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Pypreclin: An automatic pipeline for macaque functional MRI preprocessing

Jordy Tasserie, Antoine Grigis, Lynn Uhrig, Morgan Dupont, Alexis Amadon, Béchir Jarraya
2019 NeuroImage  
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.  ...  Acknowledgments We thank, Thomas Janssens, Marie-France Hang Foucarde, Michel Luong, Edouard Chazel, Eric Giacomini, J er emy Bernard, Laurent Laribi ere, Franck Mauconduit and the NeuroSpin MRI and informatics  ... 
doi:10.1016/j.neuroimage.2019.116353 pmid:31743789 fatcat:bndqh4ng3rcg3oqgobaqyvslfq

Thalamic_DBS_restores_consicousness

Jordy TASSERIE, Lynn UHRIG, Jacobo D SITT, Dragana MANASOVA, Morgan DUPONT, Stanislas DEHAENE, Béchir JARRAYA
2021 Zenodo  
Datasets and codes related to the article 'Deep brain stimulation of the thalamus restores signatures of consciousness in a non-human primate model' by Tasserie et al.  ...  Acknowledgments We thank, Thomas Janssens, Marie-France Hang Foucarde, Michel Luong, Edouard Chazel, Eric Giacomini, J er emy Bernard, Laurent Laribi ere, Franck Mauconduit and the NeuroSpin MRI and informatics  ...  teams for help with monkey's coils and MRI sequences, J erôme Cayla, Wilfried Piannezzola and S ebastien M eriaux for help within the animal facility, Timo van Kerkoerle, Qi Zhu, Vincent Frouin and Jean-Robert  ... 
doi:10.5281/zenodo.5762156 fatcat:jiqeeln2qveuvmgpu6a54q2to4

Integration of ultra-high field MRI and histology for connectome based research of brain disorders

Shan Yang, Zhengyi Yang, Karin Fischer, Kai Zhong, Jörg Stadler, Frank Godenschweger, Johann Steiner, Hans-Jochen Heinze, Hans-Gert Bernstein, Bernhard Bogerts, Christian Mawrin, David C. Reutens (+2 others)
2013 Frontiers in Neuroanatomy  
the network analyses currently performed with in vivo MRI.  ...  However, this is still the unchallenged domain of histological studies, which long played an important role in the investigation of neuropsychiatric disorders.  ...  ACKNOWLEDGMENTS The authors would like to thank DFG (Wa2673/3-1, SFB-779), Chinese National Nature Science Foundation (U1232212) and the federal state of Saxony-Anhalt (CBBS) for project grant and DAAD  ... 
doi:10.3389/fnana.2013.00031 pmid:24098272 pmcid:PMC3784919 fatcat:r7jlhxsd2zazhfql3vyjdezpiq

Construction and assessment of a 3-T MRI brain template

Florent Lalys, Claire Haegelen, Jean-Christophe Ferre, Omar El-Ganaoui, Pierre Jannin
2010 NeuroImage  
We developed a three-dimensional digitised mono-subject anatomical template of the human brain based on 3T MR images.  ...  Results demonstrated that such a template also improved inter-patient registration for population comparison in DBS.  ...  The Colin27 MRI brain template has been lightly validated in the original work of Holmes et al., (1998) by computing intensity profiles to demonstrate the improvement in image quality, but no such studies  ... 
doi:10.1016/j.neuroimage.2009.08.007 pmid:19682582 fatcat:6xpx7hlcpvgxdhuug35ov5i4qu

Neurodevelopmental MRI brain templates for children from 2 weeks to 4 years of age

Carmen E. Sanchez, John E. Richards, C. Robert Almli
2011 Developmental Psychobiology  
These average, age-specific templates were constructed from brain scans of individual children obtained from two sources: (1) the NIH MRI Study of Normal Brain Development and (2) MRIs from University  ...  Widely used processing programs (FSL, SPM, and ANTS) extracted the brain and constructed average templates separately for 1.5T and 3T MRI volumes.  ...  Some intensity variations occur in the MRI scans. First, bias field inhomogeneity was corrected with a N4 bias field correction procedure (Avants et al., 2011; Tustison et al., 2010) .  ... 
doi:10.1002/dev.20579 pmid:21688258 pmcid:PMC3184192 fatcat:ikbwco4obrcpfliv4jmsa433w4

Non-invasive monitoring of cortical volume alterations in rat brains using a clinical 3T whole body MRI scanner [chapter]

K. -H. Herrmann, S. Schmidt, M. Metzler, C. Gaser, O. W. Witte, J. R. Reichenbach
2009 International Federation for Medical and Biological Engineering Proceedings  
In this study we show that deformation based morphometry of the rat brain can be achieved with data acquired on a human 3T whole body system using a multi purpose 8-channel coil with overlapping coil elements  ...  Therefore, noninvasive detection of local changes in cerebral volume which can be accomplished by MRI, is in focus of clinical investigations.  ...  ACKNOWLEDGEMENT We thank Noras MRI products GmbH and Siemens Medical Solutions for their support and the MR technician Ines Krumbein for her active participation in all the MRI experiments.  ... 
doi:10.1007/978-3-642-03879-2_115 fatcat:zn7lwwywqjefdorn4z54tokbhm

Whole-brain atrophy assessed by proportional- versus registration-based pipelines from 3T MRI in multiple sclerosis

Christopher C. Hemond, Renxin Chu, Subhash Tummala, Shahamat Tauhid, Brian C. Healy, Rohit Bakshi
2018 Brain and Behavior  
Conclusion: Whole-brain atrophy metrics may not be interchangeable between proportional-and registration-based automated pipelines from 3T MRI in patients with MS.  ...  Whole-brain atrophy was assessed by two automated pipelines: (a) SPM8 to derive brain parenchymal fraction (BPF, proportional-based method); (b) SIENAX to derive normalized brain parenchymal volume (BPV  ...  MRI was obtained within 3 months of the neurological examination. Demographic and clinical data are summarized in Table 1 .  ... 
doi:10.1002/brb3.1068 pmid:30019857 pmcid:PMC6085901 fatcat:laiosovnpvh7deqsoojz6dgoim

Ultra-high field MRI reveals mood-related circuit disturbances in depression: A comparison between 3-Tesla and 7-Tesla [article]

Laurel S Morris, Prantik Kundu, Sara Costi, Abigail Collins, Molly Schneider, Gaurav Verma, Priti Balchandani, James W Murrough
2018 bioRxiv   pre-print
To date, few studies have quantified the advantage of resting state functional MRI (fMRI) at 7T compared to 3-Tesla (3T).  ...  of MDD but difficult to discern with standard 3T MRI.  ...  , DLPFC at the same whole-brain cluster-corrected thresholds (Fig 4A-B , Table 1 for statistics).  ... 
doi:10.1101/459479 fatcat:24cxgfknkjaj7khscwazclr7su

Measuring brain atrophy with a generalized formulation of the boundary shift integral

Ferran Prados, Manuel Jorge Cardoso, Kelvin K. Leung, David M. Cash, Marc Modat, Nick C. Fox, Claudia A.M. Wheeler-Kingshott, Sebastien Ourselin
2015 Neurobiology of Aging  
Brain atrophy measured using structural magnetic resonance imaging (MRI) has been widely used as an imaging biomarker for disease diagnosis and tracking of pathologic progression in neurodegenerative diseases  ...  This method adaptively estimates a non-binary exclusive OR region of interest from probabilistic brain segmentations of the baseline and repeat scans to better localize and capture the brain atrophy.  ...  Fig. 2 . 2 Extra N3 correction. (A) Initial scan with the template-12-dof mask overlaid. (B) Corrected scan. (C) Subtraction between initial scan and corrected scan.  ... 
doi:10.1016/j.neurobiolaging.2014.04.035 pmid:25264346 pmcid:PMC4288791 fatcat:pkjd24c6kraetpafo3skmnyxde

Quantitative relaxation templates for the human brain at 3T

Fang Cao, Olivier Commowick, Camille Maumet, Christian Barillot
2014 2014 IEEE 11th International Symposium on Biomedical Imaging (ISBI)  
In this paper, we have developed 3D qMRI statistical templates consisting of T 1 , T 2 , T * 2 and ρ * maps from the human brain at 3T.  ...  Quantitative MRI (qMRI) templates of relaxation times and proton density can be of particular interest for dedicated clinical applications such as characterizing brain tissue abnormalities, as well as  ...  This may be due to the B 1 inhomogeneities in the T 1 map that needs further investigation.  ... 
doi:10.1109/isbi.2014.6867808 dblp:conf/isbi/CaoCMB14 fatcat:pthquq54kbc5hgx4dlscr3iz7i

The impact of B1+ correction on MP2RAGE cortical T1 and apparent cortical thickness at 7T

Roy A.M. Haast, Dimo Ivanov, Kâmil Uludağ
2018 Human Brain Mapping  
7T) MRI, transmit and receive B 1 -related image inhomogeneities can hamper correct classification of tissue types.  ...  Overall, the changes in cortical thickness ranged between a 5% decrease to a 70% increase after B 1 Hum Brain Mapp.  ...  In this study, we investigated the effect of residual B 1 1 inhomogeneities on T 1 and cortical thickness estimates based on T 1 (w) MP2RAGE data.  ... 
doi:10.1002/hbm.24011 pmid:29457319 pmcid:PMC5969159 fatcat:jf5lndzx7jchtazmyax2jmomvy

Efficient Variational Approach to Multimodal Registration of Anatomical and Functional Intra-Patient Tumorous Brain Data

Alvar-Ginés Legaz-Aparicio, Rafael Verdú-Monedero, Jorge Larrey-Ruiz, Juan Morales-Sánchez, Fernando López-Mir, Valery Naranjo, Ángela Bernabéu
2017 International Journal of Neural Systems  
in the brain.  ...  Functional images of the brain (fMRI and PET) provide information about brain function and metabolism whereas anatomical images (MRI and CT) supply the localization of structures with high spatial resolution  ...  The datasets used in the registration process are based on studies of 10 patients.  ... 
doi:10.1142/s0129065717500149 pmid:28093049 fatcat:umv7iebudvap7mbohjfq72al5q

A Single-Scan, Rapid Whole-Brain Protocol for Quantitative Water Content Mapping With Neurobiological Implications

Ana-Maria Oros-Peusquens, Ricardo Loução, Zaheer Abbas, Vincent Gras, Markus Zimmermann, N. J. Shah
2019 Frontiers in Neurology  
MRI can be used to measure changes in brain water content, but as these changes are usually in the low percentage range, highly accurate and precise methods are required for detection.  ...  correction.  ...  This becomes difficult at 3T and higher fields, mainly due to the effect of the B 1 inhomogeneity correction.  ... 
doi:10.3389/fneur.2019.01333 pmid:31920951 pmcid:PMC6934004 fatcat:lulbdf4fbfaqdgnftz4rbh6vri

Automatic segmentation of MR images of the developing newborn brain

Marcel Prastawa, John H. Gilmore, Weili Lin, Guido Gerig
2005 Medical Image Analysis  
The analysis and study of newborn brain MRI is of great interest due to its potential for studying early growth patterns and morphological changes in neurodevelopmental disorders.  ...  This paper describes an automatic tissue segmentation method for newborn brains from magnetic resonance images (MRI).  ...  Acknowledgments We acknowledge Koen van Leemput for providing the MATLAB code that aids the development of the bias correction software and the Insight Toolkit community (Insight Consortium, 2004) for  ... 
doi:10.1016/j.media.2005.05.007 pmid:16019252 fatcat:il3nak6j6bfndmae3rkfu2dmem

Reliability of neuroanatomical measurements in a multisite longitudinal study of youth at risk for psychosis

Tyrone D. Cannon, Frank Sun, Sarah Jacobson McEwen, Xenophon Papademetris, George He, Theo G.M. van Erp, Aron Jacobson, Carrie E. Bearden, Elaine Walker, Xiaoping Hu, Lei Zhou, Larry J. Seidman (+17 others)
2013 Human Brain Mapping  
However, siterelated variations were trivial (<1%) among sites using the same scanner model and 12-channel coil or when correcting for between-scanner differences in gradient nonlinearity and scaling.  ...  In this study 8 healthy volunteers were scanned twice on successive days at 8 sites participating in the North American Prodrome Longitudinal Study (NAPLS).  ...  Brain Imaging (to RF).  ... 
doi:10.1002/hbm.22338 pmid:23982962 pmcid:PMC3843968 fatcat:yd2jwnbblvc5fnxzmzb7wq2uhe
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