{"id":18091267,"url":"https://github.com/dfsp-spirit/system_config","last_synced_at":"2026-04-20T19:31:58.289Z","repository":{"id":98535390,"uuid":"141824998","full_name":"dfsp-spirit/system_config","owner":"dfsp-spirit","description":"My system configuration (bash_profile, bashrc, vimrc, ...) including my setup for popular neuroimaging software. 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I use the `bash` shell under both GNU/Linux and MacOS, and I do my best to keep this setup consistent between these two operating systems.\n\n## About\n\nThese are my personal config files to setup my environment in the bash shell under Linux and MacOS. Whenever I use or install a new machine, or get a user account on some new server, I grab this from here. They include the setup for neuroimaging software like FreeSurfer and FSL. This setup doesn't do any magic:\n\n* configure the shell prompt to `user@host: workdir`\n* add stuff the the `$PATH` environment variable, including general stuff like `~/bin/` but also my neuroimaging software installations (it won't hurt if you don't have them, it checks for them first).\n* colour some shell output\n* add my aliases\n* configure the `vim` editor with syntax highlighting, line number display, the solarized colour scheme, ...\n* more stuff I forgot\n\nThis setup is not *really* intended to be used by anybody else, but please feel free to do so.\n\nThe neuroimaging software that I check for:\n* FSL (FMRIB Software Library, see https://fsl.fmrib.ox.ac.uk/fsl/)\n* FreeSurfer (see https://surfer.nmr.mgh.harvard.edu/)\n* PALM (Permutation Analysis of Linear Models, see https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM)\n* Anaconda2 (for PySurfer etc, see https://anaconda.org/anaconda/python)\n\n\n## Usage\n\nThis is a collection of system configuration files and a script, `install_sysconfig.bash`, that copies all of these files into place.\n\nWARNING: The script overwrites your current files and does NOT make a backup (this repo is my backup).\n\nIt is very likely that you will at least have to adapt the installation paths of your neuroimaging software in the `bash_profile` file. I check for my installation paths and defaults if available, but as you may have installed to a different location, you have to adapt the paths.\n\nSo what you should do is:\n1) Download/clone the repo and have a look at the files (especially the paths in `bash_profile`) and adapt stuff to your needs.\n    * To download, click the green `Clone or download` button near the top of this page, then click `Download ZIP`.\n2) Make a backup of your current config files.\n3) Run the install script from within its directory: `./install_sysconfig.bash`\n\nIf you only want a minimum setup, you can omit step 3 and copy the files you want manually. To use only my basic bash shell setup (and not the vim and ssh config files, etc), do:\n\n```bash\n   cp bash_profile ~/.bash_profile\n   cp bashrc ~/.bashrc\n```\n\n\n## Recommended usage\n\nIf you use Github, I would recommend forking this repo and using/maintaining/updating your own copy in the future.\n\n## External tools\n\nThis repo contains some external tools created by others and software which does NOT fall under the license of the repo.\n\n* `tools/solarized/solarized.vim`: solarized colour scheme by [Ethan Schoonover](http://ethanschoonover.com/solarized), implementation for the vim editor by [altercation](https://github.com/altercation/vim-colors-solarized)\n* `bin/obj2surf` and `bin/surf2obj`: shell scripts by [Anderson M. Winkler](https://brainder.org/) to convert surface files (meshes) between the obj and FreeSurfer ASCII formats\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdfsp-spirit%2Fsystem_config","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdfsp-spirit%2Fsystem_config","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdfsp-spirit%2Fsystem_config/lists"}