{"id":20566173,"url":"https://github.com/aces/cbrain-plugins-freesurfer","last_synced_at":"2025-06-16T07:37:06.106Z","repository":{"id":25769271,"uuid":"29207500","full_name":"aces/cbrain-plugins-freesurfer","owner":"aces","description":"(Deprecated) FreeSurfer models and tasks for CBRAIN","archived":false,"fork":false,"pushed_at":"2015-08-31T20:19:35.000Z","size":928,"stargazers_count":0,"open_issues_count":0,"forks_count":3,"subscribers_count":11,"default_branch":"master","last_synced_at":"2025-03-06T08:57:40.443Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Ruby","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/aces.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-01-13T19:42:16.000Z","updated_at":"2015-08-31T20:19:52.000Z","dependencies_parsed_at":"2022-08-23T11:20:09.722Z","dependency_job_id":null,"html_url":"https://github.com/aces/cbrain-plugins-freesurfer","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/aces/cbrain-plugins-freesurfer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aces%2Fcbrain-plugins-freesurfer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aces%2Fcbrain-plugins-freesurfer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aces%2Fcbrain-plugins-freesurfer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aces%2Fcbrain-plugins-freesurfer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/aces","download_url":"https://codeload.github.com/aces/cbrain-plugins-freesurfer/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aces%2Fcbrain-plugins-freesurfer/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":260119833,"owners_count":22961609,"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":"2024-11-16T04:40:18.583Z","updated_at":"2025-06-16T07:37:06.036Z","avatar_url":"https://github.com/aces.png","language":"Ruby","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# DEPRECATED\n\nThe content of this package is deprecated; please use the combined package [cbrain-plugins-neuro](https://github.com/aces/cbrain-plugins-neuro) instead,\nwhich include the code here as well as the plugins in `cbrain-plugins-fsl` and\n`cbrain-plugins-mni`.\n\n## Introduction\n\nThis repository is a package containing a set of plugins for the\n[CBRAIN](https://github.com/aces/cbrain) platform.\n\n## Contents of this package\n\nThis package provides some tasks and models supporting\nparts of the [FreeSurfer](http://freesurfer.net/) suite.\n\n**Important Note** : Because this package required the NiftiFile userfile model, you must\nalso install the [MNI plugin package for CBRAIN](https://github.com/aces/cbrain-plugins-mni).\nThis can be done separately, before or after this package is installed.\n\n#### 1. Userfile models\n\n| Name                         | Description                                                                                     |\n|------------------------------|-------------------------------------------------------------------------------------------------|\n| ReconAllCrossSectionalOutput | Model for recon-all cross sectional output, result of the first step in longitudinal studies    |\n| ReconAllBaseOutput           | Model for recon-all unbiased base output, result of the second step in longitudinal studies     |\n| ReconAllLongiOutput          | Model for recon-all longitudinal output, result of the third step in longitudinal studies       |\n| ReconAllOutput               | Model for recon-all collection (not directly used). All the ReconAll*Output inherits this model |\n\n#### 2. CbrainTasks\n\n| Name          | Description                                                                                    |\n|---------------|------------------------------------------------------------------------------------------------|\n| ReconAll      | To run [recon-all](https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all)                        |\n| ReconAllLongi | To run [Longitudinal Stream](https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) |\n\n## How to install this package\n\nAn existing CBRAIN installation is assumed to be operational before\nproceeding.\n\nThis package must be installed once on the BrainPortal side of a\nCBRAIN installation, and once more on each Bourreau side.\n\n**Important** : The prerequisite [MNI plugin package for CBRAIN](https://github.com/aces/cbrain-plugins-mni)\nmust also be installed.\n\n#### 1. Installation on the BrainPortal side:\n\n  * Go to the `cbrain_plugins` directory under BrainPortal:\n\n```bash\ncd /path/to/BrainPortal/cbrain_plugins\n```\n\n  * Clone this repository. This will create a subdirectory called\n  `cbrain-plugins-freesurfer` with the content of this repository:\n\n```bash\ngit clone git@github.com:aces/cbrain-plugins-freesurfer.git\n```\n\n  * Run the following rake task:\n\n```bash\nrake cbrain:plugins:install:all\n```\n\n  * Restart all the instances of your BrainPortal Rails application.\n\n#### 2. Installation on the Bourreau side:\n\n**Note**: If you are using the Bourreau that is installed just\nbesides your BrainPortal application, you do not need to make\nany other installation steps, as they share the content of\nthe directory `cbrain_plugins` through a symbolic link; you\nonly need to *restart your Bourreau server*.\n\n  * Go to the `cbrain_plugins` directory under BrainPortal\n  (yes, *BrainPortal*, because that's where files are installed; on\n  the Bourreau side `cbrain_plugins` is a symbolic link):\n\n```bash\ncd /path/to/BrainPortal/cbrain_plugins\n```\n\n  * Clone this repository:\n\n```bash\ngit clone git@github.com:aces/cbrain-plugins-freesurfer.git\n```\n  * Run the following rake task (which is not the same as for\n  the BrainPortal side):\n\n``` bash\nrake cbrain:plugins:install:plugins\n```\n\n  * Restart your execution server (with the interface, click stop, then start).\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faces%2Fcbrain-plugins-freesurfer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faces%2Fcbrain-plugins-freesurfer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faces%2Fcbrain-plugins-freesurfer/lists"}