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TAPAS ceode toolbox

Current Version: Release 09.2020

Copyright (C) 2020
Dario Schöbi
<dschoebi(at)biomed.ee.ethz.ch>

Translational Neuromodeling Unit (TNU)
Institute for Biomedical Engineering
University of Zurich and ETH Zurich

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Purpose

The general purpose of this Matlab toolbox is the robust estimation of convolution based Dynamic Causal Models (DCMs) for evoked responses (ERPs). Core goals for the toolbox are: flexibility, robustness, and quality assurance. It ties modularly into the existing software suite (SPM12) for the estimation of Dynamic Causal Models for ERP.

Some highlights:

  1. Efficient integration of delay differential equations underlying convolution based DCMs for ERPs for three (ERP model) and four (canonical microcircuit (CMC)) populations. The integration method uses the concept of a Continuous Extension of ODE methods (CEODE).

Installation and Usage

  1. Start MATLAB

  2. Add SPM12 -> EEG toolboxes (e.g. type spm eeg in command window) to the MATLAB path

  3. Replace y{c} = spm_int_L(Q, M, U) with y{c} = tapas_ceode_int_euler(Q, M, U) in spm_gen_erp (line 84)

    For three (ERP) / four (CMC) population DCMs

     Replace f = 'spm_fx_erp' with f = 'tapas_ceode_fx_erp' in spm_dcm_x_neural.m (line 53)
 Replace f = 'spm_fx_cmc' with f = 'tapas_ceode_fx_cmc' in spm_dcm_x_neural.m (line 79)

  4. Run tapas_ceode_init()

    Your setup is compatible, if all of the following information is displayed:

    • Checking for SPM version: You are currently using SPM version: SPM12 (XXXX)

    • Running test scripts: Successful test for your model (ERP/CMC).

    • Checking integrator settings: Your setup currently runs with the tapas/ceode integrator. (No compatibility warning with your model (ERP/CMC))

Tutorial

To see the overall predictions by the integrators, run

tapas_ceode_compare_integrators_erp()

or

tapas_ceode_compare_integrators_cmc()

This will create a figure showing the impact of the delays to the responses in a simple two region setup. We assume a delay on the forward connection (from region 1 to region 2).

To change the delay magnitude, adjust the spacing of tau in line 35 of

tapas_ceode_compare_integrators_erp.m

and

tapas_ceode_compare_integrators_cmc.m

respectively.

To change the parameters of the synthetic setup, change

tapas_ceode_synData_erp.m

or

tapas_ceode_synData_cmc.m

Notes and Troubleshooting

Failed test script

If only the test scripts fail, compare the scaling factors of the dynamical equations between the integration scheme. (see spm_fx_erp/tapas_ceode_fx_erp or spm_fx_cmc/tapas_ceode_fx_cmc, respectively). also see: Contact/Support

Changing the integration step size

By default, the stepsize of the integration for ceode is set to 1 ms .

To change the integration stepsize, either:

a) Add field DCM.M.intstep to the DCM.M structure. This defines a sampling rate for the integration.

b) In tapas_ceode_int_euler.m (line 44): Replace default = 1E-3 to the desired subsampling rate.

Scaling parameters for delays

To change the scaling parameters, either

a) Add field DCM.M.pF.D to the DCM.M structure. This should define a 1x2 matrix with the desired scaling factors for delays.

b) In tapas_ceode_compute_itau.m (line 24): Replace D = [2, 16] (ERP) or D = [1, 8] (CMC) to the desired scaling factors.

Contact/Support

In case you encouter problems with this toolbox, please refer to the GitHub Issue Forum.

Documentation

Documentation for this toolbox is provided in the following forms

  1. Overview and guide to further documentation: README.md and CHANGELOG.md
    • README.md: this file, purpose, installation, getting started, pointer to more help
    • CHANGELOG.md: List of all toolbox versions and the respective release notes, i.e. major changes in functionality, bugfixes etc.
  2. For the general purpose documentation of DCM for ERPs, we refer to the SPM manual.

Compatibility

  • MATLAB (tested with MATLAB R2017b)
  • SPM12 (tested with SPM12, ver.7219 and ver.7771)

Contributors

  • Lead Programmer:
  • Coding and Revision:
    • Cao Tri Do, TNU Zürich
  • Project Team:
    • Jakob Heinzle, TNU Zurich
    • Klaas Enno Stephan, TNU Zurich

Requirements

  • MATLAB
  • SPM12 (also see Compatibility)

References

Main Toolbox Reference

Schöbi D., Do C.T., Heinzle J., Stephan K.E., Technical Note: A novel delay differential integration method for DCM for ERP (in prep)

Schöbi D. Dynamic causal models for inference on neuromodulatory processes in neural circuits. ETH Zürich (Dissertation; Chapter 2)

Related Papers

  1. Schöbi D., Jung F., Frässle S., Endepols H., Moran R.J., Friston K.J., Tittgemeyer M., Heinzle J., Stephan K.E. Model-based prediction of muscarinic receptor function from auditory mismatch negativity responses. bioRXiv. https://doi.org/10.1101/2020.06.08.139550

Copying/License

The ceode Toolbox is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program (see the file LICENSE). If not, see http://www.gnu.org/licenses/.