{"id":23442557,"url":"https://github.com/mvdoc/nipype-tutorial","last_synced_at":"2025-08-22T11:09:12.484Z","repository":{"id":75577340,"uuid":"360893404","full_name":"mvdoc/nipype-tutorial","owner":"mvdoc","description":"A short tutorial on Nipype","archived":false,"fork":false,"pushed_at":"2021-04-26T00:54:43.000Z","size":3162,"stargazers_count":9,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-27T02:38:41.036Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/mvdoc.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-04-23T13:28:56.000Z","updated_at":"2024-01-16T10:21:10.000Z","dependencies_parsed_at":"2023-06-06T23:30:21.329Z","dependency_job_id":null,"html_url":"https://github.com/mvdoc/nipype-tutorial","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/mvdoc%2Fnipype-tutorial","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mvdoc%2Fnipype-tutorial/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mvdoc%2Fnipype-tutorial/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mvdoc%2Fnipype-tutorial/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mvdoc","download_url":"https://codeload.github.com/mvdoc/nipype-tutorial/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248704012,"owners_count":21148268,"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":[],"created_at":"2024-12-23T17:32:45.556Z","updated_at":"2025-04-13T11:23:26.805Z","avatar_url":"https://github.com/mvdoc.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# A minimal tutorial on Nipype by Matteo Visconti dOC\n\nThis repository contains a very, very short tutorial on\n[Nipype](https://nipype.readthedocs.io/en/latest/). It is far from being a\ncomplete tutorial of all features of Nipype. It shows how I would go about creating\na simple workflow for QA, which generates a temporal SNR volume and framewise displacement \nparameters. In the process, it highlights some useful features and practices to iterate\nworkflows over multiple files (largely inspired by [fMRIPrep](https://fmriprep.org/en/stable/)).\n\nThis tutorial was written rather quickly, and the narrative needs to be improved.\nThat said, I think it accomplishes the goal of showcasing the benefits of using Nipype. \nThe audience is assumed to be researchers who already know a great deal about\nneuroimaging, and who are trying to switch to a better way of writing pipelines.\n\nMore exhaustive tutorials are available elsewhere. To learn more about Nipype, I\nhighly recommend checking the following links:\n\n- [Nipype example's page](https://nipype.readthedocs.io/en/latest/examples.html)\n- [Michael Notter's Nipype tutorials](https://miykael.github.io/nipype_tutorial/)\n\nIf you need help, do the following\n\n1. Search through [Nipype's issues](https://github.com/nipy/nipype/issues).\n2. Search on [Neurostars](https://neurostars.org/).\n3. If 1. and 2. do not answer your question, post on Neurostars.\n\nMore advanced users might want to check the following packages containing tested workflows. \nIf you can use them without reinventing the wheel, that's fantastic. Otherwise they are\ngreat for inspiration.\n\n- [nipreps/niworkflows](https://github.com/nipreps/niworkflows) for common MRI workflows\n- [nipreps/sdcflows](https://github.com/nipreps/sdcflows) for distortion-correction workflows.\n\n\n## Installation\n\nPython packages required by this tutorial are listed under `requirements.txt`. Install them with\n\n```bash\npip install -r requirements.txt\n```\n\nin your favorite conda/non-conda environment. Feel free to open an issue or a\nPR if I forgot some packages.\n\nYou also need a working version of FSL and AFNI to run some steps of the\nexample workflows. The tutorial uses [DataLad](https://datalad.org) to download\na dataset from [OpenNeuro](https://openneuro.org). You might need to install\n[git-annex](https://git-annex.branchable.com/).\n\n## Content\n\n- [01-example-interface](01-example-interface.ipynb) describes\n  what an `Interface` object is, one of the building blocks of Nipype workflows.\n- [02-example-simple-workflow](02-example-simple-workflow.ipynb) creates a\n  simple quality-assurance workflow that performs motion correction, computes\n  tSNR on the motion corrected volumes, and computes framewise displacement. In\n  the process, it explains some core concepts of writing Nipype workflows.\n- [03-extending-our-first-workflow](03-extending-our-first-workflow.ipynb)\n  extends the workflow so that it can be run over multiple files. It showcases\n  the `Function` interface, some advanced features of Nipype to rename\n  filenames, one way to create subworkflows for each input file, and how to use\n  a `DataSink` node.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmvdoc%2Fnipype-tutorial","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmvdoc%2Fnipype-tutorial","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmvdoc%2Fnipype-tutorial/lists"}