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Software Installation

Software Stack

Written by Luke Chang

For this course, we will be providing hands on tutorials working with real data using open source software written in the Python programming language. We have included some introductory tutorials in the Background Resources section to help you get up to speed on using Python and in particular how to manipulate data with pandas, plot data, and work with neuroimaging data. All of our tutorials will be provided in the form of a Jupyter Notebook. These notebooks are distributed via a jupyter-book and can be downloaded to run on your personal computer.

Throughout this course various tutorials will use the following libraries:

  • datalad - data versioning software (see Download Data tutorial for installation instructions and overview)
  • nibabel - a library to read and write common neuroimaging file formats.
  • nilearn - a neuroimaging toolbox for performing statistical learning
  • brainiak - a neuroimaging toolbox for performing advanced fMRI analyses
  • nltools - a neuroimaging toolbox for performing multivariate analyses
  • hypertools - a toolbox for visualizing high dimensional data
  • timecorr - a toolbox for calculating dynamic correlations
  • pliers - a toolbox for extracting features from multimodal data

Installing Software

First, if you have never worked with Python before, we recommend installing Python via the Anaconda distribution. This includes many popular packages used in scientific computing. Be sure to install Python 3.7.

Package management in Python can be a little tricky. Anaconda has provided their own system called conda, which includes precompiled packages that are theoretically tested to reduce conflicts. Conda is usually a good place to start when installing packages. If a package isn't included in conda, you will next try installing the package using the Python packaging system called pip. This tends to be our main workhorse for installing packages. If a package isn't in PyPI, then you may have to install from a github repository. This can be done using `pip.

Package installation is probably easiest through the command line in a terminal, but you can also run commands in the shell by using the ! cell magic.

If you use Python for many different projects, you may find it helpful to create a conda environment, which provides a way to install a specific collection of packages. This can be useful if you use different versions of the same library for different projects, or if you want to avoid conflicts across packages.

Conda

Some packages can be installed with conda. The more established scientific packages are already included in the anaconda distribution and usually can be installed via conda. The advantages of installing via conda is that distributions usually undergo an extra round of testing to make sure they are compatible and are precompiled. Smaller scale projects can often be installed via conda using a specific channel such as conda-forge. We have found some of the brainiak dependencies to be finicky to install with pip and instead recommend installing it with conda.

If you would like to create a conda environment for this course, run the following command in the terminal or with a ! in front of it within a jupyter notebook.

conda create -n naturalistic python=3.7 anaconda

To activate your environment:

conda activate naturalistic

If you would like would like to exit your environment:

conda deactivate

One neat thing about conda environments is that you can select a specific one to serve as your kernel for a jupyter notebook. To get this to work, run:

conda install -c anaconda ipykernel

and then

python -m ipykernel install --user --name=naturalistic

Ok, let's install the packages we need from conda first.

!conda install numpy scipy scikit-learn pandas matplotlib seaborn
!conda install -c brainiak -c defaults -c conda-forge brainiak

Github

Some packages are not released on Anaconda or PyPI and must be installed directly from their github repository. For example, one of the dependencies in the timecorr toolbox requires a package called brainconn, which must be installed from their github repository.

!pip install git+https://github.com/FIU-Neuro/brainconn#egg=brainconn

Pip

Otherwise, pip will be the main way you install packages. Let's now install the rest of the packages you will need for this course.

!pip install nibabel datalad nilearn nltools hypertools timecorr pliers statesegmentation networkx nltk requests urllib3

Jupyter Notebooks

Jupyter notebooks are a great way to have your code, comments and results show up inline in a web browser. Work for this course will be done in Jupyter notebooks so you can reference what you have done, see the results and someone else could redo it in the future, similar to a typical lab notebook.

Rather than writing and re-writing an entire program, you can write lines of code and run them one at a time. Then, if you need to make a change, you can go back and make your edit and rerun the program again, all in the same window.

Finally, you can view examples and share your work with the world very easily through nbviewer. One easy trick if you use a cloud storage service like dropbox is to paste a link to the dropbox file in nbviewer. These links will persist as long as the file remains being shared via dropbox.

If you would like to get a quick overview of Jupyter Notebooks check out talk1 and talk2 from the MIND summer school.

R

You can also connect notebooks not just to Python kernels, but also to other languages such as R.

The easiest way to get started is to install R and the r-irkernel package using conda.

Alternatively, if this doesn't work you can also install R directly from their website. To connect this version of R to jupyter, we need to manually install the IRkernel from within the version of R that you downloaded.

Start R, then run the following commands:

install.packages('IRkernel')
IRkernel::installspec()  # to register the kernel in the current R installation

If you end up using R in your work, you will likely also find RStudio as well as packages from the tidyverse to be helpful.

!conda install -c r r-irkernel