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Issues with threshold masking in voxel-based morphometry of atrophied brains

2009 NeuroImage  
We show that one of the most commonly used strategies for defining this mask runs a major risk of excluding from the analysis precisely those voxels where the subjects' brains were most vulnerable to atrophy  ...  Voxel-Based Morphometry (VBM) is one of the most widely used of such techniques. VBM performs voxel-wise statistical analysis of smoothed spatially normalised segmented Magnetic Resonance Images.  ...  Introduction In essence, Voxel-Based Morphometry (VBM) (Ashburner and Friston, 2000) involves voxelwise statistical analysis of data derived from structural Magnetic Resonance (MR) brain images of multiple  ... 
doi:10.1016/j.neuroimage.2008.08.045 pmid:18848632 fatcat:j2tut5kmefdqrfcicnzofkm5ni

Building Confidence in fMRI Results with Model Diagnosis [article]

Thomas Nichols
2017 Figshare  
Talk given during the "How Not to Analyze Your Data: A Skeptical Introduction to Modeling Methods" workshop at the 2013 Organization for Human Brain Mapping (OHBM) conference in Seattle, 16-20 June.  ...  Issues with threshold masking in voxel-based morphometry of atrophied brains. NeuroImage, 44(1), 99-111. Compute mean: make_average! Estimate mask: opt_thresh('','','')!  ...  More MaskingMasking not just a VBM issue • SPM fMRI -Single-subject maskThreshold, 80% of global of BOLD images after smoothing -Intersection group analysis mask • If but one subject  ... 
doi:10.6084/m9.figshare.5484154.v1 fatcat:xzxc4c5ptnfiro4scancdvaao4

Extrahippocampal gray matter loss and hippocampal deafferentation in patients with temporal lobe epilepsy

Leonardo Bonilha, Jonathan C. Edwards, Stephen L. Kinsman, Paul S. Morgan, Julius Fridriksson, Chris Rorden, Zoran Rumboldt, Donna R. Roberts, Mark A. Eckert, Jonathan J. Halford
2010 Epilepsia  
Methods-Three different MRI studies were performed involving 23 patients with unilateral MTLE (8 left and 15 right) and 34 healthy controls: (1) voxel-based morphometry (VBM), (2) diffusion tensor imaging  ...  Purpose-Medial temporal epilepsy (MTLE) is associated with extrahippocampal brain atrophy. The mechanisms underlying brain damage in MTLE are unknown.  ...  Acknowledgments We confirm that we have read the Journal's position on issues involved in ethical publication and affirm that this report is consistent with those guidelines.  ... 
doi:10.1111/j.1528-1167.2009.02506.x pmid:20163442 pmcid:PMC2855766 fatcat:x7nk7fklavfg7ai3au6ctk2kri

Detection of grey matter loss in mild Alzheimer's disease with voxel based morphometry

G B Frisoni
2002 Journal of Neurology, Neurosurgery and Psychiatry  
These results support the use of this tool to study regional atrophy in AD. Three studies have performed voxel based morphometry in AD.  ...  Caudate atrophy in AD has been reported by other investigators with voxel based morphometry 10 11 and has been explained in view of the demonstrated involvement of striatial nuclei by neurofibrillary  ... 
doi:10.1136/jnnp.73.6.657 pmid:12438466 pmcid:PMC1757361 fatcat:7txbxv53djd6hkm7sfsigav5oy

A Bayesian Morphometry Algorithm

E.H. Herskovits, H. Peng, C. Davatzikos
2004 IEEE Transactions on Medical Imaging  
Most methods for structure-function analysis of the brain in medical images are usually based on voxel-wise statistical tests performed on registered magnetic resonance (MR) images across subjects.  ...  We demonstrate our methods in the context of determining associations between regional brain atrophy (as demonstrated on MR images of the brain), and functional deficits.  ...  Chickering for assistance with latent-variable BC methods. They would also like to thank the reviewers for their insightful comments.  ... 
doi:10.1109/tmi.2004.826949 pmid:15191147 fatcat:eovqpj25dreqhjfqr2b2yw3py4

Grey and White Matter Changes across the Amyotrophic Lateral Sclerosis-Frontotemporal Dementia Continuum

Patricia Lillo, Eneida Mioshi, James R. Burrell, Matthew C. Kiernan, John R. Hodges, Michael Hornberger, Emmanuel Andreas Stamatakis
2012 PLoS ONE  
imaging using voxel-based morphometry (VBM) and diffusion tensor imaging (DTI) analysis of magnetic resonance brain imaging to examine grey and white matter differences and commonalities across the continuum  ...  of the other.  ...  Voxel-based Morphometry Differences with controls.  ... 
doi:10.1371/journal.pone.0043993 pmid:22952843 pmcid:PMC3430626 fatcat:fhsahjyyongulok3ymn6rrwhpi

Severe Traumatic Brain Injury Patients without Focal Lesion but with Behavioral Disorders: Shrinkage of Gray Matter Nuclei and Thalamus Revealed in a Pilot Voxel-Based MRI Study

Alexis Ruet, Françoise Joyeux, Shailendra Segobin, Corine Jokic, Béatrice Desgranges, Francis Eustache, Anne-Lise Pitel
2018 Journal of Neurotrauma  
These individual maps were then thresholded in order to obtain a value of 1 in voxels with significant atrophy and a value of 0 elsewhere.  ...  First, gray and white matter (GM and WM) volumes were compared between groups using Voxel-Based Morphometry.  ... 
doi:10.1089/neu.2017.5242 pmid:29648977 fatcat:dfvjkwg6y5crbfm74aealraluu

Terra incognita—cerebellar contributions to neuropsychiatric and cognitive dysfunction in behavioral variant frontotemporal dementia

Rachel H. Tan, Emma Devenney, Matthew C. Kiernan, Glenda M. Halliday, John R. Hodges, Michael Hornberger
2015 Frontiers in Aging Neuroscience  
Based on cortico-cerebellar connectivity maps, these findings in the cerebellum are consistent with the neural connections with the cortices involved in these domains in patients with bvFTD.  ...  The present study assessed whether degeneration in specific cerebellar subregions associate with indices of cognition and neuropsychiatric performance in bvFTD.  ...  The first step involved extracting the brain FIGURE 1 | 1 FIGURE 1 | Voxel-based morphometry analyses showing cerebellar regions in which gray matter intensity correlates significantly with memory, language  ... 
doi:10.3389/fnagi.2015.00121 pmid:26191000 pmcid:PMC4488961 fatcat:urplnu6ebvekzmz5xodeu3gf4a

A voxel based morphometry study on mild cognitive impairment

C Pennanen
2005 Journal of Neurology, Neurosurgery and Psychiatry  
Methods: Thirty two controls and 51 individuals with MCI deriving from population based cohorts were studied by MRI using voxel based morphometry. The threshold of t maps was set at p,0.001.  ...  Objective: To study the pattern of brain atrophy in MCI.  ...  ACKNOWLEDGEMENTS The study was supported by the Research Council for Health of the Academy of Finland, and an EVO grant 5772720 from the Kuopio University Hospital.  ... 
doi:10.1136/jnnp.2004.035600 pmid:15607988 pmcid:PMC1739300 fatcat:yvg52shuivfr3ebfwhuykqlffa

Higher midlife CAIDE score is associated with increased brain atrophy in a cohort of cognitively healthy middle-aged individuals

Xulin Liu, Maria-Eleni Dounavi, Karen Ritchie, Katie Wells, Craig W. Ritchie, Li Su, Graciela Muniz-Terrera, John T. O'Brien
2021 Journal of Neurology  
Voxel-based morphometry was performed in FSL 6.0.1 to identify areas of grey matter (GM) volume differences both cross-sectionally and longitudinally between subjects with high and low baseline CAIDE score  ...  The Cardiovascular Risk Factors, Aging, and Dementia (CAIDE) score has been suggested to be associated with accelerated brain atrophy in middle-aged subjects but the regional specificity of atrophic areas  ...  Acknowledgements We thank all the PREVENT-Dementia participants for their enthusiastic participation in this study. We thank the NIHR Cambridge Biomedical Centre for support.  ... 
doi:10.1007/s00415-020-10383-8 pmid:33423129 fatcat:k37z365ko5fbtlrqezyakzhase

Regional grey matter atrophy in clinically isolated syndromes at presentation

R G Henry, M Shieh, D T Okuda, A Evangelista, M L Gorno-Tempini, D Pelletier
2008 Journal of Neurology, Neurosurgery and Psychiatry  
Voxel-based analyses allow detection of regional atrophy throughout the brain and, therefore, may be sensitive to regional atrophy in CIS patients, and these changes may correspond with clinical disability  ...  Methods: This study used a modified voxel-based morphometry (VBM) method to correct for lesion effects to analyse regional atrophy and perform voxel-wise correlations between volume and clinical metrics  ...  Acknowledgements We would like to acknowledge the funding of this work by the National Multiple Sclerosis Society research grant RG3240A1.  ... 
doi:10.1136/jnnp.2007.134825 pmid:18469033 pmcid:PMC4827711 fatcat:kwq6jk6whjehfnj2hldjbmfrsi

Association of total tau and phosphorylated tau 181 protein levels in cerebrospinal fluid with cerebral atrophy in mild cognitive impairment and Alzheimer disease

Philipp A Thomann, Elmar Kaiser, Peter Schönknecht, Johannes Pantel, Marco Essig, Johannes Schröder
2009 Journal of Psychiatry & Neuroscience  
We performed voxel-based morphometry to investigate the association between tau levels in cerebrospinal fluid (CSF) and cerebral grey matter density throughout the entire brain.  ...  Among participants with AACD, elevated levels of p-tau181 (but not t-tau) in CSF were correlated with a pronounced atrophy in the right hippocampus.  ...  Voxel-based morphometry analysis of the entire study sample revealed that elevated t-tau and p-tau181 concentrations were significantly associated with reduced grey matter density in a variety of brain  ... 
pmid:19270764 pmcid:PMC2647572 fatcat:sk3ltgqxtvcr3lpayfscshj64a

Cerebellar Integrity in the Amyotrophic Lateral Sclerosis - Frontotemporal Dementia Continuum

Rachel H. Tan, Emma Devenney, Carol Dobson-Stone, John B. Kwok, John R. Hodges, Matthew C. Kiernan, Glenda M. Halliday, Michael Hornberger, Jan Kassubek
2014 PLoS ONE  
of the inferior cerebellum and vermis in ALS patients, while ALS-bvFTD patients had both patterns of atrophy.  ...  Taken together, these findings indicate an important role of the cerebellum in the ALS-bvFTD disease spectrum, with all three clinical phenotypes demonstrating specific patterns of subregional atrophy  ...  We would like to thank Lauren Bartley for the collection and processing of blood samples for genetic testing; Dr David Mowat, Marianne Hallupp, Kirsten Coupland, Jessica Lazarus, Yue Huang, Mia MacMillan  ... 
doi:10.1371/journal.pone.0105632 pmid:25144223 pmcid:PMC4140802 fatcat:52sqezokwvfu5gnzumq2vabbai

The impact of skull-stripping and radio-frequency bias correction on grey-matter segmentation for voxel-based morphometry

Julio Acosta-Cabronero, Guy B. Williams, João M.S. Pereira, George Pengas, Peter J. Nestor
2008 NeuroImage  
., The impact of skull-stripping and radio-frequency bias correction on grey-matter segmentation for voxel-based morphometry, NeuroImage (2007) ,  ...  (nonparametric nonuniform intensity normalisation (N3), bias field corrector (BFC) and FMRIB's automated segmentation tool (FAST)) as pre-processing pipelines for the technique of voxel-based morphometry  ...  Hodges for identifying patients as well as the participants themselves and their relatives for their continued support with our research.  ... 
doi:10.1016/j.neuroimage.2007.10.051 pmid:18065243 fatcat:z3ejhzwy5bfshjdn767wz5jg3i

Grey and white matter brain network changes in frontotemporal dementia subtypes

Tim Nguyen, Maxime Bertoux, Claire O'Callaghan, Samrah Ahmed, John Hodges, Michael Hornberger
2013 Translational Neuroscience  
Methodology: In 94 participants, including bvFTD (n = 16), SV-PPA (n = 16) and NFV-PPA (n = 16), as well as an age-matched control group (n = 46), we employed voxel-based morphometry (VBM) and diffusion  ...  Grey and whIte matter braIn network chanGes In frontotemporal dementIa subtypes abstract Background: Frontotemporal dementia (FTD) comprises of three clinical syndromes, behavioural-variant frontotemporal  ...  [24] Voxel-based morphometry (VBM) analysis Voxel based morphometry was conducted on the three dimensional T1-weighted scans using the FLS-VBM toolbox in the FMRIB software library package (http:/  ... 
doi:10.2478/s13380-013-0141-2 fatcat:yxu3ahqx2jabjcngmwo3qzhtuq
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