Lev Lafayette

This tutorial illustrates Advanced Normalization Tools (ANTs) to do image registration in 3D using data from Brain/MINDS data portal and how to apply the transforms/inverse transforms from image registration using the Slurm Workload Manager.

ANTs is described on their repository as follows:

"Advanced Normalization Tools (ANTs) is a C++ library available through the command line that computes high-dimensional mappings to capture the statistics of brain structure and function. It allows one to organize, visualize and statistically explore large biomedical image sets. Additionally, it integrates imaging modalities in space + time and works across species or organ systems with minimal customization."

The tutorial is derived from the tutorial at the Brain/MINDS data portal.

The basic Linux command for directory creation is mkdir $DIRNAME, with the most common options being -p to create parent directories and the handy verbose flag (-v) to print the directories to standard output as they are created. An array of subdirectories can also be created. e.g.,


$ mkdir -p -v examples/{dir1,dir2,dir3}
mkdir: created directory 'examples'
mkdir: created directory 'examples/dir1'
mkdir: created directory 'examples/dir2'
mkdir: created directory 'examples/dir3'


Converting between filesystems can be fraught with difficulties, especially if one is dealing with a proprietary filesystem. One such system is APFS, the Apple File System, designed by Apple for its devices, introduced originally for macOS Sierra in 2017 and later, iOS 10.3, tvOS 10.2, watchOS 3.2, and all versions of iPadOS, and designed to replace HFS Plus. The question here is how does one access APFS on Linux when a kind individual has provided you, for example, a USB device that has been written with this filesystem.

Several months ago, YouTube began "a global effort" to prevent users from blocking advertisements. This process included allowing users with an adblocker, once detected, a few videos, then a warning, and then outright prevention. There was an implicit suggestion that one could receive the desired ad-free service from a Premium subscription. Methods employed by YouTube to implement these blocks include embedding advertisements in the video itself, serving advertisements from the same domain as the video, or using browser fingerprinting to detect ad-blocking extensions.

Supercomputing Asia 2024 was held in Sydney from the 19th to 23rd of February with over 1,000 attendees, most of whom were from Australia, the United States, Singapore, Japan, Thailand, and Aotearoa New Zealand, with a notable exception from the conference was China given their importance to both supercomputing and Asia, and one speaker noted wryly that "Australia is now apparently part of Asia". The program consisted of plenary sessions in the morning and multiple streams in the afternoon of each day.

Since late in 2007 I have been involved in the field of high performance computing. Initially, this was at the Victorian Partnership for Advanced Computing, but just before that organisation closed its doors in December 2015 I accepted a similar role at the University of Melbourne. The end of the year provides a reason for reflection, an annual report if one likes, and whilst activities not related to my vocation and profession will be dealt with in a subsequent entry, the opportunity is taken here to review workplace activities and in particular, changes in the environment for the University's general HPC system, Spartan. Spartan now has 6159 accounts across 2109 projects in diverse disciplines in the life sciences, engineering, economics, mathematics, and more and has been cited in 62 papers in the past year.

Following the successful first conference last year, this year’s 2023 International Conference on Green and Innovation-driven Development in Cities and Towns was hosted in Suzhou with proceedings held at the recently opened Suzhou International Conference Hotel. The lead host of the conference was the Foreign Affairs Office of the Jiangsu Provincial People’s Government, and the main organiser was the Xiangcheng District People’s Government of Suzhou City.

Way back in 2015 the University of Melbourne had a general-purpose high performance computer system called "Edward", which itself replaced an even smaller system called "Alfred", both named after the Kings of Wessex. Edward was a fairly typical machine for its vintage and, as is normal, when a system is being retired the main researchers were asked what should be different in the new system. What was also normal was their answers; more cores, faster CPUs, etc.

The expression "Not all members of set N have characteristic r, but all elements with characteristic r are in set N" can be represented with standard set notation as follows.

1. There exist some elements in N that do not have characteristic r. Using the "∃" symbol, to denote "there exists", and the "∉" symbol, which denotes "not an element of."

∃x ∈ N : x ∉ R

This reads as "There exists an element x in N such that x is not an element of R."

2. For the second part, all elements with characteristic r are in set N:

For the past few years, I have delivered some guest lectures and training for the University of Melbourne master's level course Cluster and Cloud Computing. This year's contribution has been expanded, which is not surprising as the course is apparently required for data science students as well as computer science students. Thus, for 2023 four presentations were given, with the workshop repeated three times!