Installation for Linux

Install R

Before you do anything, you need to have the programming language R (version >= 3.2.3). Specific instructions for installing R on the different flavors of Linux are described on CRAN. For Debian, if you are installing in a Windows Subsystem for Linux, you would do the following:

sudo apt-get update
sudo apt-get install r-base r-base-dev

Install Python if you do not have it

To test whether you have Python, you can do:

python --version

If this does not return something useful indicating the Python version, you probably do not have Python installed, and you can install it with your package manager.

For Debian and Ubuntu:

sudo apt-get install python

For Red Hat and other derivatives:

sudo yum install python

If you are just beginning to work with Python and are interested in having a lot of data science libraries ready to go, you might consider installing the Anaconda Python distribution. Both can exist simultaneously on your system, increasing the chances that one will work.

After your travails, Python should be in your path (you might have to start a new terminal window) and you should be able to see what version of Python you are running.

python --version

Download neuropointillist

There are two ways to install neuropointillist. The first is to download the package as a zip (archive) file from the Github repository. Here, we pull it using wget, unzip it, and rename it to be called neuropointillist.

wget https://github.com/IBIC/neuropointillist/archive/master.zip
unzip master.zip
mv neuropointillist-master neuropointillist

The second way is to clone it using Git. You can install Git for your Linux flavor if it is not installed.

git clone https://github.com/IBIC/neuropointillist.git

Install dependencies and neuropointillist

Change into the directory where you have downloaded neuropointillist. There will be a subdirectory called neuropointillist within that directory; this contains the R package.

Start R at the bash command line.

R

Within R, install the dependencies argparse, RNifti, doParallel and reticulate.

install.packages("argparse")
install.packages("RNifti")
install.packages("doParallel")
install.packages("reticulate")

Depending on what version of R you are running, you might also need to install nlme.

install.packages("nlme")

Once all prerequisites are installed, you can install neuropointillist. Once again, make sure you are in the directory where you downloaded neuropointillist, or change into that directory from within R.

install.packages("neuropointillist", repos=NULL, type="source")

Modify Your Path

Finally, put the repository directory that contains the scripts npoint, npointrun and npointmerge into your PATH variable. You can do this on the command line every time you start a new terminal as follows. Make sure you put the path where YOU downloaded the github repository for neuropointillist.

export PATH=$PATH:~/neuropointillist

Alternatively, you can put this line into your .bashrc file.