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

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

New paper: conscious vision proceeds from global to local

Campana F, Rebello I, Urai AE, Wyart V & Tallon-Baudry C. (2016) Visual consciousness proceeds from global to local content in goal-directed tasks and spontaneous vision. Journal of Neuroscience 36(19).

During my MSc at the ENS in Paris, I did my internship in the laboratory of Dr. Catherine Tallon-Baudry, where I worked on a project about the hierarchical nature of conscious perception. This project, led by Dr. Florence Campana, aimed to experimentally address several predictions made by the Reverse Hierarchy Theory (Hochstein & Ahissar, 2002). Continue reading

NVP best poster prize

At the Dutch Society for Psychonomics conference (NVP), which takes place every other year in beautiful beach-side Egmond aan Zee, I won the best poster prize for my work Pupil dilation signals decision uncertainty and predicts response alternation.

Since I didn’t take any photos at NVP, here’s me presenting the study at the Society for Neuroscience meeting in Chicago earlier this year.

DonnerLab now on Twitter

I’ve been on Twitter for a couple of years now, and I find it to be a great addition to my usual diet of journal-specific rss feeds and PubMed keyword alerts for keeping up with the literature. I’ve also connected with many people in my field, joined the #PLOS #SfN15 twitter team and even got invited to speak at a symposium. See also this great post by Dorothy Bishop introducing Twitter for academics, and another post by Micah Allen asking how useful Twitter is in getting articles read by colleagues.

I’ve now also convinced my lab of the powers of social media, and our twitter account has gone live this week. We will also soon announce our new lab website, that should go live in the beginning of the new year. So yes, you know you want to click these buttons and keep track of what we’re up to!


We’re off to a good start with some great promo:

Matlab-based IPython notebooks

21 February 2018, update: the new JupyterLab was just released, and according to this tweet is really easy to integrate with Matlab. Probably worth checking out instead of the reasonably outdated instructions below!

I really like Python’s philosophy, but over the last years I haven’t been able to switch the code for my research from Matlab. At this point, the transition costs are too high for me, but it’s a move I have planned for some point in the future.

Now, Python has the awesome Jupyter (formerly IPyton notebook) feature, that allows for comments, code, and most importantly graphical output (i.e. figures you’ve just generated) to be shown in one document. This is a great way to share and explain the code you’re writing, since the reader immediately sees how output is generated without having to run all the analyses themselves.

Continue reading

Decision-making in ten minutes

During the Montenegrin Open Science Days in 2014, I gave a short talk on models and neural bases of decision-making. A video of the talk is now online, so check it out if you’re interested in a crash course on how psychologists and neuroscientists think about the process of decision-making. If you’re interested in the slides, don’t hesitate to get in touch. And while you’re at it, check out the other talks by Nuno, Elena, Merina and Nikola!