Source Analysis Head Models - Revision history

Jaehyun at 14:03, 5 May 2021

2021-05-05T14:03:18Z

Jaehyun: /* Spherical Head Model for MEG */

2021-05-05T13:47:38Z

‎Spherical Head Model for MEG

Harald at 12:22, 4 May 2021

2021-05-04T12:22:45Z

Harald: /* Using Individual FEM Models in BESA Research */

2021-05-04T12:16:37Z

‎Using Individual FEM Models in BESA Research

Harald: /* Overview */

2021-05-04T12:15:14Z

‎Overview

Jaehyun at 09:36, 16 July 2019

2019-07-16T09:36:55Z

Jamie: /* Individual FEM Model */

2019-03-27T09:58:01Z

‎Individual FEM Model

Jaehyun: /* Spherical and Ellipsoidal Head Models for EEG */

2017-10-05T13:58:58Z

‎Spherical and Ellipsoidal Head Models for EEG

Jaehyun: /* Spherical Head Model for MEG */

2017-08-09T10:51:28Z

‎Spherical Head Model for MEG

Jaehyun: /* Spherical and Ellipsoidal Head Models for EEG */

2017-06-21T14:41:37Z

‎Spherical and Ellipsoidal Head Models for EEG

@@ Line 2: / Line 2: @@
 |title = Module information
 |module = BESA Research Standard or higher
-|version = 6.1 or higher
+|version = BESA Research 6.1 or higher
 }}

@@ Line 254: / Line 254: @@
 == Spherical Head Model for MEG ==
-BESA Research currently uses the spherical head model by Sarvas (1987). If no coregistration with the individual MRI has been performed in BESA Research (i.e. no individual MRI has been specified, see chapter ''[[Integration_with_MRI_and_fMRI|Integration with MRI and fMRI]]''), you can define the center for the sphere using the individual MRI by seeding a dipole at the assumed center using BrainVoyager. Then perform the <span style="color:#ff9c00;">Write Sphere Center File (*.cot)</span> entry of the <span style="color:#3366ff;">'''Head Box'''</span> popup menu.
+BESA Research currently uses the spherical head model by Sarvas (1987). If no coregistration with the individual MRI has been performed in BESA Research (i.e. no individual MRI has been specified, see chapter ''[[Integration_with_MRI_and_fMRI|Integration with MRI and fMRI]]''), you can define the center for the sphere using the individual MRI by seeding a dipole at the assumed center using BrainVoyager. Then perform the ''Write Sphere Center File (*.cot)'' entry of the <span style="color:#3366ff;">'''Head Box'''</span> popup menu.
 For additional information please see the BrainVoyager help system at [http://www.brainvoyager.com www.brainvoyager.com].

← Older revision		Revision as of 12:22, 4 May 2021
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	* Wendel, K, N G Narra, M Hannula, P Kauppinen, and J Malmivuo. “The Influence of CSF on EEG Sensitivity Distributions of Multilayered Head Models.” IEEE Transactions on Bio-Medical Engineering 55, no. 4 (April 2008): 1454–1456. doi:10.1109/TBME.2007.912427.		* Wendel, K, N G Narra, M Hannula, P Kauppinen, and J Malmivuo. “The Influence of CSF on EEG Sensitivity Distributions of Multilayered Head Models.” IEEE Transactions on Bio-Medical Engineering 55, no. 4 (April 2008): 1454–1456. doi:10.1109/TBME.2007.912427.
		+
		+
		+	== Individual BEM Model: Realistic head model for EEG and MEG (requires BESA Research 7.1 or higher) ==
		+
		+	The boundary element method (BEM) model implemented in BESA MRI uses a 3-layer realistic head model (scalp, skull, and brain). In comparison to FEM, BEM can be applied for a piecewise constant conductivity field, resulting in a simplified description of the head geometry on the boundaries of head tissue. To generate nested closed surface meshes, less detailed volume conductor segmentation is applied for BEM in BESA MRI. To compute the BEM forward solution, BESA MRI uses the OpenMEEG (Kybic et al., 2005; Gramfort et al., 2010) which was developed within the Athena project-team at INRIA Sophia-Antipolis. The OpenMEEG is used solving forward problems in the field of EEG and MEG, and it consists of the symmetric BEM.
		+
		+	=== Using Individual BEM Models in BESA Research ===
		+
		+	Similar to the individual FEM model, individual BEM models can be also used in BESA Research after coregistration has been performed in BESA MRI. In the coregistration process BESA MRI will generate a leadfield table, and a description of the source space. The leadfield table contains the simulated EEG potentials or MEG signals for sources in x-, y-, and z-direction distributed on a regular grid (4 mm resolution) covering the entire source space. The source space specifies the locations where BESA Research is allowed to place dipole sources. In simultaneous EEG and MEG recordings, the same coregistration and source space can be used for both EEG and MEG data.
		+
		+	After successfully running the coregistration, the coregistration dialog in BESA Research indicates that an individual BEM model is defined.
		+
		+	The BEM head model can be used in the Source Analysis module by selecting the entry Individual BEM from the head model selection dropdown list in the Parameter box or the context menu of the EEG/MEG button in the Channel box. After selecting the entry, BESA Research will load the leadfield table and the source space definitions. During dipole fitting BESA Research computes the EEG potentials or MEG signals for any given dipole source employing cubic Bezier-spline interpolation. In this way, the individual BEM model can be used for the source analysis like any of the other head models.
		+
		+
		+	'''References:'''
		+	* Gramfort A., Papadopoulo T., Olivi E., Clerc M. OpenMEEG: opensource software for quasistatic bioelectromagnetics, BioMedical Engineering OnLine 45:9, 2010
		+
		+	* Kybic J., Clerc M., Abboud T., Faugeras O., Keriven R., Papadopoulo T. A common formalism for the integral formulations of the forward EEG problem. IEEE Transactions on Medical Imaging, 24:12-28, 2005.
		+

	== Standardized FEM Model: Realistic Approximation for EEG ==		== Standardized FEM Model: Realistic Approximation for EEG ==

@@ Line 38: / Line 38: @@
 Individual FEM models can be used in BESA Research after coregistration has been performed in BESA MRI. Detailed instructions on how to perform the coregistration can be found in the ''BESA help'' or in the quick-guides which are available on the BESA homepage.
-In the coregistration process BESA MRI will generate a leadfield table, and a description of the source space. The leadfield table contains the simulated EEG potentials or MEG signals for sources in x-, y-, and z-direction distributed on a regular grid covering the entire source space. The source space specifies the locations where BESA Research is allowed to place dipole sources.
+In the coregistration process BESA MRI will generate a leadfield table, and a description of the source space. The leadfield table contains the simulated EEG potentials or MEG signals for sources in x-, y-, and z-direction distributed on a regular grid covering the entire source space. The source space specifies the locations where BESA Research is allowed to place dipole sources. In simultaneous EEG and MEG recordings, the same coregistration and source space can be used for both EEG and MEG data.
 After successfully running the coregistration the coregistration dialog in BESA Research indicates that an individual FEM model is defined. The model can now be used in the Source Analysis module. To do so select the entry Individual FEM from the head model selection dropdown list. BESA Research will now load the leadfield table and the source space definitions. During dipole fitting BESA Research computes the EEG potentials or MEG signals for any given dipole source employing '''cubic Bezier-spline interpolation'''. This way, the individual FEM model can be used for the source analysis like any of the other head models.

@@ Line 7: / Line 7: @@
 == Overview ==
-BESA Research provides head models that are based either on multi-shell spherical head models, standardized realistic head models using finite elements (FEM), or individual realistic FEM models that were created in BESA MRI. Standard FEM models are currently only available for EEG.
+BESA Research provides head models that are based either on multi-shell spherical head models, standardized realistic head models using finite elements (FEM), or individual realistic FEM or BEM (boundary element method) models that were created in BESA MRI. Standard FEM models are currently only available for EEG.
 It is highly recommended that you carefully read the specifications of the different head models below to understand what assumptions you are making in your data analysis when selecting a particular head model.
-The ''Head Model'' chapter is subdivided into four sections:
+The ''Head Model'' chapter is subdivided into the following sections:
 * '''Individual FEM model''': Realistic head model for EEG and MEG
 * '''Standardized FEM model''': Realistic approximation for EEG
 * '''Age-appropriate template models:''' Realistic head models from infancy to adulthood
@@ Line 19: / Line 20: @@
 To select a different head model, use the ''Head Model Selection'' list in the ''parameter box''. If you right click onto the ''Head Model dropdown list in'' the ''parameter box'' or on the EEG/MEG button in the ''channel box'', a special <span style="color:#3366ff;">'''Head Model Selection'''</span> popup menu will appear.
 == Individual FEM Model ==

@@ Line 34: / Line 34: @@
-'''Using Individual FEM Models in BESA Research'''
+=== Using Individual FEM Models in BESA Research ===
-−
 Individual FEM models can be used in BESA Research after coregistration has been performed in BESA MRI. Detailed instructions on how to perform the coregistration can be found in the ''BESA help'' or in the quick-guides which are available on the BESA homepage.
@@ Line 41: / Line 40: @@
 In the coregistration process BESA MRI will generate a leadfield table, and a description of the source space. The leadfield table contains the simulated EEG potentials or MEG signals for sources in x-, y-, and z-direction distributed on a regular grid covering the entire source space. The source space specifies the locations where BESA Research is allowed to place dipole sources.
-After successfully running the coregistration the coregistration dialog in BESA Research indicates that an individual FEM model is defined. The model can now be used in the Source Analysis module. To do so select the entry Individual FEM from the head model selection dropdown list. BESA Research will now load the leadfield table and the source space definitions. During dipole fitting BESA Research computes the EEG potentials or MEG signals for any given dipole source employing cubic Bezier-spline interpolation. This way, the individual FEM model can be used for the source analysis like any of the other head models.
+After successfully running the coregistration the coregistration dialog in BESA Research indicates that an individual FEM model is defined. The model can now be used in the Source Analysis module. To do so select the entry Individual FEM from the head model selection dropdown list. BESA Research will now load the leadfield table and the source space definitions. During dipole fitting BESA Research computes the EEG potentials or MEG signals for any given dipole source employing '''cubic Bezier-spline interpolation'''. This way, the individual FEM model can be used for the source analysis like any of the other head models.
@@ Line 108: / Line 107: @@
-'''Practical implementation of the FEM model'''
+=== Practical implementation of the FEM model ===
 When selecting a realistic approximation model from the '''Head Model Selection list''' or from the '''Head Model Selection popup menu''', a precalculated leadfield table is loaded. Each table contains the forward solution for a standard set of electrode locations and orthogonal dipoles at fixed grid points in the brain. Different tables have been precalculated for the various conductivity ratios using the same standard MRI average of 50 subjects. Individual realistic models will simply need separate tables and MRI volume and surface files.
@@ Line 163: / Line 162: @@
 == Spherical and Ellipsoidal Head Models for EEG ==
-<br>
+=== 4 shell ellipsoidal ===
-'''4 shell ellipsoidal'''
 The basis of this model is the multi-shell spherical head model with the fast algorithm by P. Berg and M. Scherg ([https://doi.org/10.1016/0013-4694(94)90113-9 A fast method for forward computation of multiple-shell spherical head models. Electroenceph. clin. Neurophysiol., 1994: 90, 58-64]). The 4 homogeneous shells are the brain, the CSF, the bone and the skin. You can modify the thicknesses of the shells and their conductivities in the parameter box. The center of the sphere is determined from the 3D electrode locations. If you use standard electrodes without 3D coordinates (see chapter [[Electrodes_and_Surface_Locations#Electrode_Conventions|Electrodes / Electrode Conventions]]), the multi-shell model is spherical. If 3D electrode coordinates have been defined, the spherical shells are distorted into an ellipsoid that best fits the 3D electrode cloud. The transformation from spherical to ellipsoidal is achieved via a 3×3 distortion-rotation matrix calculated by a least squares fit of the true 3D electrodes with their projection onto the best fitting sphere.
@@ Line 222: / Line 220: @@
 |}
+=== 3 shell Ary approximation ===
-'''3 shell Ary approximation'''
 The forward solution is calculated using a homogeneous head model after transforming the eccentricity of the dipole according to a non-linear equation (Scherg 1990; Ary 1981). Essentially, this model uses the similarity of the voltage topography of a dipole within a homogeneous sphere at a deeper location (e.g. 60% eccentricity) with the topography of a dipole in a 3-shell spherical model at a shallower location (e.g. 84% eccentricity).
+=== Homogenous sphere ===
-'''Homogenous sphere'''
 This model uses a dipole in a sphere with homogeneous conductivity. The homogeneous model is most suitable for the calculation of epicortical potentials.
+=== Polynomial 4 shells ===
-'''Polynomial 4 shells'''
 This model employs the widely-used polynomial expansion to calculate an iterative forward model using multiple spherical shells. This model is much slower than the fast 4-shell ellipsoidal head model, but has been provided for the purpose of comparison.

@@ Line 37: / Line 37: @@
-Individual FEM models can be used in BESA Research after coregistration has been performed in BESA MRI. Detailed instructions on how to perform the coregistration can be found in the ''BESA help'' or in the quick guide which is available on the BESA homepage (http://www.besa.de/downloads/quick-guides/ <!-- www.besa.de/tutorials/quickguides-->).
+Individual FEM models can be used in BESA Research after coregistration has been performed in BESA MRI. Detailed instructions on how to perform the coregistration can be found in the ''BESA help'' or in the quick-guides which are available on the BESA homepage.
 In the coregistration process BESA MRI will generate a leadfield table, and a description of the source space. The leadfield table contains the simulated EEG potentials or MEG signals for sources in x-, y-, and z-direction distributed on a regular grid covering the entire source space. The source space specifies the locations where BESA Research is allowed to place dipole sources.
@@ Line 61: / Line 61: @@
 * Wendel, K, N G Narra, M Hannula, P Kauppinen, and J Malmivuo. “The Influence of CSF on EEG Sensitivity Distributions of Multilayered Head Models.” IEEE Transactions on Bio-Medical Engineering 55, no. 4 (April 2008): 1454–1456. doi:10.1109/TBME.2007.912427.
 == Standardized FEM Model: Realistic Approximation for EEG ==

@@ Line 167: / Line 167: @@
 '''4 shell ellipsoidal'''
-The basis of this model is the multi-shell spherical head model with the fast algorithm by P. Berg and M. Scherg (A fast method for forward computation of multiple-shell spherical head models. Electroenceph. clin. Neurophysiol., 1994: 90, 58-64). The 4 homogeneous shells are the brain, the CSF, the bone and the skin. You can modify the thicknesses of the shells and their conductivities in the parameter box. The center of the sphere is determined from the 3D electrode locations. If you use standard electrodes without 3D coordinates (see chapter [[Electrodes_and_Surface_Locations#Electrode_Conventions|Electrodes / Electrode Conventions]].), the multi-shell model is spherical. If 3D electrode coordinates have been defined, the spherical shells are distorted into an ellipsoid that best fits the 3D electrode cloud. The transformation from spherical to ellipsoidal is achieved via a 3*3 distortion-rotation matrix calculated by a least squares fit of the true 3D electrodes with their projection onto the best fitting sphere.
+The basis of this model is the multi-shell spherical head model with the fast algorithm by P. Berg and M. Scherg ([https://doi.org/10.1016/0013-4694(94)90113-9 A fast method for forward computation of multiple-shell spherical head models. Electroenceph. clin. Neurophysiol., 1994: 90, 58-64]). The 4 homogeneous shells are the brain, the CSF, the bone and the skin. You can modify the thicknesses of the shells and their conductivities in the parameter box. The center of the sphere is determined from the 3D electrode locations. If you use standard electrodes without 3D coordinates (see chapter [[Electrodes_and_Surface_Locations#Electrode_Conventions|Electrodes / Electrode Conventions]]), the multi-shell model is spherical. If 3D electrode coordinates have been defined, the spherical shells are distorted into an ellipsoid that best fits the 3D electrode cloud. The transformation from spherical to ellipsoidal is achieved via a 3×3 distortion-rotation matrix calculated by a least squares fit of the true 3D electrodes with their projection onto the best fitting sphere.
 Bone thickness and conductivity is age dependent, with children having higher bone conductivities as compared to adults. Precise conductivity values are generally not known. Rough estimates have been obtained by comparing the depth of sources in subjects of different age groups. For that purpose, in combined EEG/MEG recordings of SEP/SEFs and epileptic spikes, the dipole fit results to the EEG and the MEG data were compared and matched. This resulted in the following recommendations for bone thickness and conductivity depending on the subject's age:
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 |}