For the last eight years, I called myself a cognitive neuroscientist. Throughout undergrad and grad school, I spent my days finding out how humans make decisions based on the information they extract from the outside world, and what factors play a role in determining our choices.

Half a year ago I started working with mice, asking many of the same questions. I was (and am) excited about the possibilities of recording from actual cells. I was (and am) inspired by the many genetic tools available, and the opportunities for collecting quantities of data from single individuals that are very rare in human subjects research. I also thought it would be cool to do something different – wrap my head around some fresh ideas, and perhaps build up a useful combined skill set.

“Science would be ruined if (like sports) it were to put competition above everything else, and if it were to clarify the rules of competition by withdrawing entirely into narrowly defined specialties. The rare scholars who are nomads-by-choice are essential to the intellectual welfare of the settled disciplines.”

– Benoit Mandelbrot

Continue reading →

I strongly believe in the value of openness and transparency, and I encourage the authors to make their data and analysis code publicly available. Over and above increasing the transparency and reproducibility of scientific findings as a whole, sharing data and code increases the visibility and impact of individual papers (McKiernan et al. 2016 eLife). Please see the standards of the Peer Reviewers’ Openness Initiative (https://opennessinitiative.org/the-initiative/) for guidelines.

I hope this is useful to others – so far this has always worked (but my N is pretty small).

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.

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

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 →

Check out my answer to the question ‘does psychology need neuroscience?’, published in Spiegeloog magazine. If you don’t read Dutch, or are interested in hearing more about this topic, check out this episode of the UnsupervisedThinking podcast. Continue reading →

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 →

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 cfg.style = ‘both’ (with contour lines) or cfg.style = ‘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 →

I’m starting to explore fellowship programs to fund my future postdoctoral adventures.  Thanks to many on Twitters who responded to my request, here’s a list of the agencies and programs I’ve come across so far.

Continue reading →

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 →