XNAT upload app

We have built an own XNAT application suitable to process raw MRI data to a project-specific, quality-controlled and anonymized BIDS data format.

Documentation

Slides

 

Fig.: A) Overview of the XNAT app. Raw files are decompressed, anonymized, defaced (using pydeface), converted into the Nifti format, structured into folders and subfolders. There is an option to convert MRI raw data to the BIDS format¹. Finally all data can be uploaded to a server. B) In addition, a data quality control is automatically carried out. The signal-to-noise ratio (SNR) is calculated, motion artifacts are determined (using FSL McFlirt), and the field of view is displayed.

References:

¹Gorgolewski KJ et al. (2016). Sci Data 3: 160044