (basic workflow is for evoked localisation only, maybe mention covariance estimation but details left to separate document/page)
• coordinate frame alignment, incl. tools available (this is important: would be great to have a clear description of the why and how of coregistration, illustrations welcome)

Things to leave out here (more advanced topics)

• choice and generation of head model
• covariance, rank-deficiency, inverse operator

[sarathykousik]

_Coregistration_ MNE-C: Uses the ICP algorithm. Perfroms best in my view http://martinos.org/mne/dev/manual/sample_dataset.html#meg-mri-coordinate-system-alignment

MNE-Py: Better GUI. Seems issues were fixed recently. Perhaps mje knows better here (at the cost of repeating) http://www.slideshare.net/mne-python/mnepython-coregistration

Fieldtrip: Nothing great about their coreg tool. They suggest using the MEG manufacturer's tool anyway. http://www.fieldtriptoolbox.org/faq/how_to_coregister_an_anatomical_mri_with_the_gradiometer_or_electrode_positions

[sarathykousik]

Update on Fieldtrip & coreg - FT does have a not-so-good GUI for co-registration. Can be launched with the following code: Note: You need to first register as much as possible -> mri_ra. The let the ICP do a better job. It doesn't work that well in my experience. cfg = []; cfg.method = 'headshape'; cfg.coordsys = 'neuromag'; cfg.headshape.headshape = headshape; cfg.headshape.icp = 'yes'; cfg.headshape.interactive = 'yes'; mri_fine = ft_volumerealign(cfg, mri_ra);