{"id":13676325,"url":"https://github.com/bids-apps/antsCorticalThickness","last_synced_at":"2025-04-29T06:31:37.960Z","repository":{"id":73504488,"uuid":"106866069","full_name":"bids-apps/antsCorticalThickness","owner":"bids-apps","description":"BIDS App for calculating cortical thickness using ANTs","archived":false,"fork":false,"pushed_at":"2024-11-04T08:32:01.000Z","size":42,"stargazers_count":0,"open_issues_count":1,"forks_count":2,"subscribers_count":5,"default_branch":"master","last_synced_at":"2024-11-11T18:40:59.326Z","etag":null,"topics":["bids","bidsapp"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-10-13T19:36:36.000Z","updated_at":"2024-11-04T08:32:02.000Z","dependencies_parsed_at":"2024-04-08T22:32:05.936Z","dependency_job_id":"0bbd94d5-c55e-4323-9abe-0d8fa9f6489c","html_url":"https://github.com/bids-apps/antsCorticalThickness","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2FantsCorticalThickness","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2FantsCorticalThickness/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2FantsCorticalThickness/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2FantsCorticalThickness/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bids-apps","download_url":"https://codeload.github.com/bids-apps/antsCorticalThickness/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251450656,"owners_count":21591407,"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"],"created_at":"2024-08-02T13:00:22.858Z","updated_at":"2025-04-29T06:31:34.113Z","avatar_url":"https://github.com/bids-apps.png","language":"Python","funding_links":[],"categories":["BIDS Apps"],"sub_categories":["others"],"readme":"## BIDS App for calculating cortical thickness using ANTs\n\nThis BIDS App runs ANTs cortical thickness estimation pipeline.\n\nFor more information about the specification of BIDS Apps see [here](https://docs.google.com/document/d/1E1Wi5ONvOVVnGhj21S1bmJJ4kyHFT7tkxnV3C23sjIE/edit#).\n\n### Description\nThe app finds all T1w files for each subject and runs antsCorticalThickness.sh (if there is only one T1w file per subject) or\nantsLongitudinalCorticalThickness.sh (if there are more than one T1w files).\n\n### Documentation\nhttps://github.com/ANTsX/ANTs\n\n### How to report errors\nhttps://github.com/BIDS-Apps/antsCorticalThickness/issues\n\n### Acknowledgements\nhttps://github.com/ANTsX/ANTs#boilerplate-ants\n\n### Usage\nThis App has the following command line arguments:\n\n\t\tusage: run.py [-h]\n                  [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]\n                  [--n_cpus N_CPUS]\n                  [--stage {brain_extraction,template_registration,tissue_segmentation,qc,cortical_thickness}]\n                  [-v]\n                  bids_dir output_dir {participant}\n\n    Cortical thickness estimation using ANTs.\n\n    positional arguments:\n      bids_dir              The directory with the input dataset formatted\n                            according to the BIDS standard.\n      output_dir            The directory where the output files should be stored.\n                            If you are running group level analysis this folder\n                            should be prepopulated with the results of\n                            theparticipant level analysis.\n      {participant}         Level of the analysis that will be performed. Multiple\n                            participant level analyses can be run independently\n                            (in parallel) using the same output_dir.\n\n    optional arguments:\n      -h, --help            show this help message and exit\n      --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]\n                            The label(s) of the participant(s) that should be\n                            analyzed. The label corresponds to\n                            sub-\u003cparticipant_label\u003e from the BIDS spec (so it does\n                            not include \"sub-\"). If this parameter is not provided\n                            all subjects should be analyzed. Multiple participants\n                            can be specified with a space separated list.\n      --n_cpus N_CPUS       Number of CPUs/cores available to use.\n      --stage {brain_extraction,template_registration,tissue_segmentation,qc,cortical_thickness}\n                            Which stage of ACT to run\n      -v, --version         show program's version number and exit\n\nTo run it in participant level mode (for one participant):\n\n    docker run -i --rm \\\n\t\t-v /Users/filo/data/ds005:/bids_dataset:ro \\\n\t\t-v /Users/filo/outputs:/outputs \\\n\t\tbids/antscorticalthickness \\\n\t\t/bids_dataset /outputs participant --participant_label 01\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-apps%2FantsCorticalThickness","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbids-apps%2FantsCorticalThickness","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-apps%2FantsCorticalThickness/lists"}