Abstract In order to calculate SUVmax for GE data, the following formula has to be utilized: To be more precise, below is the same formula, but with more specific information on the voxel and DICOM metadata fields required: For more information, please refer to the article below. Introduction An algorithm for calculating SUVmax value for PET/CT GE scanner will be […]
I wanted to learn how to configure a proxy for Jupyter Notebook with Nginx. For such test, it was easier to use dockerized environment rather than a remote server because the configuration could be simply reset to the defaults. The final, working version of the setup: nginx, Jupyter Notebook, Ubuntu, docker, is available at my GitLab repository. Source of the […]
Create a new user For this example, we will be using a Linux username hyperion. In order to create a new user in Linux and set up a password, use the following commands: Note: -m is required in order to create user’s home directory the command to remove the user is: userdel hyperion To make sure that the user has been created, […]
Previously I described how to use GNU screen to run bash commands in background. In addition to that, if sometimes it happens that a detached command terminates before completion, we would like to have logs for that command, e.g., in order to determine why and when an error occurred. This post explains how to log the progress of a command […]
Recently I needed to quickly perform a one sample t-test in an Excel spreadsheet. Unfortunately, this functionality is not implemented in Excel by default. However, I found a very nice post by Zach at Statology on how to calculate this test using some build-in Excel functions and objects. For my convenience what I did was to put the whole procedure […]
Based on R Bioconductor Sushi package I created a step-by step guide of how to produce a Manhattan plot for a genom-wide associaction study (GWAS).
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 […]
It is very important to set password for your instance. Why? Otherwise, if, e.g., something will go wrong with you network interface, you will not be able to access the instance via VNC console. Hence, you will not be able to access your instance at all, at least from the OpenStack’s web GUI. Although it is of course possible to […]
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 […]