[FieldTrip] {SpamScore: ssss} fieldtrip Digest, Vol 60, Issue 17

[K Jeffrey Eriksen]

Hi John,

This was more than I expected, thanks for the detail. I will start with what you suggest. Thanks,
-Jeff

PS. Are you using FEM because you have EEG, as opposed to MEG data? I really need to model the whole head for 256-channel EGI EEG coverage.


-----Original Message-----
From: RICHARDS, JOHN [mailto:RICHARDS at mailbox.sc.edu] 
Sent: Friday, November 20, 2015 6:02 AM
To: fieldtrip at science.ru.nl; K Jeffrey Eriksen <eriksenj at ohsu.edu>
Subject: Re: {SpamScore: ssss} fieldtrip Digest, Vol 60, Issue 17

I have learned FT recently.  The “SimBio” external tool is used for a full segmented head FEM model.  It works well, though needs some tweaking if you use grid (source dipole points) that are too dense.

Re the “source model”.  I presume you mean the source dipoles.  The FT procedure is ft_prepare_sourcemodel, which has documentation on the www.

The tutorial for the MNE estimation tells how to get this from free surfer;  but there are a number of other tutorials on the FT site that show how to get this by other means.  I have been using the segmented GM (or brain) and getting a volume grid that includes only the GM points; or points on the surface from my own grids or with the FT procedures.  You can use normal dipoles or the 3-moment direction dipoles.  I do this with a segmented GM done outside of FT, and use the GM MRI volume to get the grid positions for the volumetric dipoles; also have used the surface (on the GM, or on the brain-inner-compartment).  I think the FT procedures to get the segmented MRI call SPM calls to get the GM/WM.

Here are a list of tutorials I have used.  The SimBio one is mostly complete, but overall there is less help in the FT materials for the FEM models than for the BEM models.  If I were doing BEM models, the tutorials are pretty self-sufficient; for the FEM model I have had to put a couple of incomplete code snippets together from different locations.

John

http://fieldtrip.fcdonders.nl/tutorial/natmeg/dipolefitting#construct_the_eeg_volume_conduction_model
http://fieldtrip.fcdonders.nl/development/simbio
http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg?s[]=ft&s[]=prepare&s[]=mesh 
<http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg?s%5B%5D=ft&s%5B%5D=prepare&s%5B%5D=mesh>
http://fieldtrip.fcdonders.nl/example/compute_forward_simulated_data_and_apply_a_beamformer_scan
http://fieldtrip.fcdonders.nl/development/minimum_norm_estimate_new
http://fieldtrip.fcdonders.nl/development/simbio
http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg?s[]=ft&s[]=prepare&s[]=mesh 
http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg?s%5B%5D=ft&s%5B%5D=prepare&s%5B%5D=mesh
http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_brain_atlas_based_mni_space
http://fieldtrip.fcdonders.nl/example/compute_forward_simulated_data_and_apply_a_beamformer_scan
http://fieldtrip.fcdonders.nl/development/minimum_norm_estimate_new
http://fieldtrip.fcdonders.nl/tutorial/natmeg/dipolefitting#construct_the_eeg_volume_conduction_model
http://fieldtrip.fcdonders.nl/development/minimum_norm_estimate_new