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Multiple testing correction over contrasts for brain imaging [article]

Bianca Alessandra Visineski Alberton, Thomas E. Nichols, Humberto R. Gamba, Anderson M. Winkler
2019 bioRxiv   pre-print
The multiple testing problem arises not only when there are many voxels or vertices in an image representation of the brain, but also when multiple contrasts of parameter estimates (that is, hypotheses  ...  Here we argue that a correction for this multiplicity must be performed to avoid excess of false positives.  ...  Contrast correction and brain imaging Accommodating correction over contrasts with brain imaging requires that both types of multiple testing, that is, across space (mtp-i), and across contrasts (mtp-ii  ... 
doi:10.1101/775106 fatcat:drewqx7wdrhwxfwmjhoijjfn6q

472 ImmunoPET-informed sequence for focused ultrasound-targeted mCD47 blockade controls glioma

Natasha Sheybani, Soumen Paul, Katelyenn McCauley, Victoria Breza, Stuart Berr, G Wilson Miller, Kiel Neumann, Richard Price
2020 Journal for ImmunoTherapy of Cancer  
Significance assessed by RM 2-way ANOVA followed by Sidak's multiple comparison test. (D) Contrast-enhanced T1-weighted MR images of GL261 tumors on days 14, 17 and 20 post-implantation. ?  ...  (C) Mean greyscale intensity (MGI) of contrast enhancement pre- and post-FUS over three separate BBB/BTB-D sessions conducted every three days. Calculated as fold change over contralateral brain.  ...  Significance assessed by RM 2-way ANOVA followed by Sidak's multiple comparison test. (D) Contrast-enhanced T1-weighted MR images of GL261 tumors on days 14, 17 and 20 post-implantation. ?  ... 
doi:10.1136/jitc-2020-sitc2020.0472 fatcat:ivn65pm5pzcihpyx2ynkz4kc5q

Multiple testing correction overcontrasts for brain imaging

Bianca A.V. Alberton, Thomas E. Nichols, Humberto R. Gamba, Anderson M. Winkler
2020 NeuroImage  
The multiple testing problem arises not only when there are many voxels or vertices in an image representation of the brain, but also when multiple contrasts of parameter estimates (that represent hypotheses  ...  Various methods for correction have been proposed in the literature, but few have been applied to brain imaging.  ...  Acknowledgements We would like to thank the anonymous reviewers for their thoughtful comments. We also thank the Child Mind Institute (CMI) for providing data.  ... 
doi:10.1016/j.neuroimage.2020.116760 pmid:32201328 pmcid:PMC8191638 fatcat:p6h2zrnbsbaw7nhwb7zmks2tfm

An Investigation of Neural Correlates in Adults with Developmental Dyscalculia Using fMRI

Seylan Sahin
2015 The Journal of Neurobehavioral Sciences  
Figure 2 . 2 Brain activation in the incorrect item contrast (left image) and the correct item contrast (right image) in the multiplication task for participants with dyscalculia and the controls.  ...  Brain activation in the correct item contrast (left image) and the incorrect item contrast (right image) in the subtraction task for participants with dyscalculia and the controls. 4.56 Z= 5.05 R  ... 
doi:10.5455/jnbs.1433794984 fatcat:ehdwk6efrnbkjlwy3kltizwo74

Statistical Parametric Mapping

Geraint Rees
2004 Practical Neurology  
THE BASIC IDEA Brain responses are recorded using an imaging technique such as fMRI, which allows the repeated measurement of brain activity at hundreds of thousands of points, or voxels, throughout the  ...  This requires that a statistical test be carried out to assess any differences in brain activity between the two different conditions, rather than just simply subtracting the activity in the two conditions  ...  I thank Daniel Glaser and Rebecca Roylance for helpful comments.  ... 
doi:10.1111/j.1474-7766.2004.00266.x fatcat:pfevtmtqknh3jdsau252r7xf7m

Individual differences in learning correlate with modulation of brain activity induced by transcranial direct current stimulation

Brian Falcone, Atsushi Wada, Raja Parasuraman, Daniel E. Callan, Tifei Yuan
2018 PLoS ONE  
This same region showed greater activity during the training session for target feedback of incorrect (target-error feedback) over correct trials for the tDCS stim over sham group indicating greater attention  ...  However, many recent studies have called into question the reliability and efficacy of tDCS to induce modulatory changes in brain activity.  ...  Acknowledgments We would like to thank Chie Kawakami for her extensive assistance in conducting the experiment and Akiko Callan for her assistance in translating instructions from English to Japanese.  ... 
doi:10.1371/journal.pone.0197192 pmid:29782510 pmcid:PMC5962315 fatcat:6ddqgce4cjcg3iax7grh7dxsgi

Longitudinal stability of MRI for mapping brain change using tensor-based morphometry

Alex D. Leow, Andrea D. Klunder, Clifford R. Jack, Arthur W. Toga, Anders M. Dale, Matt A. Bernstein, Paula J. Britson, Jeffrey L. Gunter, Chadwick P. Ward, Jennifer L. Whitwell, Bret J. Borowski, Adam S. Fleisher (+8 others)
2006 NeuroImage  
Although SPGR/FLASH images showed least deviation here, pulse sequence selection for the ADNI project was based on multiple additional image analyses, to be reported elsewhere. D  ...  N3 correction reduced coil type and pulse sequence differences and improved scan reproducibility, except for Synthetic T1 images (which were intrinsically corrected for B1inhomogeneity).  ...  ADNI is funded by the National Institute of Aging, the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the Foundation for the National Institutes of Health, through generous contributions  ... 
doi:10.1016/j.neuroimage.2005.12.013 pmid:16480900 pmcid:PMC1941663 fatcat:mww52hmmcfhehednbkzeg6ubw4

Revealing architectural order with polarized light imaging and deep neural networks [article]

Syuan-Ming Guo, Anitha Priya Krishnan, Jenny Folkesson, Ivan Ivanov, Bryant Chhun, Nathan Cho, Manuel Leonetti, Shalin B. Mehta
2019 bioRxiv   pre-print
We recover birefringence, orientation, brightfield, and degree of polarization contrasts simultaneously by using Stokes formalism to model image formation.  ...  Our open-source python software for reconstruction of optical properties and training the neural networks is available on GitHub.  ...  ACKNOWLEDGEMENTS We thank Spyros Dermanis (CZ Biohub), Bing Wu (CZ Biohub), May Han (Stanford), and Ezzat Hashemi (Stanford) for providing the mouse brain slice used for acquiring data shown in Fig. 1  ... 
doi:10.1101/631101 fatcat:grjmxtbj4bewzjkpakh6zh4jsu

Guidelines for Developing Automated Quality Control Procedures for Brain Magnetic Resonance Images Acquired in Multi-Centre Clinical Trials [chapter]

Elias Gedamu
2011 Applications and Experiences of Quality Control  
SNR, contrast-to-noise ratio) for different scanners at multiple sites.  ...  MRIs that do not meet the criteria for acceptable image quality are assessed for correctability.  ...  Guidelines for Developing Automated Quality Control Procedures for Brain Magnetic Resonance Images Acquired in Multi-Centre Clinical Trials, Applications and Experiences of Quality Control, Prof.  ... 
doi:10.5772/14515 fatcat:37d4nspayrc6jhu7mevonc6xam

Classifying magnetic resonance image modalities with convolutional neural networks

Samuel Remedios, Snehashis Roy, Dzung L. Pham, John A. Butman, Kensaku Mori, Nicholas Petrick
2018 Medical Imaging 2018: Computer-Aided Diagnosis  
Many MR brain image processing techniques, such as tissue segmentation, require multiple MR contrasts as inputs, and each contrast is treated differently.  ...  The proposed CNN automatically identifies the MR contrast of an input brain image volume.  ...  ACKNOWLEDGEMENTS Support for this work included funding from the Intramural Research Program of the NIH and the Department of Defense in the Center for Neuroscience and Regenerative Medicine.  ... 
doi:10.1117/12.2293943 dblp:conf/micad/RemediosPBR18 fatcat:2goze4zhkfhxtpko4zqkn2be5q

Effects of T2-weighted MRI based cranial volume measurements on studies of the aging brain

Phong Vuong, David Drucker, Chris Schwarz, Evan Fletcher, Charles DeCarli, Owen Carmichael, David R. Haynor, Sebastien Ourselin
2013 Medical Imaging 2013: Image Processing  
T1-weighted Magnetic Resonance Imaging (MRI) sequences are commonly used to measure TIV, but T2-weighted MRI sequences provide superior contrast between the cerebrospinal fluid (CSF) bounding the premorbid  ...  In this study, we compared T1-based and T2-based TIV measurements to assess the practical impact of this superior contrast on studies of brain aging. 810 Alzheimer's Disease Neuroimaging Initiative (ADNI  ...  The number of individuals in each regression model (N), the test statistic for significance of the brain volume predictor in the Poisson regression model (z), and the significance of that test statistic  ... 
doi:10.1117/12.2006727 pmid:24353391 pmcid:PMC3864960 dblp:conf/miip/VuongDSFDC13 fatcat:bpbpmatiy5czbfjkuwqcgapvle

Exploring fMRI Results Space: 31 Variants of an fMRI Analysis in AFNI, FSL, and SPM

Ruth Pauli, Alexander Bowring, Richard Reynolds, Gang Chen, Thomas E. Nichols, Camille Maumet
2016 Frontiers in Neuroinformatics  
Results were thresholded with a voxel-wise threshold of familywise error rate p ≤ 0.05 with correction for multiple comparisons.  ...  Voxel-Wise FDR p ≤ 0.05 Results were thresholded with a voxel-wise threshold of false discovery rate p ≤ 0.05 correction for multiple comparisons.  ...  We would like to thank Russell Poldrack for giving advice on re-using the data. We also gratefully acknowledge Krzysztof Gorgolewski, William Triplett, and others at OpenfMRI for their feedback.  ... 
doi:10.3389/fninf.2016.00024 pmid:27458367 pmcid:PMC4932120 fatcat:kk7jw2q6fjf53jnqgalmclkjfu

Recommendations to improve imaging and analysis of brain lesion load and atrophy in longitudinal studies of multiple sclerosis

H. Vrenken, M. Jenkinson, M. A. Horsfield, M. Battaglini, R. A. van Schijndel, E. Rostrup, J. J. G. Geurts, E. Fisher, A. Zijdenbos, J. Ashburner, D. H. Miller, M. Filippi (+5 others)
2012 Journal of Neurology  
Focal lesions and brain atrophy are the most extensively studied aspects of multiple sclerosis (MS), but the image acquisition and analysis techniques used can be further improved, especially those for  ...  Briefly, they are (1) images should be acquired using 3D pulse sequences, with nearisotropic spatial resolution and multiple image contrasts to allow more comprehensive analyses of lesion load and atrophy  ...  It would clearly be advantageous to define a set of 3D imaging techniques with multiple contrasts that capture as many of the known aspects of brain changes in MS as possible in both the GM and WM, with  ... 
doi:10.1007/s00415-012-6762-5 pmid:23263472 pmcid:PMC3824277 fatcat:s727aflyjrcrpip7d3nuissbhq

Single Image-based Vignetting Correction for Improving the Consistency of Neural Activity Analysis in 2-Photon Functional Microscopy [article]

Dong Li, Guangyu Wang, René Werner, Hong Xie, Ji-Song Guan, Claus C. Hilgetag
2021 bioRxiv   pre-print
Using immediate-early-gene-based 2-photon microscopic neural image data of the mouse brain, we show the necessity of correcting both image brightness and contrast to improve within- and across-image intensity  ...  In the present report, we propose a straightforward protocol for single image-based vignetting correction.  ...  Thus, for single image-based vignetting correction, the multiple image-based prior information is essentially replaced by the hypothesis that the image background intensity and the image contrast distribution  ... 
doi:10.1101/2021.03.01.433412 fatcat:5auqjo3bbvhddh5zf6lyqiawm4

Page 968 of Journal of Cognitive Neuroscience Vol. 20, Issue 6 [page]

2008 Journal of Cognitive Neuroscience  
Due to the multiple ¢ test compar- isons with the same variable, a Bonferroni correction was applied and the minimum threshold of p = .0125 was taken to determine significant effects.  ...  One-sample ¢ tests were employed for the group analyses across the contrast images of all subjects, which indicated whether observed differences between conditions were significantly distinct from zero  ... 
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