This README.txt file was generated on 20201208 by Mats Forssell # # General instructions for completing README: # For sections that are non-applicable, mark as N/A (do not delete any sections). # Please leave all commented sections in README (do not delete any text). # ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: Simulation files for current field computation in layer-homogeneous media, applied to skull-transparent currents # # Authors: Include contact information for at least the # first author and corresponding author (if not the same), # specifically email address, phone number (optional, but preferred), and institution. # Contact information for all authors is preferred. # 2. Author Information First Author Contact Information Name: Mats Forssell Institution: Carnegie Mellon University Address: 5000 Forbes Avenue, Pittsburgh, PA 15232, USA Email: mforssel@andrew.cmu.edu Phone Number: NA Author Contact Information Name: Pulkit Grover Institution: Carnegie Mellon University Address: 5000 Forbes Avenue, Pittsburgh, PA 15232, USA Email: pgrover@andrew.cmu.edu Phone Number: NA Author Contact Information Name: Chaitanya Goswami Institution: Carnegie Mellon University Address: 5000 Forbes Avenue, Pittsburgh, PA 15232, USA Email: cgoswami@andrew.cmu.edu Phone Number: NA --------------------- DATA & FILE OVERVIEW --------------------- # # Directory of Files in Dataset: List and define the different # files included in the dataset. This serves as its table of # contents. # Simulation files used in paper "Effect of skull thickness and conductivity on current propagation for noninvasively injected currents" (M Forssell, C Goswami, A Krishnan, M Chamanzar, and P Grover) Directory of Files: A. Filename: COMSOL_cuboid_setup.mph Short description: COMSOL file containing the setup of the cuboidal model simulation, sweeping over different parameters of scalp and skull thickness and conductivity (ran on COMSOL v5.5) B. Filename: COMSOL_spherical_setup.mph Short description: COMSOL file containing setup of the spherical model simulation, sweeping over different parameters of scalp and skull thickness and conductivity (ran on COMSOL v5.5) C. Filename: 20201022_NYhead_5elD_in.mph Short description: COMSOL file containing setup for the NY head model simulation using the 5 electrode pattern (pattern A) (ran on COMSOL v5.5) D. Filename: 20200303_spherical_pointsource.mat Short description: result from the spherical COMSOL simulation, as a MATLAB file: "data" table contains values of the voltage and current density in an X,Y,Z grid for different tskull, Sskull, tscalp, Sscalp conditions. The order of columns is specified in the "parameters" variable E. Filename: 20190524_cuboidal_pointsource.mat Short description: result from the cuboidal COMSOL simulation, as a MATLAB file: similar data as the previous file F. Filename: 20201024_NYhead_1elD_output_Sskull_0.02_Sscalp_0.41_Sbrain_0.47_dummy_1.mat Short description: result from the COMSOL simulation in the NY head model, with the single electrode injection, for a 3-layer head. G. Filename: 20201024_NYhead_1elD_output_Sskull_1_Sscalp_1_Sbrain_1_dummy_1.mat Short description: result from the COMSOL simulation in the NY head model, with the single electrode injection, for a homogeneous head. H. Filename: 20201022_NYhead_5elD_output_d_12_Sskull_0.02_Sscalp_0.41_Sbrain_0.47_dummy_1.mat Short description: result from the COMSOL simulation in the NY head model, with the 5 electrode pattern (pattern A) injection, for a 3 Layer head. I. Filename: 20201022_NYhead_5elD_output_d_12_Sskull_1_Sscalp_1_Sbrain_1_dummy_1.mat Short description: result from the COMSOL simulation in the NY head model, with the 5 electrode pattern (pattern A) injection, for a homogeneous head. J. Filename: 20201023_NYhead_VHF_output_F_4_Sskull_0.02_Sscalp_0.41_Sbrain_0.47_dummy_1.mat Short description: result from the COMSOL simulation in the NY head model, with the high frequency pattern (pattern C) injection, for a 3 Layer head. K. Filename: 20201023_NYhead_VHF_output_F_4_Sskull_1_Sscalp_1_Sbrain_1_dummy_1.mat Short description: result from the COMSOL simulation in the NY head model, with the high frequency pattern (pattern C) injection, for a homogeneous head. L. Filename: MATLAB_code.zip Short description: contains code for the computation of current field in the cuboidal, spherical and planar models. The code was executed using Matlab R2018a. The following files are included in this archive: a. model/VH.m description: calculates voltage field resulting from a point current source in a semi-infinite homogeneous medium b. model/V2L.m description: calculates voltage field resulting from a point current source in a semi-infinite 2-layer homogeneous medium c. model/V3L.m description: calculates voltage field resulting from a point current source in a semi-infinite 3-layer homogeneous medium d. model/JHx.m description: calculates current density field in x resulting from a point current source in a semi-infinite homogeneous medium e. model/JHz.m description: calculates current density field in z resulting from a point current source in a semi-infinite homogeneous medium f. model/JHn.m description: calculates current density field norm resulting from a point current source in a semi-infinite homogeneous medium g. model/J1x.m description: calculates current density field in x resulting from a point current source in a semi-infinite 2-layer homogeneous medium h. model/J1y.m description: calculates current density field in y resulting from a point current source in a semi-infinite 2-layer homogeneous medium i. model/J1z.m description: calculates current density field in z resulting from a point current source in a semi-infinite 2-layer homogeneous medium j. model/J1z3L.m description: calculates current density field in z resulting from a point current source in a semi-infinite 3-layer homogeneous medium k. model/J2L.m description: calculates field of interrest resulting from a pattern of point current sources in a semi-infinite 2-layer homogeneous medium l. model/J2L_n_XYZ.m description: calculates current density field norm resulting from a pattern of point current sources in a semi-infinite 2-layer homogeneous medium m. model/J3L.m description: calculates field of interrest resulting from a pattern of point current sources in a semi-infinite 3-layer homogeneous medium n. model/cuboid_TF_full.m description: calculates the transfer function for a pattern of point current sources in an arbitrary cuboidal model o. model/cuboid_TF_approx.m description: calculates the approximate transfer function for a pattern of point current sources in an arbitrary cuboidal model p. model/cuboid_full.m description: calculates field of interest for a pattern of point current sources in an arbitrary cuboidal model q. model/cuboid_approx.m description: calculates approximate field of interest for a pattern of point current sources in an arbitrary cuboidal model r. model/fft_cube.m description: calculates the cosine transform amplitudes for a given input current field in an arbitrary cuboidal model s. model/ifft_cube.m description: calculates the inverse cosine transform amplitudes for a given cosine transform in an arbitrary cuboidal model t. model/sphere_TF_full.m description: calculates the transfer function for a pattern of point current sources in an arbitrary spherical model u. model/sphere_TF_approx.m description: calculates the approximate transfer function for a pattern of point current sources in an arbitrary spherical model v. model/sphere_full.m description: calculates field of interest for a pattern of point current sources in an arbitrary spherical model w. model/sphere_approx.m description: calculates approximate field of interest for a pattern of point current sources in an arbitrary spherical model x. model/fft_sphere.m description: calculates the spherical harmonic transform for a given input current field in an arbitrary spherical model y. model/ifft_sphere.m description: calculates the inverse spherical harmonic transform for a given harmonic field in an arbitrary spherical model z. model/elpattern_sph.m description: returns the electrode pattern in the spherical system for an input electrode pattern in a cartesian system aa. plot_TF_comp.m description: plot comparisons of transfer functions for cuboidal and spherical models in different conditions ab. plot_pattern_comp.m description: plot comparisons of voltage/current fields resulting from an electrode pattern for semi-infinite, cuboidal and spherical models ac. plot_tsdel_comp.m description: plot comparisons of current fields resulting from varying electrode patterns for semi-infinite, cuboidal and spherical models ad. cuboid_transparency_distance_size.m description: plot comparisons of current fields resulting from varying electrode patterns for cuboidal and spherical models, comparing homogeneous conductivity case with 2 or 3-layer models af. cuboid_FFT_remove_reconstruct.m description: plot electrode pattern and resulting field in a cuboidal model resulting from eliminating some spatial frequencies from a given input pattern ag. sphere_FFT_remove_reconstruct.m description: plot electrode pattern and resulting field in a spherical model resulting from eliminating some spatial frequencies from a given input pattern ae. pattern_tsdel_comp_FFTfreq.m description: plot comparisons of current fields resulting from varying electrode patterns with some spatial frequencies removed for cuboidal and spherical models, comparing homogeneous conductivity case with 2 or 3-layer models Additional Notes on File Relationships, Context, or Content (for example, if a user wants to reuse and/or cite your data, what information would you want them to know?): NA # # File Naming Convention: Define your File Naming Convention # (FNC), the framework used for naming your files systematically # to describe what they contain, which could be combined with the # Directory of Files. # File Naming Convention: NA # # Data Description: A data description, dictionary, or codebook # defines the variables and abbreviations used in a dataset. This # information can be included in the README file, in a separate # file, or as part of the data file. If it is in a separate file # or in the data file, explain where this information is located # and ensure that it is accessible without specialized software. # (We recommend using plain text files or tabular plain text CSV # files exported from spreadsheet software.) # ----------------------------------------- DATA DESCRIPTION FOR: 20200303_spherical_pointsource.mat ----------------------------------------- 1. Number of variables: 2 2. Number of cases/rows: 5436030 3. Missing data codes: Code/symbol Definition NaN undefined value 4. Variable List # # Example. Name: Gender # Description: Gender of respondent # 1 = Male # 2 = Female # 3 = Transgender # 4 = Nonbinary # 5 = Other gender not listed # 6 = Prefer not to answer # A. Name: parameters Description: List of the column headers for the data variable Value labels if appropriate B. Name: data Description: voltage and current density field for the simulated electrode pattern. The quantities are arranged in the following columns, as indicated in the parameters variable: Column 1: X coordinate (in m): range: -0.015 to 0.015, step: 0.0001 Column 2: Y coordinate (in m): range: -0.015 to 0.015, step: 0.0001 Column 3: Z coordinate (in m): range: 0.07 to 0.079, step: 0.001 Column 4: skull thickness (in m): value: 0.001 Column 5: skull conductivity (in S/m): values: 0.1, 1, 10 Column 6: scalp thickness (in m): values: 0, 0.001 Column 7: scalp conductivity (in S/m): value: 1 Column 8: voltage (in V) Column 9: Current density along x, Jx (in A/m^2) Column 10: Current density along y, Jy (in A/m^2) Column 11: Current density along z, Jz (in A/m^2) ----------------------------------------- DATA DESCRIPTION FOR: 20200303_cuboidal_pointsource.mat ----------------------------------------- 1. Number of variables: 2 2. Number of cases/rows: 3488425 3. Missing data codes: Code/symbol Definition NaN undefined value 4. Variable List # # Example. Name: Gender # Description: Gender of respondent # 1 = Male # 2 = Female # 3 = Transgender # 4 = Nonbinary # 5 = Other gender not listed # 6 = Prefer not to answer # A. Name: parameters Description: List of the column headers for the data variable Value labels if appropriate B. Name: data Description: voltage and current density field for the simulated electrode pattern. The quantities are arranged in the following columns, as indicated in the parameters variable: Column 1: X coordinate (in m): range: -0.017 to 0.017, step: 0.0001 Column 2: Y coordinate (in m): range: -0.017 to 0.017, step: 0.0001 Column 3: Z coordinate (in m): range: 0 to 0.005, step: 0.001 Column 4: skull thickness (in m): value: 0.001 Column 5: skull conductivity (in S/m): values: 0.1, 1, 10 Column 6: scalp thickness (in m): values: 0, 0.001 Column 7: scalp conductivity (in S/m): value: 1 Column 8: voltage (in V) Column 9: Current density along x, Jx (in A/m^2) Column 10: Current density along y, Jy (in A/m^2) Column 11: Current density along z, Jz (in A/m^2) ----------------------------------------- DATA DESCRIPTION FOR: 20201024_NYhead_1elD_output_Sskull_0.02_Sscalp_0.41_Sbrain_0.47_dummy_1.mat 20201024_NYhead_1elD_output_Sskull_1_Sscalp_1_Sbrain_1_dummy_1.mat 20201022_NYhead_5elD_output_d_12_Sskull_0.02_Sscalp_0.41_Sbrain_0.47_dummy_1.mat 20201022_NYhead_5elD_output_d_12_Sskull_1_Sscalp_1_Sbrain_1_dummy_1.mat 20201023_NYhead_VHF_output_F_4_Sskull_0.02_Sscalp_0.41_Sbrain_0.47_dummy_1.mat 20201023_NYhead_VHF_output_F_4_Sskull_1_Sscalp_1_Sbrain_1_dummy_1.mat ----------------------------------------- 1. Number of variables: 6 structures are defined for each file: 2. Number of cases/rows: N/A 3. Missing data codes: Code/symbol Definition NaN undefined value 4. Variable List # # Example. Name: Gender # Description: Gender of respondent # 1 = Male # 2 = Female # 3 = Transgender # 4 = Nonbinary # 5 = Other gender not listed # 6 = Prefer not to answer # A. Name: data, fine, coarse Description: voltage and current density field for the simulated electrode pattern. The structure containing two variables. the "textdata" variable contains labels for the data. The "data" variable contains a table of the following quantities: Column 1: X coordinate (in mm) Column 2: Y coordinate (in mm) Column 3: Z coordinate (in mm) Column 4: Voltage (in V) Column 5: Current density along x, Jx (in A/m^2) Column 6: Current density along y, Jy (in A/m^2) Column 7: Current density along z, Jz (in A/m^2) Column 8: Material indication: 1=scalp 2=skull 3=brain Data range: the three structures data, fine, and coarse contain the same quantities, but computed over different ranges of X,Y, Z: data: X from 80 to 120 with spacing 0.1, Y from 80 to 120 with spacing 0.1, Z from 250 to 300 with spacing 1 fine: X from 80 to 120 with spacing 0.1, Y from 80 to 120 with spacing 0.1, Z from 260 to 270 with spacing 0.1 coarse: X from 0 to 200 with spacing 1, Y from 0 to 230 with spacing 1, Z from 0 to 300 with spacing 1 B. Name: nJ Description: Normal current density at the boundary of the simulation for the simulated electrode pattern. The structure containing two variables. the "textdata" variable contains labels for the data. The "data" variable contains a table of the following quantities: Column 1: X coordinate (in mm) Column 2: Y coordinate (in mm) Column 3: Z coordinate (in mm) Column 4: Normal current density (A/m^2) C. Name: meshS Description: Mesh size of the surface elements for the simulated electrode pattern. The structure containing two variables. the "textdata" variable contains labels for the data. The "data" variable contains a table of the following quantities: Column 1: X coordinate (in mm) Column 2: Y coordinate (in mm) Column 3: Z coordinate (in mm) Column 4: Mesh size (im mm) C. Name: meshV Description: Mesh size of the volume elements for the simulated electrode pattern. The structure containing two variables. the "textdata" variable contains labels for the data. The "data" variable contains a table of the following quantities: Column 1: X coordinate (in mm) Column 2: Y coordinate (in mm) Column 3: Z coordinate (in mm) Column 4: Mesh size (im mm) -------------------------- METHODOLOGICAL INFORMATION -------------------------- # # Software: If specialized software(s) generated your data or # are necessary to interpret it, please provide for each (if # applicable): software name, version, system requirements, # and developer. #If you developed the software, please provide (if applicable): #A copy of the software’s binary executable compatible with the system requirements described above. #A source snapshot or distribution if the source code is not stored in a publicly available online repository. #All software source components, including pointers to source(s) for third-party components (if any) 1. Software-specific information: Name: COMSOL Multiphysics Version:5.5 System Requirements:NA Open Source? (Y/N): N (if available and applicable) Executable URL:NA Source Repository URL:NA Developer: COMSOL Inc Product URL: https://www.comsol.com/ Software source components:NA Name: MATLAB Version:R2018a System Requirements:NA Open Source? (Y/N): N (if available and applicable) Executable URL:NA Source Repository URL:NA Developer: Mathworks Product URL: https://www.mathworks.com/products/matlab.html Software source components:NA Name: New York Head model Version: NA System Requirements: NA Open Source? (Y/N): Y (if available and applicable) Executable URL: https://www.parralab.org/nyhead/NYhead_mesh.mphtxt Source Repository URL: https://www.parralab.org/nyhead/ Developer: Yu (Andy) Huang, Lucas Parra Product URL: NA Software source components:NA Additional Notes(such as, will this software not run on certain operating systems?): NA # # Equipment: If specialized equipment generated your data, # please provide for each (if applicable): equipment name, # manufacturer, model, and calibration information. Be sure # to include specialized file format information in the data # dictionary. # 2. Equipment-specific information: Manufacturer:NA Model:NA (if applicable) Embedded Software / Firmware Name:NA Embedded Software / Firmware Version:NA Additional Notes:NA # # Dates of Data Collection: List the dates and/or times of # data collection. # 3. Date of data collection (single date, range, approximate date) : 2019-2020