{"id":20566165,"url":"https://github.com/aces/loris-mri","last_synced_at":"2025-08-20T04:31:39.591Z","repository":{"id":1804924,"uuid":"2728966","full_name":"aces/Loris-MRI","owner":"aces","description":"The set of scripts that preprocess and insert MRI data into the database.","archived":false,"fork":false,"pushed_at":"2024-10-18T21:15:53.000Z","size":7123,"stargazers_count":10,"open_issues_count":83,"forks_count":51,"subscribers_count":26,"default_branch":"main","last_synced_at":"2024-10-20T06:59:01.887Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"dasmoth/jni-glmnet","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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2011-11-07T20:19:37.000Z","updated_at":"2024-10-18T21:15:57.000Z","dependencies_parsed_at":"2024-02-16T17:26:14.099Z","dependency_job_id":"486d1cad-d123-4401-ae48-237d4d77f4ba","html_url":"https://github.com/aces/Loris-MRI","commit_stats":null,"previous_names":[],"tags_count":51,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aces%2FLoris-MRI","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aces%2FLoris-MRI/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aces%2FLoris-MRI/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aces%2FLoris-MRI/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/aces","download_url":"https://codeload.github.com/aces/Loris-MRI/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":230394228,"owners_count":18218707,"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":"2024-11-16T04:40:17.865Z","updated_at":"2024-12-19T07:05:53.661Z","avatar_url":"https://github.com/aces.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"This Readme covers release 26.0.* of the LORIS Imaging Insertion Pipeline for Ubuntu or CentOS systems\n\nThis repo accompanies the [LORIS neuroimaging data platform main repo](https://github.com/aces/Loris/releases)\u003c/b\u003e, release 24.1.*.\u003cbr\u003e\nFor documentation and detailed setup information, please see the [LORIS-MRI documentation](docs/) for your installed version\u003c/b\u003e.\n\nThis repo can be installed on the same VM as the main LORIS codebase, or on a different machine such as a designated fileserver where large imaging filesets are to be stored.\n\n# System Requirements\n\n* Perl\n* Python 3.11 with pip3 and venv (step 2 below)\n* MINC toolkit (step 3 below)\n* DICOM toolkit (step 4 below)\n* tpcclib (for HRRT PET only) (step 5 below)\n\nOn \u003cu\u003eUbuntu\u003c/u\u003e, DICOM toolkit will be installed by the imaging install script (step 4 below). This script will _apt-get install dcmtk_.\n\nFor \u003cu\u003eCentOS\u003c/u\u003e: The [LORIS wiki](https://github.com/aces/Loris/wiki/Imaging-Database) Imaging setup page (see Section 1, installing codebase) includes links to older transcripts for [CentOS installation](https://github.com/aces/Loris/wiki/CentOS-Imaging-installation-transcript) and notes on dependencies including [DICOM toolkit](https://github.com/aces/Loris/wiki/CentOS-Imaging-installation-transcript#7-install-dicom-toolkit).\n\nThe following installation should be run by the `$lorisadmin` user. `sudo` permission is required.\nSee [aces/Loris](https://github.com/aces/loris) README.md for further information.\n\n# Dependencies\n\n## General\n\n```bash\n# ubuntu build essential packages useful for building\nsudo apt install build-essential checkinstall cmake\n```\n\n## Perl CPAN\n\nUpdate Perl dependency with:\n\n```bash\nsudo perl -MCPAN -e shell\n\n# then enter these two commands\n\ncpan[1]\u003e install CPAN\ncpan[2]\u003e reload cpan\n```\n\n# Installation\n\n#### 1. Create directories and download Loris-MRI code\n\n```bash\nsudo mkdir -p /data/$projectname\nsudo mkdir -p /opt/$projectname/bin/mri\nsudo chown -R lorisadmin:lorisadmin /data/$projectname\nsudo chown -R lorisadmin:lorisadmin /opt/$projectname\ncd /opt/$projectname/bin\n```\n\nGet the code: Download the latest release from the\n[releases page](https://github.com/aces/Loris-MRI/releases)\nand extract it to `/opt/$projectname/bin/mri`\n\n#### 2. Install Python 3.11 with `pip` and `venv`\n\n```bash\nsudo apt install python3.11 python3.11-dev python3.11-venv\nsudo apt install python3-pip\nsudo apt install libmysqlclient-dev\n```\n\n#### 3. Install MINC toolkit from http://bic-mni.github.io/\n\n- Install MINC dependencies:\n\n```bash\n# deps\nsudo apt-get install libc6 libstdc++6 imagemagick perl\n\n# Install required dependencies such as _imagemagick_.\nsudo apt-get install libgl1-mesa-glx libglu1-mesa\n```\n\n- Download the MINC pre-compiled package for your operating system from http://bic-mni.github.io/.\n\n- Then install the MINC toolkit package:\n\n```bash\n# main minc lib\nsudo dpkg -i minc-toolkit-\u003cversion\u003e.deb\n```\n\n- Check the model is installed in `/opt/minc/share`\n\n- Then source the MINC toolkit environment, where `$mincToolsDirectory` is the path where the MINC toolkit is installed (e.g. `/opt/minc/` OR `/opt/minc/$mincToolsVersion/` for more recent installs)\n\n```bash\n# bash\nsource $mincToolsDirectory/minc-toolkit-config.sh\n\n# tcsh\nsource $mincToolsDirectory/minc-toolkit-config.csh\n```\n\n- For the defacing scripts, you will also need to download the pre-compiled `bic-mni-models` and `beast` data and model packages for you operation system.\n\n```bash\nsudo dpkg -i bic-mni-models-\u003cversion\u003e.deb\nsudo dpkg -i beast-library-\u003cversion\u003e.deb\n\n# also check they are installed in `/opt/minc/share`\n```\n\n#### 4. Run installer to set up directories, configure environment, install Perl libraries and DICOM toolkit:\n\n```bash\ncd /opt/$projectname/bin/mri/install/\nbash ./imaging_install.sh\n```\n\nYou will be asked for the following input:\n\n* What is the database name? $dbname\n* What is the database host? $dbhost\n* What is the MySQL user? $lorisuser [Use the same mysql user from the Loris installation, i.e. _lorisuser_]\n* What is the MySQL password?\n* What is the Linux user which the installation will be based on? $lorisadmin\n* What is the project name? $projectname\n* What is your email address?\n* What prod file name would you like to use? default: prod  [leave blank]\n\nIf the imaging install script reports errors in creating directories\n(due to `/data/` mount permissions), review and manually execute\n`mkdir/chmod/chown` commands starting at\n[imaging_install.sh:L97](https://github.com/aces/Loris-MRI/blob/main/install/imaging_install.sh#L97)\n\nNote: The installer will allow Apache to write to the `/data/` and `/opt/` directories by\nadding user `lorisadmin` to the Apache linux group.  To ensure this change takes\neffect, log out and log back into your terminal session before running the\nimaging pipeline. The installer will also set Apache group ownership of certain\n`/data/` and `/opt/` subdirectories.\n\n#### 5. HRRT PET\n\nFor HRRT PET, install [tpcclib](http://www.turkupetcentre.net/tpcclib-doc/md_install.html).\nFollow the [install instructions](http://www.turkupetcentre.net/petanalysis/sw_install.html).\n\n#### 6. Configure paths and environment\n\nEnsure that `/home/lorisadmin/.bashrc` includes the statement:\n\n```bash\nsource /opt/$projectname/bin/mri/environment\n```\n\nThen source the `.bashrc` file.\n\n\n**INSTALLATION COMPLETE!**\n\nPlease refer to the [Install](docs/02-Install.md) section in the\n[LORIS-MRI documentation](docs/) for your installed version for:\n- customizations and protocol configurations ([Section 2.2](docs/02-Install.md#configuration)).\n- verifying that certain fields were correctly populated by `imaging_install.sh`\n([Section 2.3](docs/02-Install.md#post-installation-checks)).\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faces%2Floris-mri","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faces%2Floris-mri","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faces%2Floris-mri/lists"}