My goals to further Diversity and Inclusion in Science

Being a visible minority and often underrepresented, I know the importance of improving diversity and inclusivity, in all the important dimensions including but not limited to gender, sexual orientation, ethnicity, race, culture, geography and school of thought. My lived experience in this domain taught me a lot of things, and provided me an important perspective …

Continue reading My goals to further Diversity and Inclusion in Science

Evaluating Visual QC protocols for Freesurfer Parcellations: error detection rate, inter-rater reliability and site differences

This page will host the study and results from systematically evaluating the visual QC protocols for Freesurfer parcellations. A preprint would be uploaded soon, but below is a poster that gives you the summary. This will be presented at OHBM 2020, at poster number 1621, titled "Site-differences and inter-rater reliability for visual quality control (QC) for …

Continue reading Evaluating Visual QC protocols for Freesurfer Parcellations: error detection rate, inter-rater reliability and site differences

Unambiguous terminology for data-splits in nested cross-validation (CV): training, tuning and reporting sets

A particularly frustrating confusion exists when referring to the different dataset splits when performing nested CV: whether the split in [the really] outer CV loop is to be called test set or validation set, and whether the "test set" in the inner-CV loop is to be called validation set or test set. There are different …

Continue reading Unambiguous terminology for data-splits in nested cross-validation (CV): training, tuning and reporting sets

Research data management for medical data with pyradigm

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

Conquering confounds and covariates in machine learning

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

Whether to reform or abandon Canadian Common CV (CCV): let’s not throw the baby out with the bathwater

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 …

Continue reading Whether to reform or abandon Canadian Common CV (CCV): let’s not throw the baby out with the bathwater

Why is Python ideal for research software development?

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?

Slides from educational course on Neuroimaging Quality Control at OHBM 2019 in Rome

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

Let’s ban alcohol at academic events to reduce sexual harassment and other unwelcome behaviour [MeToo]

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 …

Continue reading Let’s ban alcohol at academic events to reduce sexual harassment and other unwelcome behaviour [MeToo]