{"id":37109497,"url":"https://github.com/labneurocogdevel/fmri_processing_scripts","last_synced_at":"2026-01-14T13:01:12.278Z","repository":{"id":4159827,"uuid":"5274327","full_name":"LabNeuroCogDevel/fmri_processing_scripts","owner":"LabNeuroCogDevel","description":"legacy signal processing leveraging afni, ants, fsl, nipy, robex, and wavelet toolbox - brnfswdktm","archived":false,"fork":false,"pushed_at":"2025-09-25T18:06:21.000Z","size":13674,"stargazers_count":3,"open_issues_count":3,"forks_count":1,"subscribers_count":18,"default_branch":"master","last_synced_at":"2025-09-25T20:24:46.025Z","etag":null,"topics":["fmri","fmri-preprocessing"],"latest_commit_sha":null,"homepage":"","language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LabNeuroCogDevel.png","metadata":{"files":{"readme":"readme.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":"citations.txt","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2012-08-02T15:33:32.000Z","updated_at":"2025-03-27T13:45:23.000Z","dependencies_parsed_at":"2023-01-11T16:34:58.071Z","dependency_job_id":"ca4103d5-1c57-4371-808a-a37c14ae1272","html_url":"https://github.com/LabNeuroCogDevel/fmri_processing_scripts","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/LabNeuroCogDevel/fmri_processing_scripts","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LabNeuroCogDevel%2Ffmri_processing_scripts","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LabNeuroCogDevel%2Ffmri_processing_scripts/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LabNeuroCogDevel%2Ffmri_processing_scripts/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LabNeuroCogDevel%2Ffmri_processing_scripts/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LabNeuroCogDevel","download_url":"https://codeload.github.com/LabNeuroCogDevel/fmri_processing_scripts/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LabNeuroCogDevel%2Ffmri_processing_scripts/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28420816,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-14T10:47:48.104Z","status":"ssl_error","status_checked_at":"2026-01-14T10:46:19.031Z","response_time":107,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["fmri","fmri-preprocessing"],"created_at":"2026-01-14T13:01:11.676Z","updated_at":"2026-01-14T13:01:12.263Z","avatar_url":"https://github.com/LabNeuroCogDevel.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MRI Preprocessing\n\n[![DOI](https://zenodo.org/badge/5274327.svg)](https://zenodo.org/badge/latestdoi/5274327)\n\n## Tools\n\n  * `preprocessMprage`\n  * `preprocessFunctional`\n    * `sliceMotion4d`\n  * `ROI_TempCorr.R`\n\n\n## Output scheme\n\n[`preprocessFunctional`](preprocessFunctional#L=193) prepends each processing step as a prefix to each input, creating files like `brnaswutm_func.nii.gz`. In reverse order (order of name), the posible steps are:\n\n\n|prefix | desc|\n|---|-----|\n|`A` | Auto Correlation removal (optional) |\n|`b` | Bandpass filtering (optional, simultaneous with regression, for rest) |\n|`g` | Global signal regression (optional, label optional, part of *r*) |\n|`r` | Nuisance *r*egression (optional) |\n|`n` | Intensity *n*ormalization |\n|`f` | High-pass *f*iltering (optional, simultaneous with regression, for task) |\n|`a` | ICA-AROMA (optional, requires warp) |\n|`s` | Smoothing |\n|`w` | Co-registration and *w*arping to standard space (spatial normalization, optional) |\n|`u` | Field map unwarping (optional; Susceptibility Distortion Correction) |\n|`d` | Intensity/wavelet *d*espiking (optional) |\n|`k` | S*k*ull stripping and intensity thresholding |\n|`mt` | 4D slice-time motion correction ([sliceMotion4d](sliceMotion4d))|\n|`m` | *M*otion correction |\n|`t` | Slice *t*iming correction |\n|`p` | Physio/retroicor (optional) |\n|`0` | truncate (optional, if scanner output includes disacq)|\n|`_` | fslorient |\n\n## Depends\nsee [bibtex](./preproc.bib) or plain text [citations](./citations.txt) and `preprocessFunctional -check_dependencies`\n\n * [ROBEX](https://sites.google.com/site/jeiglesias/ROBEX)\n * [ANTs](http://stnava.github.io/ANTs/)\n * [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)\n * [ICA-AROMA](https://github.com/maartenmennes/ICA-AROMA)\n   * v4 `aroma`: https://github.com/rtrhd/ICA-AROMA\n   * orig repackages as `ica_aroma`: https://github.com/WillForan/ICA-AROMA/tree/maartenmennes-setup.py\n * [AFNI](https://afni.nimh.nih.gov/)\n * [MNI2009c](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009)\n * [Brain Wavelet ToolboX](http://www.brainwavelet.org/downloads/brainwavelet-toolbox/)\n * [NiPy(4dslicewarp)](https://nipype.readthedocs.io/en/0.12.0/about.html)\n\n## Testing\n\nLimited testing using [bats](https://github.com/bats-core/bats-core) in `test/`.\nsee `make test` ([Makefile](./Makefile))\n\n## See also\n * [fmriprep](https://fmriprep.readthedocs.io/en/stable/index.html), [clpipe](https://github.com/cohenlabUNC/clpipe), [xcp-d](https://github.com/PennLINC/xcp_d#when-you-should-not-use-xcp-d)\n * [afni\\_proc](https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html)\n\n## Usage Notes\n### ROI Temp Corr\nRunning `ROI_TempCorr.R` is internally parallelized (default `njobs=4`). If you are also forking in e.g. a bash for loop like `ROI_TempCorr.R ... \u0026` (and maybe paired with [lncdtool](https://github.com/lncd/lncdtools)'s [`waitforjobs`](https://lncd.github.io/lncdtools/shell/#waitforjobs), some care will need to be taken to not hit a R parallel package socket port conflict.\n1. the easiest solution is to disable internal parallelization:  `ROI_TempCorr.R ... -njobs 1`.\n1.  Alternatively, you can manually set the port for each `ROI_TempCorr.R`. Consider\n```bash \nROI_TempCorr.R ... -port \"$((11290 + $(pgrep -caf ROI_TempCorr) ))\"\n```\n\n\n## FYI OSS\n\nThe code is \"for your information.\" There are no plans (or avaiable resources) to support external usage.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flabneurocogdevel%2Ffmri_processing_scripts","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flabneurocogdevel%2Ffmri_processing_scripts","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flabneurocogdevel%2Ffmri_processing_scripts/lists"}