This is an excerpt from the official tutorial “Step 3: Request a Let’s Encrypt SSL wildcard certificate”. Some steps/commands were adjusted for the purpose of just renewing the certificate (instead of installing a new certbot instance).
macOS configuration
The collection of macOS tips and configuration settings. Change default Python version Follow the instructions from Matthew Broberg’s and Moshe Zadka’s post. In short: Cmd+arrows to jump word By default Cmd+right/left arrow sends you to end/binning of the line. The default keybind for jumping only one word is option+arrows, which is completely unusable (it is easier to use cmd). How […]
PsychoPy – a basic example
PsychoPy is an excellent tool for preparing psychological experiments in Python. However, it seems that entry-level examples one can find in the web are rather sophisticated. Hence, I prepared this basic example featuring: Installing PsychoPy on Linux Displaying a simple stimulus Simplest possible keyboard event Installing PsychoPy on Linux Open a terminal (5 Ways to Open a Terminal Console Window […]
How to use FreeSurfer – Part 2
Introduction In this chapter, we are going to take a deep dive into FreeSurfer’s output and make some clarifications about it. After data processing from in Part 1, you should see something like this: We will mainly focus on folder “stats” because it contains files with plain text. Which is good for some visualizations and analyses. I will go through […]
How to use FreeSurfer – Part 1
FreeSurfer is a great tool for gathering and extract data from fMRI images. I highly recommend use it through Jupyter Notebook because it works great and all references in this post are made in Jupyter.
(Auto)start application as a service in Linux
Two examples how to autostart services in Linux will be presented here. To run applications you have to use systemd suite. Systemd configuration files are stored at: Jupyter Create a new file at: Copy-paste the following configuration there: Where: $USER — is a username who owns the resources containing you instance/virtual environment $VENV_ID — ID of your virtual environment Start […]
When plain Bash is not enough
I recently read an excellent introductory Bash tutorial on Dev.to by Sahil Bondre. It is a really great tutorial on shell scripting basics, but I remember when I was beginning my adventure with shell scripting and I became fascinated with Bash. In fact, I was a bit over-fascinated with it. With my neuroimaging scripts becoming more and more complex, I […]
Converting NIfTI files to GIfTI
How to transform NIfTI files to GIfTI format. In other words: how to map volumetric to surface data. Case: present results in Connectome Workbench Let’s say that you have results based on parallation in MNI152. Now you’d like to present these results in Connectome Workbench. Hence, you need to convert volumetric data (NIfTI) to surface data (GIfTI). You can find […]