Local Install¶

Python¶

For the main required Python packages (numpy, scipy, etc.) we recommend using Anaconda for Python 3.6

ANTs & Convert3D (c3d)¶

If either ANTs or c3d are not installed on your machine, run install_depends.sh, located in the project directory. The required software will be installed in the depends directory

Installing package and dependencies for HippMapp3r locally¶

Clone repository

 git clone https://github.com/mgoubran/HippMapp3r.git HippMapp3r

 (or install zip file and uncompress)

 cd HippMapp3r

If you want to create a virtual environment where HippMapp3r can be run,

 conda create -n hippmapper python=3.6 anaconda
 source activate hippmapper

To end the session, deactivate the environment

 source deactivate

To delete the environment,

 conda env remove --name hippmapper

Install dependencies

 pip install git+https://www.github.com/keras-team/keras-contrib.git

If the computer you are using has a GPU:

 pip install -e .[hippmapper_gpu]

If not:

 pip install -e .[hippmapper]

Test the installation by running
```
 hippmapper --help
```
To confirm that the command line function works, and
```
 hippmapper
```
To launch the interactive GUI.

Download deep models¶

Download the models from this link and place them in the models directory

For tab completion¶

pip3 install argcomplete
activate-global-python-argcomplete

Updating HippMapp3r¶

To update HippMapp3r, navigate to the directory where HippMapp3r was cloned and run

git pull
pip install -e .[{option}] -process-dependency-links

where “option” is dependent on whether or not you have a GPU (see package installation steps above)