Containers
ReproNim Talk about Neurodesk
I was recently invited to talk about Neurodesk in the ReproNim webinar. The recording of the talk is available here: The slides are available here:
Conferences
Talk about Open Data and Neurodesk at MRItogether
This week I gave a talk about the Open Data ecosystem and how our open-source project https://NeuroDesk.org makes it very easy to access and publish open data. Here is the recording: Here are the slides:
Containers
Behind the scenes of NeuroDesk : What we learned so far in building and distributing containers in a community driven fashion
These are the slides for the talk I gave at the ARCOS Symposium in November 2021:
Containers
QSMxT: Robust masking and artifact reduction for quantitative susceptibility mapping
Our article “QSMxT: Robust masking and artifact reduction for quantitative susceptibility mapping” was just published in MRM 🙂 In this article we developed an automated, scalable, and robust QSM workflow that starts from Dicom images and produces segmentations of regions of interest: The full paper is here (unfortunately behind a Read more…
CloudStor
Neurodesk at the ANZ ISMRM reproducibility workshop
We had the fantastic opportunity to present the neurodesk project in today’s ANZ ISMRM reproducibility workshop. The 50 participants across Australia got to see the first live demo of the project and I am glad everything worked out and ran smoothly 🙂 We will post the recordings as soon as Read more…
Containers
QSMxT preprint
Our latest preprint describes the QSMxT pipeline developed by Ashley Stewart – a CIBIT PhD student in our team: QSMxT enables robust & automated quantitative susceptibility mapping and extraction of quantitative information from regions of interest. The code can be found here: https://github.com/QSMxT/QSMxT The preprint is here: QSMxT: Robust Masking Read more…
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 very slow downloads of the containers there is only a Read more…
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) The below steps are for an older version of the neurodesk project – I recommend to follow the updated instructions here: Read more…
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 still is to make them work with real data. Here Read more…
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 neuroimaging software packages with the help of containers. The feedback Read more…