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 faq:how_can_i_fine-tune_my_bem_volume_conduction_model [2013/12/05 11:12]robert updated with the triangulation methods faq:how_can_i_fine-tune_my_bem_volume_conduction_model [2015/02/03 13:54]johzum [How can I fine-tune my BEM volume conduction model?] 2015/02/03 13:54 johzum [How can I fine-tune my BEM volume conduction model?] 2014/10/01 00:11 robert added tags2013/12/05 11:13 robert 2013/12/05 11:12 robert updated with the triangulation methods2013/12/05 11:01 robert created 2015/02/03 13:54 johzum [How can I fine-tune my BEM volume conduction model?] 2014/10/01 00:11 robert added tags2013/12/05 11:13 robert 2013/12/05 11:12 robert updated with the triangulation methods2013/12/05 11:01 robert created Line 1: Line 1: + {{tag>​faq source headmodel}} + ====== How can I fine-tune my BEM volume conduction model? ====== ====== How can I fine-tune my BEM volume conduction model? ====== Line 9: Line 11: * mesh, consisting of vertices and elements (triangles, tetraheders,​ hexaheders) * mesh, consisting of vertices and elements (triangles, tetraheders,​ hexaheders) - In cas of the BEM, the volume conduction model consists of one or multiple homogenous and isotropic compartments. The compartment boundaries are closed and non-intersecting surfaces that are described by triangulated meshes. Furthermore,​ each of the compartments is described by a conductivity. + In case of the BEM, the volume conduction model consists of one or multiple homogenous and isotropic compartments. The compartment boundaries are closed and non-intersecting surfaces that are described by triangulated meshes. Furthermore,​ each of the compartments is described by a conductivity. To make the highest quality BEM volume conduction model, FieldTrip offers a number of functions to manipulate these three classes of geometrical data. If we summarize the geometrical data as **anatomy**,​ **segmentation** and **mesh**, then we can consider functions that take one type of geometrical data as input, and return the same or another type. To make the highest quality BEM volume conduction model, FieldTrip offers a number of functions to manipulate these three classes of geometrical data. If we summarize the geometrical data as **anatomy**,​ **segmentation** and **mesh**, then we can consider functions that take one type of geometrical data as input, and return the same or another type. Line 17: Line 19: ​ - ===== Functions for converting ​anatomy to anatomy ===== + ===== Converting ​anatomy to anatomy ===== * **[[:​reference:​ft_volumerealign]]** * **[[:​reference:​ft_volumerealign]]** * **[[:​reference:​ft_volumereslice]]** * **[[:​reference:​ft_volumereslice]]** - ===== Functions for converting ​anatomy to segmentation ===== + ===== Converting ​anatomy to segmentation ===== * **[[:​reference:​ft_volumesegment]]** * **[[:​reference:​ft_volumesegment]]** - ===== Functions for converting ​segmentation to segmentation ===== + ===== Converting ​segmentation to segmentation ===== Here it helps to distinguish the different representations. Examples of these are given in **[[:​reference:​ft_datatype_segmentation]]**. Here it helps to distinguish the different representations. Examples of these are given in **[[:​reference:​ft_datatype_segmentation]]**. Line 57: Line 59: The same effect can be reached with the use of another morphology function: bwlabeln. This function classifies the cluster of neighboring voxels and attaches a label to them, so that different objects can be easily distinguished (and processed) in the successive steps. The same effect can be reached with the use of another morphology function: bwlabeln. This function classifies the cluster of neighboring voxels and attaches a label to them, so that different objects can be easily distinguished (and processed) in the successive steps. - ===== Functions for converting ​anatomy to mesh ===== + ===== Converting ​anatomy to mesh ===== The **[[:​reference:​ft_prepare_mesh]]** function allows you to interactively make a mesh, i.e. by manually clicking in an anatomical MRI, by specifying cfg.method='​interactive'​. It will give you a simple user interface that allows you to add and remove points in each of the slices. The vertices in each of the slices are connected together to form a closed triangulated mesh. The **[[:​reference:​ft_prepare_mesh]]** function allows you to interactively make a mesh, i.e. by manually clicking in an anatomical MRI, by specifying cfg.method='​interactive'​. It will give you a simple user interface that allows you to add and remove points in each of the slices. The vertices in each of the slices are connected together to form a closed triangulated mesh. - ===== Functions for converting ​segmentation to mesh ===== + ===== Converting ​segmentation to mesh ===== The **[[:​reference:​ft_prepare_mesh]]** function has the '​projectmesh',​ '​iso2mesh'​ and '​isosurface'​ methods for constructing a mesh from a segmentation. The **[[:​reference:​ft_prepare_mesh]]** function has the '​projectmesh',​ '​iso2mesh'​ and '​isosurface'​ methods for constructing a mesh from a segmentation. Line 72: Line 74: - ===== Functions for converting ​mesh to mesh ===== + ===== Converting ​mesh to mesh ===== The [[http://​iso2mesh.sourceforge.net|iso2mesh]] toolbox includes very useful functions for mesh manipulations. ​ The [[http://​iso2mesh.sourceforge.net|iso2mesh]] toolbox includes very useful functions for mesh manipulations. ​ Line 88: Line 90: * spm_mesh_render.m * spm_mesh_render.m - ===== Functions for converting ​mesh to volume conduction model ===== + ===== Converting ​mesh to volume conduction model ===== The **[[:​reference:​ft_prepare_headmodel]]** function can take a single or the combination of multiple meshes as input and make a volume conduction model out of it. This construction of the volume conduction model can for example consist of fitting spheres to the mesh for a concentric sphere model, or the computation of a BEM system matrix. ​ The **[[:​reference:​ft_prepare_headmodel]]** function can take a single or the combination of multiple meshes as input and make a volume conduction model out of it. This construction of the volume conduction model can for example consist of fitting spheres to the mesh for a concentric sphere model, or the computation of a BEM system matrix. ​ Line 96: Line 98: -