Pypreclin: An automatic pipeline for macaque functional MRI preprocessing

Publication date: Available online 16 November 2019Source: NeuroImageAuthor(s): Jordy Tasserie, Antoine Grigis, Lynn Uhrig, Morgan Dupont, Alexis Amadon, Béchir JarrayaAbstractNon-human primate functional MRI (fMRI) is a growing field in neuroscience. However, there is no standardized method for monkey fMRI data analysis, specifically for data preprocessing. The preprocessing of monkey fMRI data is challenged by several technical and experimental specificities of the monkey research such as artifacts related to body movements or to intracranial leads. Here we propose to address these challenges by developing a new versatile pipeline for macaque fMRI preprocessing. We developed a Python module, Pypreclin, to process raw images using state of the art algorithms embedded in a fully automatic pipeline. To evaluate its robustness, we applied Pypreclin to fMRI data acquired at 3T in both awake and anesthetized macaques, with or without iron oxide contrast agent, using single loop or multichannel phased-array coils, combined or not with intracranial implanted electrodes. We performed both resting-state and auditory evoked fMRI and compared the results of Pypreclin to a previously employed preprocessing pipeline. Pypreclin successfully achieved the registration of the fMRI data to the macaque brain template in all the experimental conditions. Moreover, Pypreclin enables more accurate locations of auditory evoked activations in relation to the gray matter at corrected level in the aw...

Source: NeuroImage - November 18, 2019 Category: Neuroscience Source Type: research