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 very slow downloads of the containers there is only a Read more…
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 can directly access this data 🙂 Wouldn’t it be nice Read more…
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) The below steps are for an older version of the neurodesk project – I recommend to follow the updated instructions here: Read more…
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 still is to make them work with real data. Here Read more…
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 neuroimaging software packages with the help of containers. The feedback Read more…
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 on OSF: And we also built a colab notebook (described Read more…
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 on different computing platforms. Video: Code to hack along: https://hackmd.io/ep87sx8ERMWFYc4D0FisRw Read more…
For a paper we recently submitted (Improving FLAIR SAR efficiency at 7T by adaptive tailoring of adiabatic pulse power using deep convolutional neural networks – pre-print here: https://arxiv.org/abs/1911.08118 and published article here: https://doi.org/10.1002/mrm.28590) I was wondering if we can do more than just provide the source code. One problem I Read more…
NMR in Biomedicine published our special issue review article, summarising and discussing the recent developments in deep learning QSM. The paper is here: https://onlinelibrary.wiley.com/doi/abs/10.1002/nbm.4292 The preprint is here: https://arxiv.org/abs/1912.05410 We also created a github repository collecting implementations of deep learning QSM algorithms that we are keeping updated regularly: https://github.com/dlQSM/dlQSM
During our last week in Boston, I was invited to give a talk in the Science on Tap Seminar. Science on tap is a fantastic iniative driven by dedicated early career researchers that organise a talk with drinks and nibbles every Friday afternoon at the Martinos Center. The talk should Read more…