https://github.com/benoitberanger/farm
MATLAB implementation of FARM toolbox, for removing MRI artifacts from EMG recordings
https://github.com/benoitberanger/farm
artifact denoising electrophysiology emg fieldtrip fmri matlab mri
Last synced: 6 months ago
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MATLAB implementation of FARM toolbox, for removing MRI artifacts from EMG recordings
- Host: GitHub
- URL: https://github.com/benoitberanger/farm
- Owner: benoitberanger
- License: gpl-3.0
- Created: 2019-05-07T15:17:31.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2022-11-08T17:59:41.000Z (almost 3 years ago)
- Last Synced: 2025-02-13T01:25:58.395Z (8 months ago)
- Topics: artifact, denoising, electrophysiology, emg, fieldtrip, fmri, matlab, mri
- Language: MATLAB
- Homepage:
- Size: 29.8 MB
- Stars: 2
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
Awesome Lists containing this project
README
# 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](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