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Saskia and Steffen Bollmann's Science blog

Containers

World wide mirrors and load balancing for NeuroDesk Containers

Although NeuroDesk is still a young project we already have users outside of Australia. This led to a few problems: our singularity containers are stored on Swift object storage on the Nectar Research Cloud and users outside of Australia saw Read more…

By Steffen, 2 weeks2 weeks ago
Code

Connect AARNET Cloudstor with OSF

Cloudstor is a wonderful storage service providing 1TB of owncloud storage for researchers in Australia. It’s like dropbox, but your data is in Australia, very fast to access from aarnet institutions and they provide a jupyter notebook service SWAN that Read more…

By Steffen, 2 weeks2 weeks ago
Code

Run NeuroDesk on Oracle Cloud Free Tier

Here is a little tutorial on running our NeuroDesk project in the free tier of Oracle cloud 🙂 Sign up for a free account here: Try Free Tier (oracle.com) now connect to your newly created instance (the public IP is Read more…

By Steffen, 2 months2 weeks ago
Applying Deep Learning Models to medical imaging data
Conferences

Applying Deep Learning Models to Medical Imaging Data – Problems, Pitfalls, Solutions – A tutorial

For this year’s AICI artificial intelligence in clinical imaging forum I prepared a tutorial for applying deep learning models to medical imaging data. It was very interesting to prepare the tutorial and see what models exist and how difficult it Read more…

By Steffen, 3 months3 months ago
Neurodesk slides
Conferences

Neurodesk talk at eResearch Australasia conference

This week I attended the eResearch Australasia conference and gave a talk about our little hackathon project that started at the OHBM Brainhack this year: https://github.com/NeuroDesk/. In a nutshell, we are trying to make it a lot easier to use Read more…

By Steffen, 3 months1 week ago
Conferences

2020 Australian Ultra High Field Network Virtual Workshop

The Australian ultra-high field community had its first virtual workshop organized by Leigh Johnston, Markus Barth and Kieran O’Brien. I was invited to talk about high-resolution fMRI and how it is currently used for neuroscience research. I thought I share Read more…

By Saskia Bollmann, 3 months3 months ago
Deep Learning

Improving FLAIR SAR Efficiency at 7T by Adaptive Tailoring of Adiabatic Pulse Power through Deep Learning Estimation

The full publication can be found here: https://doi.org/10.1002/mrm.28590 The preprint is here: [1911.08118] Improving FLAIR SAR efficiency at 7T by adaptive tailoring of adiabatic pulse power using deep convolutional neural networks (arxiv.org) The data used to train the model is Read more…

By Steffen, 3 months2 weeks ago
Conferences

ISMRM 2020: Imaging of the pial arterial vasculature

For this year’s ISMRM, I’ve investigated how we can image the pial arterial vasculature using a time-of flight contrast. Surprisingly, we found that we are not limited by physiological parameters, but ‘simply’ by the voxel size. All the gory details Read more…

By Saskia Bollmann, 6 months6 months ago
Containers

Containers for neuroscience at OHBM Brainhack Trainhack 2020

Tom Shaw and I prepared a talk for this year’s OHBM Brainhack Trainhack where we show what containers are and how to use them for neuroscience applications. We cover docker and singularity and show how to build and run containers Read more…

By Steffen, 7 months7 months ago
Code

Introduction to Git and Github for OHBM Brainhack Traintrack 2020

For the 2020 OHBM Brainhack we made a little tutorial explaining git and github. We hope it’s useful and thanks to the organizers for putting this great event together 🙂 Video: Slides:

By Saskia Bollmann, 8 months7 months ago

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