Pypreclin: An automatic pipeline for macaque functional MRI preprocessing
Non-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 monk...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2020-02-01
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| Series: | NeuroImage |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1053811919309449 |
| _version_ | 1818145417351659520 |
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| author | Jordy Tasserie Antoine Grigis Lynn Uhrig Morgan Dupont Alexis Amadon Béchir Jarraya |
| author_facet | Jordy Tasserie Antoine Grigis Lynn Uhrig Morgan Dupont Alexis Amadon Béchir Jarraya |
| author_sort | Jordy Tasserie |
| collection | DOAJ |
| description | Non-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 awake fMRI condition. Finally, using the Primate neuroimaging Data-Exchange open access platform, we could further validate Pypreclin for monkey fMRI images that were acquired at ultra-high fields, from other institutions and using different protocols. Pypreclin is a validated preprocessing tool that adapts to diverse experimental and technical situations of monkey fMRI. Pypreclin code is available on open source data sharing platform. |
| first_indexed | 2024-12-11T12:03:08Z |
| format | Article |
| id | doaj.art-7c01df39658b4d1cbf5828353cf4f111 |
| institution | Directory Open Access Journal |
| issn | 1095-9572 |
| language | English |
| last_indexed | 2024-12-11T12:03:08Z |
| publishDate | 2020-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | NeuroImage |
| spelling | doaj.art-7c01df39658b4d1cbf5828353cf4f1112022-12-22T01:08:00ZengElsevierNeuroImage1095-95722020-02-01207116353Pypreclin: An automatic pipeline for macaque functional MRI preprocessingJordy Tasserie0Antoine Grigis1Lynn Uhrig2Morgan Dupont3Alexis Amadon4Béchir Jarraya5Commissariat à l’Énergie Atomique et aux Énergies Alternatives, Direction de la Recherche Fondamentale, NeuroSpin Center, Gif-sur-Yvette, France; Cognitive Neuroimaging Unit, Institut National de la Santé et de la Recherche Médicale U992, Gif-sur-Yvette, France; Université Paris Sud, Université Paris-Saclay, Orsay, FranceCommissariat à l’Énergie Atomique et aux Énergies Alternatives, Direction de la Recherche Fondamentale, NeuroSpin Center, Gif-sur-Yvette, France; Analysis and Information Treatment Unit, Commissariat à l’Énergie Atomique et aux Énergies Alternatives, Gif-sur-Yvette, FranceCommissariat à l’Énergie Atomique et aux Énergies Alternatives, Direction de la Recherche Fondamentale, NeuroSpin Center, Gif-sur-Yvette, France; Cognitive Neuroimaging Unit, Institut National de la Santé et de la Recherche Médicale U992, Gif-sur-Yvette, FranceCommissariat à l’Énergie Atomique et aux Énergies Alternatives, Direction de la Recherche Fondamentale, NeuroSpin Center, Gif-sur-Yvette, France; Cognitive Neuroimaging Unit, Institut National de la Santé et de la Recherche Médicale U992, Gif-sur-Yvette, FranceCommissariat à l’Énergie Atomique et aux Énergies Alternatives, Direction de la Recherche Fondamentale, NeuroSpin Center, Gif-sur-Yvette, France; Magnetic Resonance Imaging and Spectroscopy Unit, Commissariat à l’Énergie Atomique et aux Énergies Alternatives, Gif-sur-Yvette, FranceCommissariat à l’Énergie Atomique et aux Énergies Alternatives, Direction de la Recherche Fondamentale, NeuroSpin Center, Gif-sur-Yvette, France; Cognitive Neuroimaging Unit, Institut National de la Santé et de la Recherche Médicale U992, Gif-sur-Yvette, France; Neurosurgery Department, Foch Hospital, Suresnes, France; University of Versailles Saint-Quentin-en-Yvelines, Université Paris-Saclay, Versailles, France; Corresponding author. Neurospin imaging center, Inserm, CEA Saclay, Bat 145, 91191, Gif-sur-Yvette, France.Non-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 awake fMRI condition. Finally, using the Primate neuroimaging Data-Exchange open access platform, we could further validate Pypreclin for monkey fMRI images that were acquired at ultra-high fields, from other institutions and using different protocols. Pypreclin is a validated preprocessing tool that adapts to diverse experimental and technical situations of monkey fMRI. Pypreclin code is available on open source data sharing platform.http://www.sciencedirect.com/science/article/pii/S1053811919309449PreprocessingfMRIMacaqueNon-human primateAutomaticMovement artifact |
| spellingShingle | Jordy Tasserie Antoine Grigis Lynn Uhrig Morgan Dupont Alexis Amadon Béchir Jarraya Pypreclin: An automatic pipeline for macaque functional MRI preprocessing NeuroImage Preprocessing fMRI Macaque Non-human primate Automatic Movement artifact |
| title | Pypreclin: An automatic pipeline for macaque functional MRI preprocessing |
| title_full | Pypreclin: An automatic pipeline for macaque functional MRI preprocessing |
| title_fullStr | Pypreclin: An automatic pipeline for macaque functional MRI preprocessing |
| title_full_unstemmed | Pypreclin: An automatic pipeline for macaque functional MRI preprocessing |
| title_short | Pypreclin: An automatic pipeline for macaque functional MRI preprocessing |
| title_sort | pypreclin an automatic pipeline for macaque functional mri preprocessing |
| topic | Preprocessing fMRI Macaque Non-human primate Automatic Movement artifact |
| url | http://www.sciencedirect.com/science/article/pii/S1053811919309449 |
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