Installing Neurolang¶

Windows¶

First: download and install 64 bit Anaconda¶

We recommend that you install a complete 64 bit scientific Python distribution like Anaconda . Since it meets all the requirements of neurolang, it will save you time and trouble. You could also check PythonXY as an alternative.

Neurolang requires a Python installation and the following dependencies: ipython, scipy, scikit-learn, joblib, matplotlib, nibabel, nilearn.

Second: open a Command Prompt¶

(Press “Win-R”, type “cmd” and press “Enter”. This will open the program cmd.exe, which is the command prompt)

Then type the following line and press “Enter”

pip install -U --user neurolang

Third: open IPython¶

(You can open it by writing “ipython” in the command prompt and pressing “Enter”)

Then type in the following line and press “Enter”:

In [1]: import neurolang

If no error occurs, you have installed neurolang correctly.

Mac¶

First: download and install 64 bit¶

Anaconda

We recommend that you install a complete 64 bit scientific Python distribution like Anaconda. Since it meets all the requirements of neurolang, it will save you time and trouble.

Second: open a Terminal¶

(Navigate to /Applications/Utilities and double-click on Terminal)

Then type the following line and press “Enter”

pip install -U --user neurolang

Third: open IPython¶

(You can open it by writing “ipython” in the terminal and pressing “Enter”)

Then type in the following line and press “Enter”:

In [1]: import neurolang

If no error occurs, you have installed neurolang correctly.

Linux¶

If you are using Ubuntu or Debian

First: Install dependencies¶

Install or ask your system administrator to install the following packages using the distribution package manager: ipython , scipy, scikit-learn (sometimes called sklearn, or python-sklearn), joblib, matplotlib (sometimes called python-matplotlib) and nibabel (sometimes called python-nibabel).

If you do not have access to the package manager we recommend that you install a complete 64 bit scientific Python distribution like Anaconda. Since it meets all the requirements of neurolang, it will save you time and trouble.

Second: open a Terminal¶

(Press ctrl+alt+t and a Terminal console will pop up)

Then type the following line and press “Enter”

pip install -U --user neurolang

Third: open IPython¶

(You can open it by writing “ipython” in the terminal and pressing “Enter”)

Then type in the following line and press “Enter”:

In [1]: import neurolang

If no error occurs, you have installed neurolang correctly.

To Install the development version¶

Use git as an alternative to using pip, to get the latest neurolang version

Simply run the following command (as a shell command, not a Python command):

git clone https://github.com/neurolang/neurolang.git

In the future, you can readily update your copy of neurolang by executing “git pull” in the neurolang root directory (as a shell command).

If you really do not want to use git, you may still download the latest development snapshot from the following link (unziping required): https://github.com/neurolang/neurolang/archive/master.zip

Install in the neurolang directory created by the previous steps, run (again, as a shell command):

python setup.py develop --user

Now to test everything is set up correctly, open IPython and type in the following line:

In [1]: import neurolang

If no error occurs, you have installed neurolang correctly.

Installing alternative backends for Neurolang¶

By default, Neurolang uses the pandas library to manage its data. It is however possible to use an alternative backend which relies on dask-sql.

Using the dask-sql backend allows Neurolang to benefit from some query optimizations based on SQL syntax, as well as parallelism in computation by using dask instead of pandas. In other words, using the dask-sql backend might help improve the performance of specific queries which are slow to resolve with the default installation of Neurolang. It is not however guaranteed to be faster, as query optimizations are very case specific…

To install Neurolang with the dask-sql backend, it is required to first install a version of the maven library along with a running java installation with version >= 8 (dask-sql needs Java for parsing the SQL queries). There are two ways to install maven along with java:

On a linux machine, run the following command in your shell terminal:

sudo apt update && sudo apt install maven

Or, if you’re using conda to manage your python environments, you can run the following command in your active python environment:

conda install -c conda-forge maven

Once you’ve setup your machine with a working version of java and maven, you can install Neurolang with the dask-sql backend by running the following command in your active python environment from a local copy of the Neurolang repository:

pip install -U --user neurolang[dask]

Finally, to enable the dask-sql backend for Neurolang, you can either edit Neurolang’s configuration file located in your python environment path under config/config.ini, or you can call

from neurolang.config import config
config.set_query_backend("dask")

from your python shell.

Note: you need to call the set_query_backend method at the top of your script, before you import other modules from Neurolang.