{"id":13676433,"url":"https://github.com/bids-apps/rsHRF","last_synced_at":"2025-04-29T07:32:16.848Z","repository":{"id":54410213,"uuid":"102780962","full_name":"bids-apps/rsHRF","owner":"bids-apps","description":"Resting state HRF estimation from BOLD-fMRI signal","archived":false,"fork":false,"pushed_at":"2023-01-07T14:27:52.000Z","size":216257,"stargazers_count":34,"open_issues_count":5,"forks_count":10,"subscribers_count":14,"default_branch":"master","last_synced_at":"2025-04-12T15:04:57.083Z","etag":null,"topics":["bids","bidsapp","fmri","fmri-data-analysis","timeseries"],"latest_commit_sha":null,"homepage":"http://bids-apps.neuroimaging.io/rsHRF/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bids-apps.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2017-09-07T20:08:52.000Z","updated_at":"2025-02-12T23:45:46.000Z","dependencies_parsed_at":"2023-02-07T10:15:28.885Z","dependency_job_id":null,"html_url":"https://github.com/bids-apps/rsHRF","commit_stats":null,"previous_names":[],"tags_count":20,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2FrsHRF","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2FrsHRF/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2FrsHRF/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2FrsHRF/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bids-apps","download_url":"https://codeload.github.com/bids-apps/rsHRF/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251455925,"owners_count":21592263,"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":["bids","bidsapp","fmri","fmri-data-analysis","timeseries"],"created_at":"2024-08-02T13:00:26.815Z","updated_at":"2025-04-29T07:32:16.267Z","avatar_url":"https://github.com/bids-apps.png","language":"Python","funding_links":[],"categories":["BIDS Apps","Python"],"sub_categories":["others"],"readme":"Resting state HRF estimation and deconvolution.\n========\n[![PyPI version](https://badge.fury.io/py/rsHRF.png)](https://badge.fury.io/py/rsHRF)\n\nPlease refer to https://github.com/compneuro-da/rsHRF for MATLAB version\n\n![BOLD HRF](https://github.com/guorongwu/rsHRF/raw/master/docs/BOLD_HRF.png)\n\n\nThe basic idea \n-------------\n\nThis toolbox is aimed to retrieve the onsets of pseudo-events triggering an hemodynamic response from resting state fMRI BOLD voxel-wise signal.\nIt is based on point process theory, and fits a model to retrieve the optimal lag between the events and the HRF onset, as well as the HRF shape, using a choice of basis functions (the canonical shape with two derivatives, (smoothed) Finite Impulse Response, mixture of gammas).\n\n![BOLD HRF](http://users.ugent.be/~dmarinaz/example_hrf.png)\n\nOnce that the HRF has been retrieved for each voxel, it can be deconvolved from the time series (for example to improve lag-based connectivity estimates), or one can map the shape parameters everywhere in the brain (including white matter), and use the shape as a pathophysiological indicator.\n\n![HRF map](http://users.ugent.be/~dmarinaz/FIR_Height_full_layout.png)\n\nHow to use the toolbox \n-------------\n\nThe input is voxelwise BOLD signal, already preprocessed according to your favorite recipe. Important thing are:\n\n* bandpass filter in the 0.01-0.08 Hz interval (or something like that)\n* z-score the voxel BOLD time series\n\nTo be on the safe side, these steps are performed again in the code.\n\nThe input can be images (3D or 4D), or directly matrices of [observation x voxels].\n\nIt is possible to use a temporal mask to exclude some time points (for example after scrubbing).\n\nThe demos allow you to run the analyses on several formats of input data.\n\nPython Package and BIDS-app \n-------------\nA BIDS-App has been made for easy and reproducible analysis. Its documentation can be accessed at:\n\nhttp://bids-apps.neuroimaging.io/rsHRF/\n\nCollaborators \n-------------\n* Guorong Wu\n* Nigel Colenbier\n* Sofie Van Den Bossche\n* Daniele Marinazzo\n\n* Madhur Tandon (Python - BIDS)\n* Asier Erramuzpe (Python - BIDS)\n* Amogh Johri   (Python - BIDS)\n\n\n**References**\n--------\n1. Wu, G. R., Colenbier, N., Van Den Bossche, S., Clauw, K., Johri, A., Tandon, M., \u0026 Marinazzo, D. (2021). rsHRF: A toolbox for resting-state HRF estimation and deconvolution. Neuroimage, 244, 118591. [open access journal page](https://www.sciencedirect.com/science/article/pii/S1053811921008648)\n\n2. Guo-Rong Wu, Wei Liao, Sebastiano Stramaglia, Ju-Rong Ding, Huafu Chen, Daniele Marinazzo*. \"A blind deconvolution approach to recover effective connectivity brain networks from resting state fMRI data.\" Medical Image Analysis, 2013, 17:365-374. [Open access institutional repo](https://biblio.ugent.be/publication/3118166)\n\n3. Guo-Rong Wu, Daniele Marinazzo. \"Sensitivity of the resting state hemodynamic response function estimation to autonomic nervous system fluctuations.\" Philosophical Transactions of the Royal Society A, 2016, 374: 20150190. [Open access institutional repo](https://biblio.ugent.be/publication/7174286)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-apps%2FrsHRF","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbids-apps%2FrsHRF","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-apps%2FrsHRF/lists"}