How I start each paper review

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).

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.

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

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 “Thesis formatting in Latex”

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 “Pupil dilation reflects decision uncertainty and alters choice patterns”

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 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 “Rasterised topoplots in FieldTrip”

Postdoctoral fellowship programmes

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 “Postdoctoral fellowship programmes”

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 “Prettier plots in Matlab”

My favourite (science) podcasts

I highly recommend having some podcasts at hand for those moments when your life involves commuting, grocery shopping, cleaning, running or any other activity that doesn’t require much thinking.

Inspired by PsychBrief (and encouraged by Max), here is a list of the podcasts I currently listen to. I use the Pocketcast app. Please let me know if I should any additional essentials to the list!Continue reading “My favourite (science) podcasts”