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Pypreclin: a new tool for fMRI preprocessing to facilitate interpretation

NeuroSpin researchers have developed a software for preprocessing non-human primate brain raw images obtained by functional magnetic resonance imaging. The aim is to help harmonize methods, improve procedures, facilitate comparison and interpretation of the acquired images and to minimize the number of animals to be used in research.

Published on 21 January 2020

Since the 1990s, functional magnetic resonance imaging (fMRI), which indirectly reveals brain activity, has become an essential imaging modality, both clinically, for example during a pre-neurosurgical assessment, and in neuroscience and cognitive research. Current technological developments related to this methodology are associated with the use of increasingly large cohorts of healthy subjects and patients. They are also accompanied by an increasing number of images from non-human primates. Obtaining such images is a unique opportunity to compare brain functions between close species and to link them up, as well as to better understand the mechanisms behind the signals recorded in fMRI, spontaneous or in response to sensory stimulus. 

In 2018, an international consortium created a database, called PRIME-DE, of non-human primate brain imaging open to the entire scientific community. The aim is to harmonize the methods used by the different laboratories and thus to improve the procedures while keeping the number of animals as low as possible. But there is currently no fully validated automated method for analyzing images obtained in non-human primates. Specific artifacts exist for recording these images. Most of them is related to the movements of the animal, which cannot be asked not to move. Other artifacts occur under certain conditions, such as when using implants, which are equivalent to those used in the clinic for the deep brain stimulation treatment of Parkinson’s disease. 

NeuroSpin researchers have developed a module called Pypreclin, using Python computer programming language, to preprocess raw images using state of the art algorithms embedded in a fully automatic "pipeline". To evaluate its robustness, the researchers used Pypreclin to preprocess fMRI data acquired at 3 teslas under several conditions in awake or anesthetized macaques. They compared their data with a previously known preprocessing method. They also used Pypreclin on fMRI images obtained in other PRIME-DE consortium laboratories, i.e. with other devices (including 7 teslas MRIs) and other imaging protocols.

Their results show that Pypreclin is a robust image preprocessing tool that adapts to various experimental and technical fMRI situations recorded in the macaque. Pypreclin even manages to break away from the metal artifact of deep brain stimulation implants, paving the way for its translation into the world of clinical imaging, for example in patients with Parkinson’s disease. Pypreclin can make a significant contribution to the standardization of the preprocessing of fMRI in non-human primates under the international PRIME-DE initiative of which the NeuroSpin team is a member. Pypreclin code is available on the GitHub open source data sharing platform 

 Motion correction illustration

Movie illustrating motion correction on temporal series of functional images after performing the NSM preprocessing (left) or the Pypreclin preprocessing (right) (video published on NeuroImage website)

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