Contents
Tested for Ubuntu 14.04 LTS 64-bit Desktop
For installation instructions refer to doc/hoffman2.rst.
On most distributions of Linux or Macs, Boost, Thread Building Blocks, and MPI can be installed from a standard package manager. muparser, GetFEM++, and Deal.II are less standard libraries which will have to be installed from source. In addition, install_script.txt contains the commands that will install these libraries.
- Boost
- Version 1.54.0.1ubuntu1 from apt-get
- libboost-dev
- muparser
- http://muparser.beltoforion.de/ Version 2.2.3
- GetFEM++
http://download.gna.org/getfem/stable/getfem-4.2.tar.gz Version 4.2
If default install location is used, you may need to run
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/libin every terminal before you can run programs from sloc, or you can add it to your .bashrc.
- Deal.II Version 8.1.0
Make sure you use
cmake -DDEAL_II_WITH_MPI=ON .
while installing Deal.II, or Deal.II uses it's own MPI include file (mpi.h), which causes some issues with sloc code.
- Thread Building Blocks (tbb) [check if this generates an error in cmake when missing]
- libtbb-dev (Version 4.2~20130725-1.1ubuntu1) from apt-get
- MPI
- Works when installing from source
- Probably could also install with apt-get
- libopenmpi-dev
- libmpich-dev seems to be another option
- Currently using
- g++ Version 4.8.3-19
- cmake Version 2.8.12.2
Run
cmake . make all
Running code add pwd to path run icosahedron.run.sh from data/simple
- .mesh file
- this is a standard file format, not custom made by us.
- for geometric meshes (tetrahedron) created by hand; for sphere, stl file was created in blender, and then stl_to_mesh was used to convert from .stl to .mesh.
- Not sure exactly how icosahedron was created (mosalam, 6/12/14 @ 7:38pm)
- for anatomical meshes, .stl file created in Vitrea was converted to .mesh using make_head_model
- .sigma file
- custom file format made by us;
- lookup table for the material index
- each “material index” is actually an index for an interface between two materials with same or different conductivities.
- one row for each material index - eg. with a 7 layer model, there are 7 material indices
- first column: material index
- second column: inner conductivity
- third column: outer conductivity
- .mat file
- custom file format made by us;
- each mesh has a separate .mat file
- .mat stands for “material”
- the class sloc::MaterialData defined in material_data.cc creates the .mat and .sigma files.
- first line: # of triangles in mesh
- second line onwards (one row for each triangles)
- first column: index of vertex
- second column: material index (also called material number)
- .dat file
- custom file format made by Luis
- potentials on electrodes
- first line: number of electrodes N
- next N lines: electrode index (integer) and potential on electrode (floating-point)
- .stl file
- format from Vitrea
- .vtk file
- Format from the Visualization Toolkit
- contains information equivalent to .dat files, but in a format supported by the Visualization Toolkit
- .prm file
- format from deal.II Parameter Handler
- specifies parameters for a function as a text file
- .log file
- custom format
- debugging output
- not essential for later use
- .cost_at_grid_pts
- created by mosalam with this program: bem_cost_function , which reads potentials from two .dat files
- called within this shell script : head.run_grid.sh
- content: the cost computed by putting the candidate dipole source at the grid points
- stores the cost of best dipole fit at each candidate location in a grid of candidate points.
- the cost is the sum of squared errors between predicted and “measured” potentials (?)
- 7 columns: (x, y, z, angleX, angleY, angleZ, cost)
- one row for each candidate point
- .electrodes
- created by select_electrodes_given_3d_pos (see head.run_grid.sh that calls this)
- the vertex indices of the electrodes (10-20 system)
- takes .stl vertices for scalp and points for 10-20 electrode configuration and gives the vertices closest to the true locations
- example
- head.mesh - contains nearly 16,000 triangles.
- head.mat - contains the material information for each triangle, including the material index for the inside and the outside of each triangle
- head.sigma - contains a lookup table that relates the material index to the inner and outer conductivity
Need to compare results with
- eeglab - NFT (directory: mfiles) version 2.3 (Mosalam)
- includes forward problem solutions
Field Trip
To verify the units of the equation match let consider only the first term on the right hand side:
In the SI:
Let 
be the solution of the forward problem with dipole p at location r.
and 
are the location and the magnitude of the dipole used in the
forward problem to simulate the potential measurements, 
.
You can estimate the magnitude of the dipole for the given set of true potential
measurements and the true location of the dipole by 
.
If you multiply the magnitude of the dipole by a constant scalar value, c,
, you get a new set of potential measurements, 
. Then, you
can estimate the magnitude of the dipole for the given potential measurements,
.
5/5/13 (Ram)
Documentation is scanty.
An example overview of the analysis pipeline using an
icosahedron mesh is provided in data/simple/icosahedron.run.sh
prepare the dipoles select electrodes into a file run the forward forward solution using bem_forward_solver.
this produces output_vtk (for visualization) and output_phi
(the raw electrodepotentials) run measure_electrodes to add noise to the simulated
- measurement - this takes an argument that specifies SNR
- icosahedron.electrodes (the electrode locations) icosahedron.electrodes.dat (potential measurements at those
electrode locations
- run the bem_cost_function using as input the following files:
- icosahedron.electrodes.dat icosahedron.surf.mesh (surface mesh specification) icosahedron.sigma (conductivity values)
Details on the file 'bin/bem_cost_function.cc'. This file
iterates through points in the simulated brain to determine
the cost of asserting that those points are the seizure
location.
Other parts of this project include (a) the meshes and file formats that determine the various
surfaces (scalp, skull-outer, brain-outer, ventricles,
vessels). meshes are visualized using meshlab. the e-field
projected onto the mesh is visualized using paraview, which
reads the *.vtk file produced by 'bin/bem_cost_function.cc'.