Gender diversity in academia

Cross-posted from our lab blog.

Although we’d all like academia to be a true meritocracy, implicit biases shared by all of us create significant hurdles to achieving diversity in our communities.

I prepared slides to discuss the data (showing both the extent to which gender biases cause problems in science, and the different factors that may be significant contributors) and possible solutions that we can all try to live up to.

Please feel free to re-use the slides (here as pdf)!


You can call me Dr. Urai now

That’s it.
After 4+ years, a good number of triumphs and vastly more failures, I’ve defended my PhD!

For the occasion, I’d like to share a short piece about my experience as a PhD student that I originally wrote for a friend when she graduated. I recommend the original if you read Dutch.

Or let me know how I’ve got it all wrong.
Whatever, it’s Dr. Urai for you now! Continue reading

Thesis formatting in Latex

After four years of experimental design, data acquisition and analysis I just finished putting together everything into my PhD thesis. I did not find any templates that really worked for me (although classicthesis looks quite nice), so I put together my own set of random LaTex commands. I’m not a graphics designer but I’m quite happy with the end results – so here are the choices I made and the corresponding LaTex code. Continue reading

Pupil dilation reflects decision uncertainty and alters choice patterns

Three years after starting the project, two years after completing data collection and almost exactly one year after submitting the manuscript, the first paper of my PhD is now out! In this project, we investigated the relationship between pupil dilation, decision uncertainty and across-trial patterns of decisions.

When making decisions about the world, each choice is associated with a sense of uncertainty: the probability that a choice is correct or wrong, given all the available evidence. This quantity of decision uncertainty can be derived from a simple mathematical model. This model gives rise to a set of specific predictions (see top row of the figure). Based on previous work, we hypothesised that ascending brainstem systems, which release modulatory neurotransmitters such as dopamine and noradrenaline throughout the brain, may broadcast decision uncertainty signal across the brain. Continue reading

Rasterised topoplots in FieldTrip

To visualise the topographical distribution of electric or magnetic brain activity on the head, FieldTrip uses a family of topoplot functions. There are several styles to choose from, which determine o.a. if contour lines will be plotted on top of the color image.

Now, the default setting = ‘both’ (with contour lines) or = ‘straight’ (without contour lines) rely on contour or contourf, which in Matlab 2014b and later plot a set of triangles rather than one rasterised figure. This massively increases file sizes, and can cause weird artefacts when saving and viewing as pdf (elaborate rant here). Continue reading

Prettier plots in Matlab

Rather than prettifying all plots in Illustrator, I prefer doing as much as possible already in Matlab. Chances that you’ll have to regenerate the figures at some point (because you decide to change one step somewhere in your analysis pipeline, say…), and by scripting the plots as much as possible you can replace your pdfs with an updated one with just one click.

Here, I’ll make an overview of several types of plots I use a lot, and my strategies for making them look good. Some final touches in Illustrator might not be possible to avoid, but this should get you quite far. Continue reading