For my PhD at the University of Amsterdam, I am collaborating with a lot of researchers from different departments who are working with (f)MRI data. Additionally, I’m working at the faculty’s neuroimaging centre (“Spinoza Centre for Neuroimaging”, location REC) as ‘technical manager’ to improve and standardize data management, preprocessing, and analysis.
For my recent projects, I’ve converted my data to BIDS (using an in-house developed converter) and used fmriprep (with the fmriprep-docker package) to preprocess the data on our dedicated neuroimaging analysis servers (56 cores, 126GB RAM). These projects include two large datasets with together more than 500 subjects, whose (3T MRI) data includes anatomical data (T1-weighted), DWI data, and functional data (four tasks). I’m using both phasediff-unwarping (in some datasets) and topup-unwarping (in other datasets).
Next year, I hope to implement a protocol that converts all data acquired at our centre to BIDS and (optionally, if desired by the researcher) preprocesses the data using fmriprep.
You can contact me at the email address listed on my Github page.
Also, importantly: a big thank you for the fmriprep developers for this awesome tool!