random walk at the cross roads of neuroimaging, machine learning, brain disorders, informatics and open science.
Here are the slides from my talk the US Research Software Engineering (RSE) association workshop, titled "Research data management for medical data with pyradigm". pyradigm is a Python-based data structure for biomedical data to manage multiple tables (of diverse data types) linked via common patient info (or any other hashable ID). Allowing continuous validation, this …
Continue reading Research data management for medical data with pyradigm
News: here is the video pitch I've made for the OHBM hackathon 2020. The associated slides are here. As I tried to study impact of different deconfounding methods, as well as offer covariate regression ability in neuropredict, I realized the tools and methods I need to implement would be useful to broader machine learning and …
Continue reading Conquering confounds and covariates in machine learning
TL;DR: CCV interface indeed sucks, and must be redesignedTerrible interface does not obviate the need for tracking dataFree-format CVs are not a viable solutionTri-council must facilitate and lead a fully open discussion to completely redesign its interface, architecture and services around itTri-council must harmonize the CV format across all agenciesI am happy to help with …
Python is showing an incredible growth in many fields, including academia. By enumerating the challenges we face in sustainable research software development and how Python's unique strengths are catering to these challenges in this video below, I hope to explain this growth and encourage further adoption of python for research software development! A closely related …
Continue reading Why is Python ideal for research software development?
I am very delighted to let you know our course was attended well and received very well. The slides for each of the talks can be downloaded here: Raamana: Overview and Anatomical MRIDownload Raamana: niQC Tools and informaticsDownload Martina F. Callaghan : Functional MRI QA QCDownload Esther Kuehn : 7T fMRI QCDownload Joset Etzel: Dataset …
Continue reading Slides from educational course on Neuroimaging Quality Control at OHBM 2019 in Rome
As the discussion around harassment in academia (sexual and otherwise) is increasing, we learn that it is not healthy, definitely not rare and not reported as often as it happens. While thinking of various solutions to prevent or reduce its occurrence, I had been contemplating on the possibility and effectiveness of banning (or minimizing) alcohol …
News: slides and photos from this course are now posted here. I am very delighted to announce that our proposal for educational workshop titled "Taking Control Of Your Neuroimaging Data: Understanding Artefacts And Quantifying Quality" has been accepted for inclusion in the program for the 2019 OHBM Annual Meeting. Stay tuned for slides and related …
Continue reading Educational workshop on Neuroimaging Quality Control at OHBM 2019
To: The NeuroImaging Community Across the World Invitation to Contribute to the Development of Best Practices for niQC The niQC special interest group (SIG) aims to standardize and develop best practices for neuroimaging QC and Quality Assurance (QA). We invite you to fill this survey, to help us to get a sense of various types …
Continue reading Status quo in neuroimaging quality control – survey
TL;DR: New visitors from survey broadcast: fill the survey here. Thanks.Quality control of neuroimaging data is hard, needs purpose-built tools and standardizationThere is a need for development of best practices and QC protocolsWe formed a new special interest group (SIG) @ INCF called Neuroimaging Quality Control (niQC)Join us in the google group to stay tuned, …
cross invalidation 