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 Read more…
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:
Our latest work just got published in Medical Image Analysis: Deep learning based Quantitative Susceptibility Mapping (QSM) has shown great potential in recent years, obtaining similar results to established non-learning approaches. Many current deep learning approaches are not data consistent, Read more…
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:
Our latest work is out in eLife: https://elifesciences.org/articles/71186 We show how small pial arteries can be targeted effectively with high-resolution in vivo MR imaging. The data is openly available (https://doi.org/10.17605/OSF.IO/NR6GC) and may be used for building models of brain physiology. Read more…
Oracle Cloud recently launched a platform to host scientific datasets and we uploaded our unique Hippocampus dataset (Towards Optimising MRI Characterisation of Tissue (TOMCAT) Dataset including all Longitudinal Automatic Segmentation of Hippocampal Subfields (LASHiS) data – ScienceDirect): https://opendata.oraclecloud.com/ords/r/opendata/opendata/details?data_set_id=28&bucket_name=TOMCAT&prefix=&clear=RR&session=610618357889967&cs=1o7GdDLNfm3PHWwxI2thFXrA8jHPcvjZCdFibkYYIPPofNfOuvVt8B6S0B7YTnzIOf6cDk9BXW5hSV9b8LmhoQA More background Read more…
Sometimes it’s necessary to downgrade packages in google colab to restore compatibility with an older version (e.g. pytorch). One way of doing this is using conda within colab and a few tricks make this work. Here is the colab notebook: Read more…
These are the slides for the talk I gave at the ARCOS Symposium in November 2021:
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 Read more…
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 Read more…