[FieldTrip] Cortical surface VS brain volume source models

[RICHARDS, JOHN]

See part of my note below.  I think the answer is:

1—the Freesurfer reference is to develop a surface model of the head, and results in a surface-based mesh (pos, tri).  This mesh can be used in the ft_source_model.  Free surfer also is used to extract the brain surface; which might be a better model for where the sources are.

2—FT does provide tools to create either a surface-based or volume-based source model.  I use our segmented GM from other methods (FSL, SPM, …) and do a volume model of points only on the GM.  FT can do surface source meshes without using Freesurfer; (e.g., surface of the GM; surface of the brain; surface of a realistic inner compartment).   Part of this is because I use infant participants and have not been able to use the Freesurfer tool to identify GM surfaces.

3—There are some theoretical rationales for EEG to use surface models, with the dipoles pointed normal to the surface.  Presumably this reflects the columnar arrangement of neurons that generate a current flow across the column and thus the estimated dipoles are normal to the surface.  The three-direction moment dipole models used with volume models allow the direction of the dipole on each source dipole location to vary, and presumably capture more variance as the EEG source.  I have found in some single-dipole-fitting models that the volume models provide a better fit, and I have assumed this is because they allow more flexibility in the estimation.  The EEG source analysis and some of the methods have very large resolutions compared to the normal-surface model, so this is an artificial restriction because of the relatively poor resolution of the inverse techniques (in cm range rather than in mm range).

4—I have preferred volume models; there are some points in the GM that probably have active current dipoles that can be modeled as a volume; e.g., inside gyri, inside rather than on the surface, in convoluted structures, etc.  I also have volumetric atlases that I can use more easily with volume models; I currently am using the volumes which correspond to fMRI clusters; and some other reasons.  I use the GM as the volume, rather than the whole brain (which is theoretically questionable).

5—The “pos” matrix in surface models and volume models acts the same; the pos are only on the surface, or in the volume, but their structure is the same.  The surface-normal models only need a “pow” matrix as output, since the direction of the moment vector is not estimated, whereas the non-normal models (usually volume) require the “pow" be calculated from the “mom" matrix.  


Some of this is “practical” rather the “theoretical” (e.g., pos pow mom matrices).  Perhaps someone has a reference that is more theoretically descriptive?

John


***********************************************
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
***********************************************




>
>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.
>
>Date: Fri, 20 Nov 2015 18:49:10 +0100
>From: Maris Skujevskis <icelandhouse at gmail.com>
>To: fieldtrip at science.ru.nl
>Subject: [FieldTrip] Cortical surface VS brain volume source models
>Message-ID:
>	<CAKEvDidXE5_dmVCroYqtok8U31-zOiUYS4c7RAOZi7LjjcfSSg at mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>Dear Fieldtrip users,
>
>I am currently working on source reconstruction (EEG) of both ERPs and of
>oscillatory activity.
>
>I have 3 short and related questions of clarification:
>(1)
>Why are MNE suite and Free Surfer used to construct the
>cortical-surface-based source model in the MNE tutorial (
>http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate)?
>Is it simply because discretizing the source model into locations on the
>cortical surface (as opposed to a 3D volume of grid points) is a
>functionality not provided by Fieldtrip directly?
>
>(2)
>So, if I prefer to have a 3D grid as the source model for my MNE source
>reconstruction, can I simply make use of Fieldtrip's own function
>ft_prepare_sourcemodel and forget about MNE Suite & Free Surfer?
>
>(3)
>Does the choice between a cortical-surface-based an a brain-volume-based
>source model depend primarily on the expectation of where the sources would
>most likely be located?
>Or are there other reasons why the MNE source reconstruction approach would
>make use of a cortical-surface-based source space instead of a 3D
>volumetric grid (as found in all the beamformer tutorials)?
>
>
>
>Thanks!
>
>Maris
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