{"id":17131859,"url":"https://github.com/raamana/niatlas","last_synced_at":"2026-01-05T16:09:38.169Z","repository":{"id":46083977,"uuid":"196403685","full_name":"raamana/niatlas","owner":"raamana","description":"Atlas methods and classes for neuroimaging","archived":false,"fork":false,"pushed_at":"2022-12-26T20:47:40.000Z","size":22,"stargazers_count":2,"open_issues_count":2,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2024-04-24T14:30:07.061Z","etag":null,"topics":["atlas","neuroimaging","neuroimaging-analysis","neuroscience","nibabel","nilabels","nilearn","nipy","parcellation","roi-analysis","roi-segmentation","template"],"latest_commit_sha":null,"homepage":null,"language":"Makefile","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/raamana.png","metadata":{"files":{"readme":"README.rst","changelog":"HISTORY.rst","contributing":"CONTRIBUTING.rst","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-07-11T13:48:24.000Z","updated_at":"2023-10-20T04:07:37.000Z","dependencies_parsed_at":"2023-01-31T01:31:08.276Z","dependency_job_id":null,"html_url":"https://github.com/raamana/niatlas","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/raamana%2Fniatlas","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/raamana%2Fniatlas/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/raamana%2Fniatlas/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/raamana%2Fniatlas/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/raamana","download_url":"https://codeload.github.com/raamana/niatlas/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245212311,"owners_count":20578443,"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":["atlas","neuroimaging","neuroimaging-analysis","neuroscience","nibabel","nilabels","nilearn","nipy","parcellation","roi-analysis","roi-segmentation","template"],"created_at":"2024-10-14T19:25:07.957Z","updated_at":"2026-01-05T16:09:38.101Z","avatar_url":"https://github.com/raamana.png","language":"Makefile","funding_links":[],"categories":[],"sub_categories":[],"readme":"=======\nniatlas\n=======\n\n\n.. image:: https://img.shields.io/pypi/v/niatlas.svg\n        :target: https://pypi.python.org/pypi/niatlas\n\n.. image:: https://img.shields.io/travis/raamana/niatlas.svg\n        :target: https://travis-ci.org/raamana/niatlas\n\n\nAtlas classes and methods for neuroimaging\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n\nThis is a placeholder repository for potential development of ``nibabel``-like python package that is intended to make the management of Atlases for neuroimaging seamless, in all their diverse use-cases. We will collect and link to various relevant resources to facilitate this discussion and project development.\n\n\nAs I currently envision it, a decent ``niatlas`` package would offer the following features (consider it a **wishlist**):\n\n - easy access (including I/O) to all the popular atlases just by their name, both volumetric- and surface-based.\n - a well-defined data structure that provides, not only the parcellations, but also all the relevant ``meta-data``, such as\n    - the source of atlas, in terms of modalities and tha processes that generated it\n    - methods defining the parcellation,\n    - number, names and centroids of ROIs, along with resolution and dimensions\n    - whether it is intended to be used as a volumetric or surface atlas,\n    - **domain tags** that identify which **age-group** this atlas would be ideal for, along with other info related to target population\n    - etc\n - several convenience methods to perform the common operations on atlases including but not limited to\n    - computing ROI-based statistics\n    - masking operations\n - Methods to obtain different variations of the same atlas e.g.\n    - resampling the parcellation to a different resolution, or to different dimensions (that respects the internal parcellations)\n    - scale control in terms of number or size of ROIs i.e. methods for subdividing or clustering existing ROIs\n    - conversion to different spaces, such as between volumetric and surface-oriented spaces\n    - conversion between atlas- and subject-spaces\n - visualization routines for all the common analyses needs\n - easy integration and high interoperability with popular tools and ecosystems\n\nSome prior discussion on potential data structures for Atlas object and uniform access to parcellations at nilearn `here \u003chttps://github.com/nilearn/nilearn/issues/1489\u003e`_\n\nPrior Art (software)\n~~~~~~~~~~~~~~~~~~~~~~~\n\n - nilearn ``fetch_{atlas}`` `utilities \u003chttps://nilearn.github.io/modules/reference.html#module-nilearn.datasets\u003e`_\n - ` nilabels \u003chttps://github.com/nipy/nilabels\u003e`_ :  tools to automate simple manipulations and measurements of medical image segmentations\n - `AtlasReader` to generate coordinate tables and region labels from statistical MRI images : https://github.com/miykael/atlasreader\n - pysurfer visualization tool: https://pysurfer.github.io/auto_examples/index.html\n - python package for subparcellation of fsaverage etc: https://github.com/miykael/parcellation_fragmenter\n - shell scripts to move from atlas space to subject space https://github.com/faskowit/multiAtlasTT\n\n\nResources - atlas collections\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n - Different atlases in MNI space: http://www.lead-dbs.org/helpsupport/knowledge-base/atlasesresources/cortical-atlas-parcellations-mni-space/\n - Different atlases from Thomas Yeo's lab \n    - set 1: https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation\n    - set 2: https://github.com/ThomasYeoLab/CBIG/tree/master/data\n - `BALSA (Brain Analysis Library of Spatial maps and Atlases) \u003chttps://balsa.wustl.edu/\u003e`_ is a database for hosting and sharing neuroimaging and neuroanatomical datasets for human and primate species.\n - Brain signature patterns, atlases of regions, and meta-analysis masks from Tor Wager's lab: https://github.com/canlab/Neuroimaging_Pattern_Masks\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fraamana%2Fniatlas","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fraamana%2Fniatlas","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fraamana%2Fniatlas/lists"}