We spend a lot of our time developing code for experiments and data analyses (mostly in MATLAB). Here are some of the toolboxes and apps we find helpful:
SPM for preprocessing MRI data and GLMs
FreeSurfer for surface reconstruction
SamSrf for fitting encoding models (e.g. population receptive fields)
Psychtoolbox for stimulus presentation and data recording
Custom code: we're committed to publishing our code and data wherever possible. For individual projects, check out the publications page and OSF.
Textbooks & tutorials
Some of the links above include learning resources for the respective packages. For neuroimaging analyses we recommend the excellent Handbook of Functional MRI Data Analysis by Poldrack et al. and Statistical Analysis of fMRI Data by Ashby. To get into MATLAB, we recommend MATLAB for Neuroscientists by Wallisch and colleagues.
We also developed two tutorials for lab members beginning their coding journey and made them public- one with MATLAB exercises for MRI analyses, one with MATLAB exercises for eyetracking analyses.
In April 2021 we started PNiP: Perceptual Neuroimaging in Practice, a weekly methods seminar for researchers, which is losely based on SPM's MfD. If you're interested to take part, please ping Ben!
In September 2022 Mareike Grotheer and Ben held a one-day methods course on neuroimaging for members of the Collaborative Research Center 135. Here you can find Ben's slides on What is fMRI and what can I do with it?