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Merge pull request #43 from emersonkeenan/master
Version v1.3-alpha - Add asymmetric volume conductor modeling code
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‎.gitignore‎

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GUI/*.mat
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_site/
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testset/
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data/anatomic_models/
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data/temp/

‎CONTRIBUTING.md‎

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@@ -9,7 +9,7 @@ There are many ways to contribute to the _FECGSYN_:
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* **Fork it** Feel free to fork the repository on the project's main page
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+ **Create a pull request** We welcome novel algorithms and improvements to the <em>FECGSYN</em> toolbox. We strongly believe that open-source is the way to go with NI-FECG analysis.
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+ **Eeww bugs!** In case you in encounter a bug and cannot figure out the solution, please have a look on the opened issues before creating a new bug issue
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+ **Eeww bugs!** In case you encounter a bug and cannot figure out the solution, please have a look on the opened issues before creating a new bug issue
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+ **Pitch in your new ideas** for future releases by suggesting an enhancement
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@@ -37,6 +37,9 @@ The current version of the <em>FECGSYN</em> was developed thanks to the followin
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- Mohsan Alvi
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- Reza Sameni
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- Sebastian Zaunseder
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- Emerson Keenan
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- Chandan Karmakar
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- Marimuthu Palaniswami
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‎README.md‎

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[![license](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](./LICENSE)
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# _FECGSYN_ toolbox, version 1.2, March 2017
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# _FECGSYN_ toolbox, version 1.3-alpha, August 2019
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### Open-source platform for reproducible NI-FECG research
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## Authors
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_FECGSYN_ is the product of a collaboration between the Department of Engineering Science, University of Oxford (DES-OX), the Institute of Biomedical Engineering, TU Dresden (IBMT-TUD) and the Biomedical Engineering Faculty at the Technion Israel Institute of Technology (BME-IIT). The authors are:
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_FECGSYN_ is the product of a collaboration between the Department of Engineering Science, University of Oxford (DES-OX), the Institute of Biomedical Engineering, TU Dresden (IBMT-TUD), the Department of Electrical and Electronic Engineering, University of Melbourne (EEE-UOM) and the Biomedical Engineering Faculty at the Technion Israel Institute of Technology (BME-IIT). The authors are:
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- Joachim Behar
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- Fernando Andreotti
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- Julien Oster
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- Sebastian Zaunseder
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- Gari D. Clifford
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- Emerson Keenan
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- Chandan Karmakar
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- Marimuthu Palaniswami
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Contacts: [email protected] & [email protected]
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## References
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When using the _FECGSYN_ please refer to:
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When using _FECGSYN_ please reference at least one of the following articles:
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Behar, Joachim, Fernando Andreotti, Sebastian Zaunseder, Qiao Li, Julien Oster, and Gari D Clifford. 2014.
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"An ECG Model for Simulating Maternal-Foetal Activity Mixtures on Abdominal ECG Recordings." _Physiol Meas_ **35(8)**, pp.1537-50, 2014.
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1. Behar, Joachim, Fernando Andreotti, Sebastian Zaunseder, Qiao Li, Julien Oster, and Gari D Clifford. 2014. "An ECG Model for Simulating Maternal-Foetal Activity Mixtures on Abdominal ECG Recordings." _Physiol Meas_ **35(8)**, pp.1537-50, 2014.
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Andreotti F., Behar J., Zaunseder S.,Oster J. and Clifford G D., An Open-Source Framework for Stress-Testing Non-Invasive Foetal ECG Extraction Algorithms. _Physiol Meas_ **37(5)**, pp. 627-648, 2016.
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and/or
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2. Andreotti F., Behar J., Zaunseder S.,Oster J. and Clifford G D., An Open-Source Framework for Stress-Testing Non-Invasive Foetal ECG Extraction Algorithms. _Physiol Meas_ **37(5)**, pp. 627-648, 2016.
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If you are using _FECGSYN's_ asymmetric volume conductor modeling capability, please reference the following article:
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3. Keenan E., Karmakar C K. and Palaniswami M., The effects of asymmetric volume conductor modeling on non-invasive fetal ECG extraction. _Physiol Meas_ **39(10)**, pp. 105013, 2018.
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## License
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- _arrow.m_, by Dr. Erik A. Johnson, [available here](https://uk.mathworks.com/matlabcentral/fileexchange/278-arrow), (BSD license)
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- _fwhm.m_, v1.2, by Patrick Egan, [available here](http://uk.mathworks.com/matlabcentral/fileexchange/10590-fwhm), (BSD license)
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- _pcorr2.m_, by Peter Rydesäter, [available here](https://uk.mathworks.com/matlabcentral/fileexchange/4012-prcorr2-10-times-faster-correlation-coef) (BSD license)
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- _FieldTrip: The MATLAB toolbox for MEG and EEG analysis_, v20190828, by Robert Oostenveld, Pascal Fries, Eric Maris, and Jan-Mathijs Schoffelen, [available here](https://github.com/fieldtrip/fieldtrip) (licensed under GNU GPL 2.0)
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- _Iso2Mesh_, v1.9.0-1, Qianqian Fang, [available here](https://github.com/fangq/iso2mesh) (licensed under GNU GPL 2.0)
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Not provided with package, ocasionally required, see [install instructions](http://fernandoandreotti.github.io/fecgsyn/pages/install.html):
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- **WFDB Toolbox for MATLAB and Octave**, v.0.9.9, by Dr. Ikaro Silva, [available here](https://www.physionet.org/physiotools/matlab/wfdb-app-matlab/) (licensed under GNU GPL 2.0)
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- **Pre-processed anatomic models**, by Emerson Keenan, [available here](https://github.com/emersonkeenan/fecgsyn-anatomic-models) (licensed under CC BY-NC-SA 2.0 FR)

‎cinc_animation.mp4‎

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‎subfunctions/data-generation/calculate_lead_field.m‎

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function model = calculate_lead_field(model)
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% function model = calculate_lead_field(model)
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% Calculate lead field matrix from input model
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%
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% inputs:
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% model: Struct of anatomic model
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% model.header = information on anatomic model type
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% model.compartments = struct array of model compartments
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% model.variants = struct array of model variants
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% model.folder = folder of anatomic model
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% model.name = name of anatomic model
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% model.sources = name of sources file
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% model.sensors = name of sensors file
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% model.fem = finite element mesh ready for solver
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%
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% outputs:
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% model: Struct of anatomic model
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% model.header = information on anatomic model type
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% model.compartments = struct array of model compartments
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% model.variants = struct array of model variants
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% model.folder = folder of anatomic model
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% model.name = name of anatomic model
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% model.sources = name of sources file
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% model.sensors = name of sensors file
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% model.fem = finite element mesh ready for solver
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% model.leadfield = struct array of maternal and fetal lead field matrices
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%
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%
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% --
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% fecgsyn toolbox, version 1.3-alpha, August 2019
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% Released under the GNU General Public License
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%
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% Copyright (C) 2019 Emerson Keenan
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% Department of Electrical and Electronic Engineering, University of
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% Melbourne
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% [email protected]
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%
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% For more information visit: http://www.fecgsyn.com
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%
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% Referencing this work
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%
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% Keenan E., Karmakar C K. and Palaniswami M., The effects of asymmetric volume conductor modeling on non-invasive fetal ECG extraction.
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% Physiol Meas 39(10), pp. 105013, 2018.
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%
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%
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% Last updated : 05-09-2019
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%
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% This program is free software: you can redistribute it and/or modify
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% it under the terms of the GNU General Public License as published by
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% the Free Software Foundation, either version 3 of the License, or
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% (at your option) any later version.
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%
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% This program is distributed in the hope that it will be useful,
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% but WITHOUT ANY WARRANTY; without even the implied warranty of
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% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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% GNU General Public License for more details.
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%
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% You should have received a copy of the GNU General Public License
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% along with this program. If not, see <http://www.gnu.org/licenses/>.
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%
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% Write variables to temporary storage
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sensors = model.fem.sensors;
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sources = model.fem.sources;
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conductivity = model.fem.conductivity;
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ft_sources = [sources.maternal; sources.fetal];
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% Create a set of electrodes at chosen sensor positions
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sens.elecpos = sensors;
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sens.label = {};
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nsens = size(sens.elecpos,1);
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sens.unit = 'mm';
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for ii=1:nsens
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sens.label{ii} = sprintf('vertex%03d', ii);
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end
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% Remove fields from model before passing to solver
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model.fem = rmfield(model.fem,'sensors');
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model.fem = rmfield(model.fem,'sources');
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model.fem = rmfield(model.fem,'conductivity');
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% Pass model to FieldTrip-Simbio solver
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headmodel = ft_headmodel_simbio(model.fem,'conductivity',conductivity);
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headmodel.unit = 'mm';
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[headmodel, ~] = ft_prepare_vol_sens(headmodel,sens);
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lf = ft_compute_leadfield(ft_sources,sens,headmodel);
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% Add fields to model after returning from solver
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model.fem.sensors = sensors;
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model.fem.sources = sources;
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model.fem.conductivity = conductivity;
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model.leadfield = struct('maternal',lf(:,1:3),'fetal',lf(:,4:6));
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end

‎subfunctions/data-generation/generate_fe_mesh.m‎

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function model = generate_fe_mesh(model)
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% function model = generate_fe_mesh(model)
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% Generate finite element mesh from input model
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%
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% inputs:
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% model: Struct of anatomic model
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% model.header = information on anatomic model type
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% model.compartments = struct array of model compartments
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% model.variants = struct array of model variants
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% model.folder = folder of anatomic model
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% model.name = name of anatomic model
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% model.sources = name of sources file
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% model.sensors = name of sensors file
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%
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% outputs:
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% model: Struct of anatomic model
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% model.header = information on anatomic model type
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% model.compartments = struct array of model compartments
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% model.variants = struct array of model variants
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% model.folder = folder of anatomic model
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% model.name = name of anatomic model
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% model.sources = name of sources file
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% model.sensors = name of sensors file
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% model.fem = finite element mesh ready for solver
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%
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% --
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% fecgsyn toolbox, version 1.3-alpha, August 2019
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% Released under the GNU General Public License
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%
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% Copyright (C) 2019 Emerson Keenan
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% Department of Electrical and Electronic Engineering, University of
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% Melbourne
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% [email protected]
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%
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% For more information visit: http://www.fecgsyn.com
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%
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% Referencing this work
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%
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% Keenan E., Karmakar C K. and Palaniswami M., The effects of asymmetric volume conductor modeling on non-invasive fetal ECG extraction.
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% Physiol Meas 39(10), pp. 105013, 2018.
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%
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%
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% Last updated : 05-09-2019
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%
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% This program is free software: you can redistribute it and/or modify
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% it under the terms of the GNU General Public License as published by
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% the Free Software Foundation, either version 3 of the License, or
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% (at your option) any later version.
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%
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% This program is distributed in the hope that it will be useful,
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% but WITHOUT ANY WARRANTY; without even the implied warranty of
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% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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% GNU General Public License for more details.
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%
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% You should have received a copy of the GNU General Public License
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% along with this program. If not, see <http://www.gnu.org/licenses/>.
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%
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conf = FECGSYN_check_platform();
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if ispc
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clear tempdir
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setenv('TEMP',char(strcat(conf.fecgsynpath, 'data', conf.slashchar, 'temp', conf.slashchar, model.name, conf.slashchar)));
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elseif isunix
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clear tempdir
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setenv('TMP',char(strcat(conf.fecgsynpath, 'data', conf.slashchar, 'temp', conf.slashchar, model.name, conf.slashchar)));
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else
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error('Platform not supported');
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end
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%% Read in models, sources and sensors
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[fetusPos, fetusTri] = FECGSYN_read_off(strcat(model.folder, conf.slashchar, model.name, conf.slashchar, model.name, '_', model.compartments.fetus.mesh.tri, '.off'));
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[amnioticPos, amnioticTri] = FECGSYN_read_off(strcat(model.folder, conf.slashchar, model.name, conf.slashchar, model.name, '_', model.compartments.amniotic_fluid.mesh.tri, '.off'));
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[abdoPos, abdoTri] = FECGSYN_read_off(strcat(model.folder, conf.slashchar, model.name, conf.slashchar, model.name, '_', model.compartments.maternal_abdomen.mesh.tri, '.off'));
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[maternalSource, fetalSource] = FECGSYN_read_sources(strcat(model.folder, conf.slashchar, model.name, conf.slashchar, model.name, '_', model.sources, '.sources'));
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sensors = FECGSYN_read_sensors(strcat(model.folder, conf.slashchar, model.name, conf.slashchar, model.name, '_', model.sensors, '.sensors'));
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sources = struct('fetal',fetalSource,'maternal',maternalSource);
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%% Define conductivities for each region
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% c(1) = Fetus
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% c(2) = Vernix Caseosa
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% c(3) = Amniotic Fluid
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% c(4) = Maternal abdomen
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c = [];
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c(1) = model.compartments.fetus.conductivity;
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c(2) = model.compartments.vernix.conductivity;
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c(3) = model.compartments.amniotic_fluid.conductivity;
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c(4) = model.compartments.maternal_abdomen.conductivity;
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%% Define internal point for each region (columns 1-3) and maxvol (column 4)
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pFetus = [model.compartments.fetus.mesh.innerpoint model.compartments.fetus.meshsize];
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pAmniotic = [model.compartments.amniotic_fluid.mesh.innerpoint model.compartments.amniotic_fluid.meshsize];
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pAbdo = [model.compartments.maternal_abdomen.mesh.innerpoint model.compartments.maternal_abdomen.meshsize];
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%% Check if vernix is present
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if isempty(model.compartments.vernix.mesh.tri) % No vernix present
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c = [c(1) c(3) c(3) c(4)];
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regions = [pFetus; pAmniotic; pAbdo];
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[fullV,fullF] = mergemesh(fetusPos,fetusTri,amnioticPos,amnioticTri,abdoPos,abdoTri);
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else % Vernix present
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[vernixPos, vernixTri] = FECGSYN_read_off(strcat(model.folder, conf.slashchar, model.name, conf.slashchar, model.name, '_vernix_', model.compartments.vernix.mesh.tri, '.off'));
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pVernix = [model.compartments.vernix.mesh.innerpoint model.compartments.vernix.meshsize];
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regions = [pFetus; pVernix; pAmniotic; pAbdo];
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[fetusAndVernixPos,fetusAndVernixTri]= FECGSYN_join_nodes(fetusPos,fetusTri,vernixPos,vernixTri);
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[fullV,fullF]=mergemesh(fetusAndVernixPos,fetusAndVernixTri,amnioticPos,amnioticTri,abdoPos,abdoTri);
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end
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%% Compute tetrahedralization using iso2mesh
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[node,elem, ~]=surf2mesh(fullV,fullF,[],[],1,[],regions,[]);
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faceRegions = elem(:,5);
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%% Fix region labels for no vernix case
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if isempty(model.compartments.vernix.mesh.tri) % No vernix present
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for i=1:length(faceRegions)
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if faceRegions(i) > 1
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faceRegions(i) = faceRegions(i)+1;
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end
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end
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end
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elem=meshreorient(node,elem(:,1:4)); % Ensure all elements are oriented
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% consistently
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elem = [elem faceRegions];
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abdoIndex = sensors(:,2);
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abdoSensors = abdoPos(abdoIndex,:);
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%% Create output finite element mesh structure
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model.fem = struct();
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model.fem.pos = node;
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model.fem.tet = elem(:,1:4);
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model.fem.tissuelabel = {'fetus','vernix','amniotic', 'abdomen'};
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model.fem.tissue = faceRegions;
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model.fem.sensors = abdoSensors;
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model.fem.sources = sources;
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model.fem.conductivity = c;
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end

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