{"id":18142471,"url":"https://github.com/benoitberanger/farm","last_synced_at":"2025-04-06T19:21:40.325Z","repository":{"id":117579974,"uuid":"185427803","full_name":"benoitberanger/FARM","owner":"benoitberanger","description":"MATLAB implementation of FARM toolbox, for removing MRI artifacts from EMG recordings","archived":false,"fork":false,"pushed_at":"2022-11-08T17:59:41.000Z","size":31286,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-13T01:25:58.395Z","etag":null,"topics":["artifact","denoising","electrophysiology","emg","fieldtrip","fmri","matlab","mri"],"latest_commit_sha":null,"homepage":"","language":"MATLAB","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/benoitberanger.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-05-07T15:17:31.000Z","updated_at":"2022-08-22T12:29:19.000Z","dependencies_parsed_at":null,"dependency_job_id":"b98a70f9-691d-4611-9a66-142bc68416cd","html_url":"https://github.com/benoitberanger/FARM","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benoitberanger%2FFARM","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benoitberanger%2FFARM/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benoitberanger%2FFARM/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benoitberanger%2FFARM/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/benoitberanger","download_url":"https://codeload.github.com/benoitberanger/FARM/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247535933,"owners_count":20954648,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["artifact","denoising","electrophysiology","emg","fieldtrip","fmri","matlab","mri"],"created_at":"2024-11-01T18:22:06.397Z","updated_at":"2025-04-06T19:21:40.288Z","avatar_url":"https://github.com/benoitberanger.png","language":"MATLAB","funding_links":[],"categories":[],"sub_categories":[],"readme":"# FARM\nThis repository is a MATLAB implementation of FARM processing, for removing fMRI artifacts from EMG recordings.\n\n# Citation\nPlease cite :\n- _The original article_ :  \n  Van der Meer, J. N., Tijssen, M. A. J., Bour, L. J., van Rootselaar, A. F., \u0026 Nederveen, A. J. (2010).  \n  **Robust EMG–fMRI artifact reduction for motion (FARM)**.  \n  Clinical Neurophysiology, 121(5), 766–776.  \n  https://doi.org/10.1016/j.clinph.2009.12.035\n- _The GitHub page of the first author_ :  \n  https://github.com/jnvandermeer\n- _This GitHub repository_ :  \n  https://github.com/benoitberanger/FARM\n\n# Requirements\n- MATLAB : https://www.mathworks.com/. Tested version : R2017b\n- FieldTrip, a MATLAB tooblox : https://github.com/fieldtrip/fieldtrip\n- **no specific MATLAB official toolbox** =\u003e if you encounter a compatibility problem, please open an issue. (except for farm_plot_spectrogram)\n\n# Exemple\nOpen and run [sample_dataset/example_denoise_sample_dataset_MEMB.m](sample_dataset/example_denoise_sample_dataset_MEMB.m)\n\n# Tips\nAll functions you need to use are in the _root_ directory.  \nThe **+farm** directory is a package (MATLAB behaviour) that contains all subfonctions. You probably don't need to use the functions in the package.  \n**src** directory contains all un-modified original functions, that have been modified later for FARM purpose.\n\n# Based on\n- Van der Meer, J. N., Tijssen, M. A. J., Bour, L. J., van Rootselaar, A. F., \u0026 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\n- 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\n- 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\n- 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\n- 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\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbenoitberanger%2Ffarm","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbenoitberanger%2Ffarm","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbenoitberanger%2Ffarm/lists"}