FARM

This repository is a MATLAB implementation of FARM processing, for removing fMRI artifacts from EMG recordings.

Citation

Please cite :

• The original article :
  Van der Meer, J. N., Tijssen, M. A. J., Bour, L. J., van Rootselaar, A. F., & Nederveen, A. J. (2010).
  Robust EMG–fMRI artifact reduction for motion (FARM).
  Clinical Neurophysiology, 121(5), 766–776.
  https://doi.org/10.1016/j.clinph.2009.12.035
• The GitHub page of the first author :
  https://github.com/jnvandermeer
• This GitHub repository :
  https://github.com/benoitberanger/FARM

Requirements

• MATLAB : https://www.mathworks.com/. Tested version : R2017b
• FieldTrip, a MATLAB tooblox : https://github.com/fieldtrip/fieldtrip
• no specific MATLAB official toolbox => if you encounter a compatibility problem, please open an issue. (except for farm_plot_spectrogram)

Exemple

Open and run sample_dataset/example_denoise_sample_dataset_MEMB.m

Tips

All functions you need to use are in the root directory.
The +farm directory is a package (MATLAB behaviour) that contains all subfonctions. You probably don't need to use the functions in the package.
src directory contains all un-modified original functions, that have been modified later for FARM purpose.

Based on

• Van der Meer, J. N., Tijssen, M. A. J., Bour, L. J., van Rootselaar, A. F., & Nederveen, A. J. (2010). Robust EMG–fMRI artifact reduction for motion (FARM). Clinical Neurophysiology, 121(5), 766–776. https://doi.org/10.1016/j.clinph.2009.12.035
• R.K. Niazy, C.F. Beckmann, G.D. Iannetti, J.M. Brady, and S.M. Smith. Removal of FMRI environment artifacts from EEG data using optimal basis sets. NeuroImage 28 (2005) 720 – 737. https://doi.org/10.1016/j.neuroimage.2005.06.067
• P.J. Allen, O. Josephs, R. Turner. A Method for Removing Imaging Artifact from Continuous EEG Recording during Functional MRI. NeuroImage 12, 230-239 (2000). https://doi.org/10.1006/nimg.2000.0599
• S.I. Gonçalves, P.J.W. Pouwels, J.P.A. Kuijer, R.M. Heethaar, J.C. de Munck. Artifact removal in co-registered EEG/fMRI by selective average subtraction. Clinical Neurophysiology 118 (2007) 2437–2450. https://doi.org/10.1016/j.clinph.2007.08.017
• Jeffrey C. Lagarias, James A. Reeds, Margaret H. Wright, and Paul E Wright. Convergence Properties of the Nelder--Mead Simplex Method in Low Dimensions. December 1998 SIAM Journal on Optimization 9(1):112-147. https://doi.org/10.1137/S1052623496303470