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

[RICHARDS, JOHN]

I am doing this with EEG, EGI’s 128-channel system, with infants. There are large individual differences in head media (e.g., CSF, GM/WM/non-myelinated axons) and the models are significantly different with FEM and BEM.  We are using individual head models from participants who are in the EEG experiments; so the FEM on individual head models is the best one can get with EEG source analysis.  John

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John E. Richards Carolina Distinguished Professor
Department of Psychology
University of South Carolina
Columbia, SC  29208
Dept Phone: 803 777 2079
Fax: 803 777 9558
Email: richards-john at sc.edu
HTTP: jerlab.psych.sc.edu
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On 11/20/15, 8:54 PM, "K Jeffrey Eriksen" <eriksenj at ohsu.edu> wrote:

>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
>