Sometimes running a bash command on the server can take several hours to complete. In such cases you would like to run the command in background and close the terminal from which the command was started (without terminating the process itself). The best way to achieve that is to use GNU screen’s detaching utility. In order to run and detach […]
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 […]
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 […]
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.
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 […]