https://github.com/dfsp-spirit/system_config
My system configuration (bash_profile, bashrc, vimrc, ...) including my setup for popular neuroimaging software.
https://github.com/dfsp-spirit/system_config
bash infrastructure linux linux-shell
Last synced: about 2 months ago
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My system configuration (bash_profile, bashrc, vimrc, ...) including my setup for popular neuroimaging software.
- Host: GitHub
- URL: https://github.com/dfsp-spirit/system_config
- Owner: dfsp-spirit
- License: unlicense
- Created: 2018-07-21T15:33:49.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2023-02-05T20:39:13.000Z (over 3 years ago)
- Last Synced: 2025-10-23T08:52:47.711Z (8 months ago)
- Topics: bash, infrastructure, linux, linux-shell
- Language: Vim Script
- Homepage:
- Size: 8 MB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# system_config
My system configuration (bash_profile, bashrc, vimrc, ...) including my setup for popular neuroimaging software. 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.
## About
These 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:
* configure the shell prompt to `user@host: workdir`
* 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).
* colour some shell output
* add my aliases
* configure the `vim` editor with syntax highlighting, line number display, the solarized colour scheme, ...
* more stuff I forgot
This setup is not *really* intended to be used by anybody else, but please feel free to do so.
The neuroimaging software that I check for:
* FSL (FMRIB Software Library, see https://fsl.fmrib.ox.ac.uk/fsl/)
* FreeSurfer (see https://surfer.nmr.mgh.harvard.edu/)
* PALM (Permutation Analysis of Linear Models, see https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM)
* Anaconda2 (for PySurfer etc, see https://anaconda.org/anaconda/python)
## Usage
This is a collection of system configuration files and a script, `install_sysconfig.bash`, that copies all of these files into place.
WARNING: The script overwrites your current files and does NOT make a backup (this repo is my backup).
It 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.
So what you should do is:
1) Download/clone the repo and have a look at the files (especially the paths in `bash_profile`) and adapt stuff to your needs.
* To download, click the green `Clone or download` button near the top of this page, then click `Download ZIP`.
2) Make a backup of your current config files.
3) Run the install script from within its directory: `./install_sysconfig.bash`
If 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:
```bash
cp bash_profile ~/.bash_profile
cp bashrc ~/.bashrc
```
## Recommended usage
If you use Github, I would recommend forking this repo and using/maintaining/updating your own copy in the future.
## External tools
This repo contains some external tools created by others and software which does NOT fall under the license of the repo.
* `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)
* `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