1. Installing junifer¶
Depending on your use-case, junifer can be installed differently:
Install the latest stable release. This is the most suitable approach for end users.
Install from latest development release. This is the most suitable approach for developers.
Either way, we strongly recommend using virtual environments.
1.1. Using a package manager¶
Use pip to install junifer from PyPI, like so:
pip install junifer
You can also install via conda, like so:
conda install -c conda-forge junifer
Attention
Installation on macOS and Windows might fail via conda due to datalad.
In that case, please refer to
Datalad installation instructions for solutions.
In case the problem persists, please install it via pip as mentioned earlier.
1.2. From the source¶
Follow the detailed contribution guidelines.
2. Installing external dependencies¶
Some preprocessors and markers will require optional external dependencies to be installed. In this section you will find a list of all external dependencies that are required for specific markers.
Important
The Docker container wrappers add the commands required by junifer. Using
these commands have some limitations, mostly related to handling files and
paths. junifer knows about this and uses these commands in the proper way.
Keep this in mind if you try to use the Docker wrappers outside of
junifer. These caveats and limitations are not documented.
2.1. AFNI¶
To install AFNI, you can always follow the AFNI official instructions. Additionally, you can also follow the following steps to install and configure the AFNI Docker container in your local system.
Install Docker. You can follow the Docker official instructions.
Pull the AFNI Docker image from Docker Hub AFNI:
docker pull afni/afni_make_build
Add the Junifer AFNI scripts to your PATH environment variable. Run the following command:
junifer setup afni-docker
Take the last line and copy it to your .bashrc or .zshrc file.
Or, alternatively, you can execute this command which will update the
~/.bashrc for you:
junifer setup afni-docker | grep "PATH=" | xargs | >> ~/.bashrc
2.2. FSL¶
To install FSL, you can always follow the FSL official instructions. Additionally, you can also follow the following steps to install and configure the FSL Docker container in your local system.
Install Docker. You can follow the Docker official instructions.
Pull the FSL Docker image from Docker Hub FSL:
docker pull brainlife/fsl
Add the Junifer FSL scripts to your PATH environment variable. Run the following command:
junifer setup fsl-docker
Take the last line and copy it to your .bashrc or .zshrc file.
Or, alternatively, you can execute this command which will update the
~/.bashrc for you:
junifer setup fsl-docker | grep "PATH=" | xargs | >> ~/.bashrc
2.3. ANTs¶
To install ANTs, you can always follow the ANTs official instructions. Additionally, you can also follow the following steps to install and configure the ANTs Docker container in your local system.
Install Docker. You can follow the Docker official instructions.
Pull the ANTs Docker image from Docker Hub ANTs:
docker pull antsx/ants
Add the Junifer ANTs scripts to your PATH environment variable. Run the following command:
junifer setup ants-docker
Take the last line and copy it to your .bashrc or .zshrc file.
Or, alternatively, you can execute this command which will update the
~/.bashrc for you:
junifer setup ants-docker | grep "PATH=" | xargs | >> ~/.bashrc
2.4. FreeSurfer¶
To install FreeSurfer, you can always follow the FreeSurfer official instructions. Additionally, you can also follow the following steps to install and configure the FreeSurfer Docker container in your local system.
Install Docker. You can follow the Docker official instructions.
Pull the FreeSurfer Docker image from Docker Hub FreeSurfer:
docker pull freesurfer/freesurfer
Add the Junifer FreeSurfer scripts to your PATH environment variable. Run the following command:
junifer setup freesurfer-docker
Take the last line and copy it to your .bashrc or .zshrc file.
Or, alternatively, you can execute this command which will update the
~/.bashrc for you:
junifer setup freesurfer-docker | grep "PATH=" | xargs | >> ~/.bashrc