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

[RICHARDS, JOHN]

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




>------------------------------
>
>Message: 6
>Date: Thu, 19 Nov 2015 23:52:51 +0000
>From: K Jeffrey Eriksen <eriksenj at ohsu.edu>
>To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
>Subject: [FieldTrip] FW: FEM head model and source model
>Message-ID: <FC8F960C75FCA14493D57C730DD538EF47799D0C at EXMB14.ohsu.edu>
>Content-Type: text/plain; charset="us-ascii"
>
>Hi again,
>
>I posted this a month ago and got no response. Is there anyone who could orient me some more to the FEM capabilities of FieldTrip please? I am a newbie, and the immensity of what is available is a bit overwhelming.
>
>Thanks,
>-Jeff
>
>
>From: K Jeffrey Eriksen
>Sent: Wednesday, October 21, 2015 4:30 PM
>To: 'fieldtrip at science.ru.nl'
>Subject: FEM head model and source model
>
>I am thinking of using FieldTrip for EEG source modeling, and wish to use an FEM formulation. I have found documentation on creating an FEM head model, but am unsure how to create a matching source model. Can someone please point me to documentation for this? Ideally I would want to place sources perpendicular to the local cortical surface. Also I would want to be able to create distributed sources combining several adjacent cortical elements.
>
>Thanks,
>-Jeff Eriksen
>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: default.vnd.ms-officetheme
Type: application/octet-stream
Size: 3131 bytes
Desc: default.vnd.ms-officetheme
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20151120/2a295f25/attachment-0001.obj>