Containers – mri.sbollmann.net

Neurodesk paper published in Nature Methods

Our www.neurodesk.org paper was published in Nature Methods today: https://rdcu.be/dvqwU And we published a blog post describing why and how we developed this platform: https://communities.springernature.com/posts/reproducible-neuroimaging-for-everyone-behind-the-scenes-of-neurodesk 🧠 As researchers in neuroimaging, we often face hurdles with software installation and inconsistent results across different computing environments. But Neurodesk helps with that! ✨ Neurodesk is a Read more…

By Steffen, 1 yearJanuary 9, 2024 ago

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:

By Steffen, 2 yearsMarch 6, 2023 ago

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:

By Steffen, 2 yearsDecember 9, 2022 ago

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:

By Steffen, 3 yearsNovember 10, 2021 ago

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…

By Steffen, 3 yearsNovember 3, 2021 ago

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…

By Steffen, 4 yearsSeptember 20, 2021 ago

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…

By Steffen, 4 yearsMay 7, 2021 ago

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…

By Steffen, 4 yearsJanuary 11, 2021 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) The below steps are for an older version of the neurodesk project – I recommend to follow the updated instructions here: Read more…

By Steffen, 4 yearsDecember 8, 2020 ago

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…

By Steffen, 4 yearsNovember 1, 2020 ago