Image analysis and statistical inference in neuroimaging with R

Preprint: Comparing DXA and MRI body composition measurements in cross-sectional and longitudinal cohorts
Nicolas Basty, Marjola Thanaj, Brandon Whitcher, Jimmy D Bell and E. Louise Thomas 2024. Preprint: Comparing DXA and MRI body composition measurements in cross-sectional and longitudinal cohorts. medRxiv. https://doi.org/10.1101/2024.12.12.24318943

MRI assessment of adipose tissue fatty acid composition in the UK Biobank and its association with diet and disease
Marjola Thanaj, Nicolas Basty, Brandon Whitcher, Jimmy D. Bell and E. Louise Thomas 2024. MRI assessment of adipose tissue fatty acid composition in the UK Biobank and its association with diet and disease. Obesity (Silver Spring). 32 (9), pp. 1699-1708. https://doi.org/10.1002/oby.24108

Preprint: MRI assessment of adipose tissue fatty acid composition in the UK Biobank and its association with diet and disease
Marjola Thanaj, Nicolas Basty, Brandon Whitcher, Jimmy D. Bell and E. Louise Thomas 2024. Preprint: MRI assessment of adipose tissue fatty acid composition in the UK Biobank and its association with diet and disease. medRxiv. https://doi.org/10.1101/2024.03.27.24304957

Precision MRI phenotyping of muscle volume and quality at a population scale
Thanaj, M., Basty, N., Whitcher, B., Sorokin, E., Liu, Y., Srinivasan, R., Cule, M., Thomas, E.L. and Bell, J.D. 2024. Precision MRI phenotyping of muscle volume and quality at a population scale. Frontiers in Physiology. 15 1288657. https://doi.org/10.3389/fphys.2024.1288657

Liver Shape Analysis using Statistical Parametric Maps at Population Scale
Thanaj, M., Basty, N., Cule, M., Sorokin, E., Whitcher, B., Bell, J.D. and Thomas, E.L. 2024. Liver Shape Analysis using Statistical Parametric Maps at Population Scale. BMC Medical Imaging. 24 15. https://doi.org/10.1186/s12880-023-01149-5

Preprint: Kidney Shape Statistical Analysis: Associations with Disease and Anthropometric Factors
Thanaj, M., Basty, N., Cule, M., Sorokin, E., Whitcher, B., Srinivasan, R., Lennon, R., Bell, J.D. and Thomas, E.L. 2023. Preprint: Kidney Shape Statistical Analysis: Associations with Disease and Anthropometric Factors. medRxiv. https://doi.org/10.1101/2023.06.26.23291901

Abdominal imaging associates body composition with COVID-19 severity
Basty, N., Sorokin, E., Thanaj, M., Srinivasan, R., Whitcher, B., Bell, J.D., Cule, M. and Thomas, E.L. 2023. Abdominal imaging associates body composition with COVID-19 severity. PLoS ONE. 18 (4) e0283506. https://doi.org/10.1371/journal.pone.0283506

Preprint: Precision MRI phenotyping of muscle volume and quality at a population scale
Marjola Thanaj, Nicolas Basty, Brandon Whitcher, Elena P. Sorokin, Yi Liu, Ramprakash Srinivasan, Madeleine Cule, E. Louise Thomas and Jimmy D. Bell 2023. Preprint: Precision MRI phenotyping of muscle volume and quality at a population scale. medRxiv. https://doi.org/10.1101/2023.03.02.23286689

Preprint: Cardiovascular measures from abdominal MRI provide insights into abdominal vessel genetic architecture
Nicolas Basty, Elena P. Sorokin, Marjola Thanaj, Brandon Whitcher, Yi Liu, Jimmy D. Bell, E. Louise Thomas and Madeleine Cule 2023. Preprint: Cardiovascular measures from abdominal MRI provide insights into abdominal vessel genetic architecture. medRxiv. https://doi.org/10.1101/2022.08.02.22278060

Artifact-Free Fat-Water Separation in Dixon MRI using Deep Learning
Basty, N., Thanaj, M., Cule, M., Sorokin, E., Liu, Y., Thomas, E.L., Bell, J.D. and Whitcher, B. 2023. Artifact-Free Fat-Water Separation in Dixon MRI using Deep Learning. Journal of Big Data. 10 4. https://doi.org/10.1186/s40537-022-00677-1

Preprint: Liver Shape Analysis using Statistical Parametric Maps at Population Scale
Thanaj, M., Basty, N., Cule, M., Sorokin, E.P., Whitcher, B., Bell, J.D. and Thomas, E.L. 2023. Preprint: Liver Shape Analysis using Statistical Parametric Maps at Population Scale. medRxiv. https://doi.org/10.1101/2022.08.18.22278951

Improving the accuracy of fatty liver index to reflect liver fat content with predictive regression modelling
Asaturyan, A.H., Basty, N., Thanaj, M., Whitcher, B., Thomas, E.L. and Bell, J.D. 2022. Improving the accuracy of fatty liver index to reflect liver fat content with predictive regression modelling. PLoS ONE. 17 (9) e0273171. https://doi.org/10.1371/journal.pone.0273171

A Randomised Crossover Trial: Exploring the Dose-Response effect Of Carbohydrate restriction on glycaemia in people with well-controlled type 2 diabetes (D-ROC2)
Al Ozairi, E., Al Awadi, R., El Samad, A., Taghadom, E., Al-Kandari, J., Abdul-Ghani, M., Oliver, N., Whitcher, B. and Guess, N. 2022. A Randomised Crossover Trial: Exploring the Dose-Response effect Of Carbohydrate restriction on glycaemia in people with well-controlled type 2 diabetes (D-ROC2). Journal of Human Nutrition and Dietetics. 36 (1), pp. 51-61. https://doi.org/10.1111/jhn.13030

Analysis of MRI-derived spleen iron in the UK Biobank identifies genetic variation linked to iron homeostasis and hemolysis
Sorokin, E., Basty, N., Whitcher, B., Liu, Y., Bell, J.D., Cohen, R.L., Cule, M. and Thomas, E.L. 2022. Analysis of MRI-derived spleen iron in the UK Biobank identifies genetic variation linked to iron homeostasis and hemolysis. American Journal of Human Genetics. 109 (6), pp. P1092-1104. https://doi.org/10.1016/j.ajhg.2022.04.013

Precision MRI Phenotyping Enables Detection of Small Changes in Body Composition for Longitudinal Cohorts
Whitcher, B., Thanaj, M., Cule, M., Liu, Y., Basty, N., Sorokin, E., Bell, J.D. and Thomas, E.L. 2022. Precision MRI Phenotyping Enables Detection of Small Changes in Body Composition for Longitudinal Cohorts. Scientific Reports. 12 3748. https://doi.org/10.1038/s41598-022-07556-y

Mass Univariate Regression Analysis for Three-Dimensional Liver Image-Derived Phenotypes
Thanaj, M., Basty, N., Liu, Y., Cule, M., Sorokin, E., Thomas, E.L., Bell, J.D. and Whitcher, B. 2021. Mass Univariate Regression Analysis for Three-Dimensional Liver Image-Derived Phenotypes. Annual Conference on Medical Image Understanding and Analysis. University of Oxford 12 - 14 Jul 2021 Springer. https://doi.org/10.1007/978-3-030-80432-9_13

Genetic architecture of 11 organ traits derived from abdominal MRI using deep learning.
Liu, Y., Basty, N., Whitcher, B., Bell, J.D., Sorokin, E., van Bruggen, Nick, Thomas, E.L. and Cule, M. 2021. Genetic architecture of 11 organ traits derived from abdominal MRI using deep learning. eLife. 10. https://doi.org/10.7554/elife.65554

Genetic evidence for different adiposity phenotypes and their opposing influence on ectopic fat and risk of cardiometabolic disease
Martin, S., Cule, M, Basty, N., Tyrrell, J., Beaumont, R.N., Wood, A.R., Frayling, T., Sorokin, E., Whitcher, B., Liu, Y., Bell, J.D., Thomas, E.L. and Yaghootkar, H. 2021. Genetic evidence for different adiposity phenotypes and their opposing influence on ectopic fat and risk of cardiometabolic disease. Diabetes. 70 (8), pp. 1843-1856. https://doi.org/10.2337/db21-0129

Large‑scale analysis of iliopsoas muscle volumes in the UK Biobank
Fitzpatrick, J., Basty, N., Cule, M., Liu, Y., Bell, J.D., Thomas, E.L. and Whitcher, B. 2020. Large‑scale analysis of iliopsoas muscle volumes in the UK Biobank. Scientific Reports. 10 20215. https://doi.org/10.1038/s41598-020-77351-0

Snacking on whole almonds for 6 weeks improves endothelial function and lowers LDL cholesterol but does not affect liver fat and other cardiometabolic risk factors in healthy adults: the ATTIS study, a randomized controlled trial
Dikariyanto, V., Smith, L., Francis, L., Robertson, M., Kusaslan, E., O’Callaghan-Latham, M., Palanche, C., D’Annibale, M., Christodoulou, D., Basty, N., Whitcher, B., Shuaib, H., Charles-Edwards, G., Chowienczyk, P.J., Ellis, P. R., Berry, S.E. and Hall, W. 2020. Snacking on whole almonds for 6 weeks improves endothelial function and lowers LDL cholesterol but does not affect liver fat and other cardiometabolic risk factors in healthy adults: the ATTIS study, a randomized controlled trial. American Journal of Clinical Nutrition. 111 (6), p. 1178–1189. https://doi.org/10.1093/ajcn/nqaa100

Ethnic differences in adiposity and diabetes risk – insights from genetic studies
Yaghootkar, H., Bell, J.D., Whitcher, B. and Thomas, E.L. 2020. Ethnic differences in adiposity and diabetes risk – insights from genetic studies. Journal of Internal Medicine. 288 (3), pp. 271-283. https://doi.org/10.1111/joim.13082

Automated Measurement of Pancreatic Fat and Iron Concentration Using Multi-Echo and T1-Weghted MRI Data
Basty, N., Liu, Y., Cule, M., Thomas, E.L., Bell, J.D. and Whitcher, B. 2020. Automated Measurement of Pancreatic Fat and Iron Concentration Using Multi-Echo and T1-Weghted MRI Data. International Symposium on Biomedical Imaging 2020. Iowa City, USA 03 - 07 Apr 2020 IEEE . https://doi.org/10.1109/ISBI45749.2020.9098650

Neuroconductor: an R platform for medical imaging analysis
Muschelli, J., Gherman, A., Fortin, J.P., Avants, B., Whitcher, B., Clayden, J.D., Caffo, B.S. and Crainiceanu, C.M. 2019. Neuroconductor: an R platform for medical imaging analysis. Biostatistics. 20 (2), pp. 218-239. https://doi.org/10.1093/biostatistics/kxx068

Machine Learning Classification of Females Susceptibility to Visceral Fat Associated Diseases
Aldraimli, M., Soria, D., Parkinson, J., Whitcher, B., Thomas, E.L., Bell, J.D., Chaussalet, T.J. and Dwek, M. 2019. Machine Learning Classification of Females Susceptibility to Visceral Fat Associated Diseases. MEDICON 2019: XV Mediterranean Conference on Medical and Biological Engineering and Computing. Coimbra, Portugal 26 - 28 Sep 2019 Springer. https://doi.org/10.1007/978-3-030-31635-8_81

Ethnic differences in intrahepatic lipid and its association with hepatic insulin sensitivity and insulin clearance between men of Black and White ethnicity with early type 2 diabetes
Hakim, O., Bello, O., Bonadonna, O.C., Mohandas, C., Shojaee-Moradie, F., Jackson, N., Boselli, L., Whitcher, B., Shuaib, H., Alberti, K.G.M.M., Peacock, J.L., Umpleby, A.M., Charles-Edwards, E., Amiel, S.A. and Goff, L.M. 2019. Ethnic differences in intrahepatic lipid and its association with hepatic insulin sensitivity and insulin clearance between men of Black and White ethnicity with early type 2 diabetes. Diabetes, Obesity and Metabolism. 21 (9), pp. 2163-2168. https://doi.org/10.1111/dom.13771

Sub‐phenotyping Metabolic Disorders Using Body Composition: An Individualized, Nonparametric Approach Utilizing Large Data Sets
Linge, J., Whitcher, B., Borga, M. and Dahlqvist Leinhard, O. 2019. Sub‐phenotyping Metabolic Disorders Using Body Composition: An Individualized, Nonparametric Approach Utilizing Large Data Sets. Obesity. 27 (7), pp. 1190-1199. https://doi.org/10.1002/oby.22510

Prostate cancer detection using quantitative T2 and T2-weighted imaging: The effects of 5-alpha-reductase inhibitors in men on active surveillance
Giganti, F., Gambarota, G., Moore, C.M., Robertson, N.L., Mccartan, N., Jameson, C., Bott, S.R., Winkler, M., Whitcher, B., Castro-Santamaria, R., Emberton, M., Allen, C. and Kirkham, A. 2018. Prostate cancer detection using quantitative T2 and T2-weighted imaging: The effects of 5-alpha-reductase inhibitors in men on active surveillance. Journal of Magnetic Resonance Imaging. 47 (6), pp. 1646-1653. https://doi.org/10.1002/jmri.25891

MRI findings in men on active surveillance for prostate cancer: does dutasteride make MRI visible lesions less conspicuous? Results from a placebo-controlled, randomised clinical trial
Giganti, F., Moore, C.M., Robertson, N.L., McCartan, N., Jameson, C., Bott, S.R.J., Winkler, M., Gambarota, G., Whitcher, B., Castro, R., Emberton, M., Allen, C. and Kirkham, A. 2017. MRI findings in men on active surveillance for prostate cancer: does dutasteride make MRI visible lesions less conspicuous? Results from a placebo-controlled, randomised clinical trial. European Radiology. 27, pp. 4767-4774. https://doi.org/10.1007/s00330-017-4858-0

Dynamic contrast-enhanced magnetic resonance imaging of regional nodal metastasis in nasopharyngeal carcinoma: Correlation with nodal staging
Huang, B., Kwong, D.L.W., Lai, V., Chan, Q., Whitcher, B. and Khong, P.-L. 2017. Dynamic contrast-enhanced magnetic resonance imaging of regional nodal metastasis in nasopharyngeal carcinoma: Correlation with nodal staging. Contrast Media and Molecular Imaging. 2017 4519653. https://doi.org/10.1155/2017/4519653

The Effect of Dutasteride on Magnetic Resonance Imaging Defined Prostate Cancer: MAPPED—A Randomized, Placebo Controlled, Double-Blind Clinical Trial
Moore, C.M., Robertson, N.L., Jichi, F., Damola, A., Ambler, G., Giganti, F., Ridout, A.J., Bott, S.R.J., Winkler, M., Ahmed, H.U., Arya, M., Mitra, A.V., McCartan, N., Freeman, A., Jameson, C., Castro, R., Gambarota, G., Whitcher, B., Allen, C., Kirkham, A. and Emberton, M. 2017. The Effect of Dutasteride on Magnetic Resonance Imaging Defined Prostate Cancer: MAPPED—A Randomized, Placebo Controlled, Double-Blind Clinical Trial. Journal of Urology. 197 (4), pp. 1006-1013. https://doi.org/10.1016/j.juro.2016.11.090

Balanced translocation linked to psychiatric disorder, glutamate, and cortical structure/function.
Thomson, P.A., Duff, B., Blackwood, D.H., Romaniuk, L., Watson, A., Whalley, H.C., Li, X., Dauvermann, M.R., Moorhead, T.W., Bois, C., Ryan, N.M., Redpath, H., Hall, L., Morris, S.W., van Beek, E.J., Roberts, N., Porteous, D.J., St Clair, D., Whitcher, B. and Dunlop, J. 2016. Balanced translocation linked to psychiatric disorder, glutamate, and cortical structure/function. Schizophrenia. 2 16024. https://doi.org/10.1038/npjschz.2016.24

Single-dose serotonergic stimulation shows widespread effects on functional brain connectivity
Klaassens, B.L., van Gorsel, H.C., Khalili-Mahani, N., van der Grond, J., Wyman, B.T., Whitcher, B., Rombouts, S.A.R.B. and van Gerven, J.M.A. 2015. Single-dose serotonergic stimulation shows widespread effects on functional brain connectivity. NeuroImage. 122, pp. 440-450. https://doi.org/10.1016/j.neuroimage.2015.08.012

The cortical thickness phenotype of individuals with DISC1 translocation resembles schizophrenia
Doyle, O.M., Bois, C., Thomson, P., Romaniuk, L., Whitcher, B., Williams, S.C.R., Turkheimer, F.E., Stefansson, H., McIntosh, A.M., Mehta, M.A. and Lawrie, S.M. 2015. The cortical thickness phenotype of individuals with DISC1 translocation resembles schizophrenia. Journal of Clinical Investigation. 125 (9), pp. 3714-3722. https://doi.org/10.1172/jci82636

Effects of a balanced translocation between chromosomes 1 and 11 disrupting the DISC1 locus on white matter integrity
Whalley, H.C., Dimitrova, R., Sprooten, E., Dauvermann, M.R., Romaniuk, L., Duff, B., Watson, A.R., Moorhead, B., Bastin, M., Semple, S.I., Giles, S., Hall, J., Thomson, P., Roberts, N., Hughes, Z.A., Brandon, N.J., Dunlop, J., Whitcher, B., Blackwood, D.H.R., McIntosh, A.M. and Lawrie, S.M. 2015. Effects of a balanced translocation between chromosomes 1 and 11 disrupting the DISC1 locus on white matter integrity. PLoS ONE. 10 (6) e0130900. https://doi.org/10.1371/journal.pone.0130900

Automated identification of brain new lesions in multiple sclerosis using subtraction images
Battaglini, M., Rossi, F., Grove, R.A., Stromillo, M.L., Whitcher, B., Matthews, P.M. and De Stefano, N. 2014. Automated identification of brain new lesions in multiple sclerosis using subtraction images. Journal of Magnetic Resonance Imaging. 39 (6), pp. 1543-1549. https://doi.org/10.1002/jmri.24293

MAPPED study design: A 6month randomised controlled study to evaluate the effect of dutasteride on prostate cancer volume using magnetic resonance imaging
Robertson, N.L., Moore, C.M., Ambler, G., Bott, S.R.J., Freeman, A., Gambarota, G., Jameson, C., Mitra, A.V., Whitcher, B., Winkler, M., Kirkham, A., Allen, C. and Emberton, M. 2013. MAPPED study design: A 6month randomised controlled study to evaluate the effect of dutasteride on prostate cancer volume using magnetic resonance imaging. Contemporary Clinical Trials. 34 (1), pp. 80-89. https://doi.org/10.1016/j.cct.2012.10.003

Brain microstructure reveals early abnormalities more than two years prior to clinical progression from mild cognitive impairment to Alzheimer's disease
Douaud, G., Menke, R.A.L., Gass, A., Monsch, A.U., Rao, A., Whitcher, B., Zamboni, G., Matthews, P.M., Sollberger, M. and Smith, S. 2013. Brain microstructure reveals early abnormalities more than two years prior to clinical progression from mild cognitive impairment to Alzheimer's disease. Journal of Neuroscience. 33 (5), pp. 2147-2155. https://doi.org/10.1523/jneurosci.4437-12.2013

BEaST: brain extraction based on nonlocal segmentation technique.
Eskildsen, S.F., Coupé, P., Fonov, V., Manjón, J.V., Leung, K.K., Guizard, N., Wassef, S.N., Østergaard, L.R., Collins, D.L., Alzheimer's Disease Neuroimaging Initiative and Whitcher, B. 2012. BEaST: brain extraction based on nonlocal segmentation technique. NeuroImage. 59 (3), pp. 2362-2373. https://doi.org/10.1016/j.neuroimage.2011.09.012

Individual subject classification for Alzheimer's disease based on incremental learning using a spatial frequency representation of cortical thickness data.
Cho, Y., Seong, J.K., Jeong, Y., Shin, S.Y., Alzheimer's Disease Neuroimaging Initiative and Whitcher, B. 2012. Individual subject classification for Alzheimer's disease based on incremental learning using a spatial frequency representation of cortical thickness data. NeuroImage. 59 (3), pp. 2217-2230. https://doi.org/10.1016/j.neuroimage.2011.09.085

Detecting global and local hippocampal shape changes in Alzheimer's disease using statistical shape models.
Shen, K.K., Fripp, J., Mériaudeau, F., Chételat,G., Salvado, O., Bourgeat, P., Alzheimer's Disease Neuroimaging Initiative and Whitcher, B. 2012. Detecting global and local hippocampal shape changes in Alzheimer's disease using statistical shape models. NeuroImage. 59 (3), pp. 2155-2166. https://doi.org/10.1016/j.neuroimage.2011.10.014

Localized hippocampus measures are associated with Alzheimer pathology and cognition independent of total hippocampal volume.
Carmichael, O., Xie, J., Fletcher, E., Singh, B., DeCarli, C., Alzheimer's Disease Neuroimaging Initiative and Whitcher, B. 2012. Localized hippocampus measures are associated with Alzheimer pathology and cognition independent of total hippocampal volume. Neurobiology of Aging. 33 (6), pp. 1124.e31-1124.e41. https://doi.org/10.1016/j.neurobiolaging.2011.08.016

Imaging vascular function for early stage clinical trials using dynamic contrast-enhanced magnetic resonance imaging
Leach, M.O., Morgan, B., Tofts, P.S., Buckley, D.L., Huang, W., Horsfield, M.A., Chenevert, T.L., Collins, D.J., Jackson, A., Lomas, D., Whitcher, B., Clarke, L., Plummer, R., Judson, I., Jones, R., Alonzi, R., Brunner, T., Koh, D.M., Murphy, P., Waterton, J.C., Parker, G., Graves, M.J., Scheenen, T.W.J., Redpath, T.W., Orton, M., Karczmar, G., Huisman, H., Barentsz, J. and Padhani, A. 2012. Imaging vascular function for early stage clinical trials using dynamic contrast-enhanced magnetic resonance imaging. European Radiology. 22, pp. 1451-1464. https://doi.org/10.1007/s00330-012-2446-x

A Comparison of Gray Matter Density in Restless Legs Syndrome Patients and Matched Controls Using Voxel-Based Morphometry
Comley, R.A., Cervenka, S., Palhagen, S.E., Panagiotidis, G., Matthews, J.C., Lai, R.Y., Halldin, C., Farde, L., Nichols, T.E. and Whitcher, B. 2012. A Comparison of Gray Matter Density in Restless Legs Syndrome Patients and Matched Controls Using Voxel-Based Morphometry. Journal of Neuroimaging. 22 (1), pp. 28-32. https://doi.org/10.1111/j.1552-6569.2010.00536.x

Verbal working memory and functional large-scale networks in schizophrenia
Dauvermann, M.R., Moorhead, T.W., Watson, A.R., Duff, B., Romaniuk, L., Hall, J., Roberts, N., Lee, G.L., Hughes, Z.A., Brandon, N.J., Whitcher, B., Blackwood, D.H., McIntosh, A.M. and Lawrie, S.M. 2012. Verbal working memory and functional large-scale networks in schizophrenia. Psychiatry Research: Neuroimaging. 270, pp. 86-96. https://doi.org/10.1016/j.pscychresns.2017.10.004

Using CSF biomarkers to replicate genetic associations in Alzheimer's disease.
Schott, J.M., ADNI Investigators and Whitcher, B. 2012. Using CSF biomarkers to replicate genetic associations in Alzheimer's disease. Neurobiology of Aging. 33 (7), pp. 1486.e9-1486.e15. https://doi.org/10.1016/j.neurobiolaging.2011.02.008

Genetic variation in GOLM1 and prefrontal cortical volume in Alzheimer's disease
Inkster, B., Rao, A.W., Ridler, K., Filippini, N., Whitcher, B., Nichols, T.E., Wetten, S., Gibson, R.A., Borrie, M., Kertesz, A., Guzman, D.A., Loy-English, I., Williams, J., Saemann, P.G., Auer, D.P., Holsboer, F., Tozzi, F., Muglia, P., Merlo-Pich, E. and Matthews, P.M. 2012. Genetic variation in GOLM1 and prefrontal cortical volume in Alzheimer's disease. Neurobiology of Aging. https://doi.org/10.1016/j.neurobiolaging.2010.04.018

DCE-MRI biomarkers of tumour heterogeneity predict CRC liver metastasis shrinkage following bevacizumab and FOLFOX-6
O'Connor, J.P.B., Rose, C.J., Jackson, A., Watson, Y., Cheung, S., Maders, F., Whitcher, B.J., Roberts, C., Buonaccorsi, G.A., Thompson, G., Clamp, A.R., Jayson, G.C. and Parker, G.J.M. 2011. DCE-MRI biomarkers of tumour heterogeneity predict CRC liver metastasis shrinkage following bevacizumab and FOLFOX-6. British Journal of Cancer. 105, pp. 139-145. https://doi.org/10.1038/bjc.2011.191

Validation and pilot application of [ 18F]FDG-PET in evaluation of a metabolic therapy for Alzheimer's disease
Tzimopoulou, S., Cunningham, V.J., Nichols, T.E., Searle, G., Bird, N.P., Mistry, P., Dixon, I.J., Hallett, W.A., Whitcher, B., Brown, A.P., Zvartau-Hind, M., Lotay, N., Lai, R.Y.K., Castiglia, M., Jeter, B., Matthews, J.C., Chen, K., Bandy, D., Reiman, E.M., Gold, M., Rabiner, E.A. and Matthews, P.M. 2011. Validation and pilot application of [ 18F]FDG-PET in evaluation of a metabolic therapy for Alzheimer's disease. Advances in Alzheimer's Disease. 2, pp. 627-642. https://doi.org/10.3233/978-1-60750-793-2-627

DTI measures in crossing-fibre areas: Increased diffusion anisotropy reveals early white matter alteration in MCI and mild Alzheimer's disease
Douaud, G., Jbabdi, S., Behrens, T.E.J., Menke, R.A., Gass, A., Monsch, A.U., Rao, A., Whitcher, B., Kindlmann, G., Matthews, P.M. and Smith, S. 2011. DTI measures in crossing-fibre areas: Increased diffusion anisotropy reveals early white matter alteration in MCI and mild Alzheimer's disease. NeuroImage. 55 (3), pp. 880-890. https://doi.org/10.1016/j.neuroimage.2010.12.008

Quantitative analysis of dynamic contrast-enhanced and diffusion-weighted magnetic resonance imaging for oncology in R
Whitcher, B. and Schmid, V.J. 2011. Quantitative analysis of dynamic contrast-enhanced and diffusion-weighted magnetic resonance imaging for oncology in R. Journal of Statistical Software. 44 (5), pp. 1-29. https://doi.org/10.18637/jss.v044.i05

Special volume on Magnetic Resonance Imaging in R
Tabelow, K. and Whitcher, B. 2011. Special volume on Magnetic Resonance Imaging in R. Journal of Statistical Software. 44 (1), pp. 1-6. https://doi.org/10.18637/jss.v044.i01

Working with the DICOM and NIfTI data standards in R
Whitcher, B., Schmid, V.J. and Thornton, A. 2011. Working with the DICOM and NIfTI data standards in R. Journal of Statistical Software. 44 (6), pp. 1-29. https://doi.org/10.18637/jss.v044.i06

Spatial patterns of brain amyloid-beta burden and atrophy rate associations in mild cognitive impairment.
Tosun, D., Schuff, N., Mathis, C.A., Jagust, W., Weiner, M.W., Alzheimer's Disease NeuroImaging Initiative and Whitcher, B. 2011. Spatial patterns of brain amyloid-beta burden and atrophy rate associations in mild cognitive impairment. Brain. 134 (4), p. 1077–1088. https://doi.org/10.1093/brain/awr044

Mild cognitive impairment: baseline and longitudinal structural MR imaging measures improve predictive prognosis.
McEvoy, L.K., Holland, D., Hagler, D.J., Fennema-Notestine, C., Brewer, J.B., Dale, A.M., Alzheimer's Disease Neuroimaging Initiative and Whitcher, B. 2011. Mild cognitive impairment: baseline and longitudinal structural MR imaging measures improve predictive prognosis. Radiology. 259 (3), pp. 834-843. https://doi.org/10.1148/radiol.11101975

Fine mapping of genetic variants in BIN1, CLU, CR1 and PICALM for association with cerebrospinal fluid biomarkers for Alzheimer's disease.
Kauwe, J.S., Cruchaga, C., Karch, C.M., Sadle, B., Lee, M., Mayo, K., Latu, W., Su'a, M., Fagan, A.M., Holtzman, D.M., Morris, J.C., Alzheimer's Disease Neuroimaging Initiative, Goate, A.M. and Whitcher, B. 2011. Fine mapping of genetic variants in BIN1, CLU, CR1 and PICALM for association with cerebrospinal fluid biomarkers for Alzheimer's disease. PLoS ONE. 6 (2) e15918. https://doi.org/10.1371/journal.pone.0015918

Asymmetry of information flow between volatilities across time scales
Gençay, R., Gradojevic, N., Selçuk, F. and Whitcher, B. 2010. Asymmetry of information flow between volatilities across time scales. Quantitative Finance. 10 (8), pp. 895-915. https://doi.org/10.1080/14697680903460143

A Multi-Center Randomized Proof-of-Concept Clinical Trial Applying [18F]FDG-PET for Evaluation of Metabolic Therapy with Rosiglitazone XR in Mild to Moderate Alzheimer's Disease
Tzimopoulou, S., Cunningham, V.J., Nichols, T.E., Searle, G., Bird, N.P., Mistry, P., Dixon, I.J., Hallett, W.A., Whitcher, B., Brown, A.P., Zvartau-Hind, M., Lotay, N., Lai, R.Y.K., Castiglia, M., Jeter, B., Matthews, J.C., Chen, K., Bandy, D., Reiman, E.M., Gold, M., Rabiner, E.A. and Matthews, P.M. 2010. A Multi-Center Randomized Proof-of-Concept Clinical Trial Applying [18F]FDG-PET for Evaluation of Metabolic Therapy with Rosiglitazone XR in Mild to Moderate Alzheimer's Disease. Journal of Alzheimer's Disease. 22 (4), pp. 1241-1256. https://doi.org/10.3233/jad-2010-100939

Longitudinal changes in white matter disease and cognition in the first year of the Alzheimer disease neuroimaging initiative.
Carmichael, O., Schwarz, C., Drucker, D., Fletcher, E., Harvey, D., Beckett, L., Jack, C.R., Weiner, M., DeCarli, C., Alzheimer's Disease Neuroimaging Initiative and Whitcher, B. 2010. Longitudinal changes in white matter disease and cognition in the first year of the Alzheimer disease neuroimaging initiative. Archives of Neurology. 67 (11), pp. 1370-1378. https://doi.org/10.1001/archneurol.2010.284

Quantitative analysis of dynamic contrast-enhanced MR images based on bayesian P-splines
Schmid, V.J., Whitcher, B., Padhani, A.R. and Yang, G.-Z. 2009. Quantitative analysis of dynamic contrast-enhanced MR images based on bayesian P-splines. IEEE Transactions on Medical Imaging. 28 (6), pp. 789-798. https://doi.org/10.1109/tmi.2008.2007326

Quantifying spatial heterogeneity in dynamic contrast-enhanced MRI parameter maps
Rose, C.J., Mills, S.J., O'Connor, J.P.B., Buonaccorsi, G.A., Roberts, C., Watson, Y., Cheung, S., Zhao, S., Whitcher, B., Jackson, A. and Parker, G.J.M. 2009. Quantifying spatial heterogeneity in dynamic contrast-enhanced MRI parameter maps. Magnetic Resonance in Medicine. 62 (2), pp. 488-499. https://doi.org/10.1002/mrm.22003

A bayesian hierarchical model for the analysis of a longitudinal dynamic contrast-enhanced MRI oncology study
Schmid, V.J., Whitcher, B., Padhani, A.R., Jane Taylor, N. and Yang, G.-Z. 2009. A bayesian hierarchical model for the analysis of a longitudinal dynamic contrast-enhanced MRI oncology study. Magnetic Resonance in Medicine. 61 (1), pp. 163-174. https://doi.org/10.1002/mrm.21807

Anatomically-distinct genetic associations of APOE e{open}4 allele load with regional cortical atrophy in Alzheimer's disease
Filippini, N., Rao, A., Wetten, S., Gibson, R.A., Borrie, M., Guzman, D., Kertesz, A., Loy-English, I., Williams, J., Nichols, T., Whitcher, B. and Matthews, P.M. 2009. Anatomically-distinct genetic associations of APOE e{open}4 allele load with regional cortical atrophy in Alzheimer's disease. NeuroImage. 44 (3), pp. 724-728. https://doi.org/10.1016/j.neuroimage.2008.10.003

Variational Bayesian inference for a nonlinear forward model
Chappell, M.A., Groves, A.R., Whitcher, B. and Woolrich, M.W. 2009. Variational Bayesian inference for a nonlinear forward model. IEEE Transactions on Signal Processing. 57 (1), pp. 223-236. https://doi.org/10.1109/tsp.2008.2005752

Reproducibility of fMRI in the clinical setting: Implications for trial designs
Bosnell, R., Wegner, C., Kincses, Z.T., Korteweg, T., Agosta, F., Ciccarelli, O., De Stefano, N., Gass, A., Hirsch, J., Johansen-Berg, H., Kappos, L., Barkhof, F., Mancini, L., Manfredonia, F., Marino, S., Miller, D.H., Montalban, X., Palace, J., Rocca, M., Enzinger, C., Ropele, S., Rovira, A., Smith, S., Thompson, A., Thornton, J., Yousry, T., Whitcher, B., Filippi, M. and Matthews, P.M. 2008. Reproducibility of fMRI in the clinical setting: Implications for trial designs. NeuroImage. 42 (2), pp. 603-610. https://doi.org/10.1016/j.neuroimage.2008.05.005

A statistical framework to characterise microstructure in high angular resolution diffusion imaging
Olhede, S. and Whitcher, B. 2008. A statistical framework to characterise microstructure in high angular resolution diffusion imaging. 2008 5th IEEE international symposium on biomedical imaging: From nano to macro. Paris, France 14 - 17 May 2008 IEEE . https://doi.org/10.1109/isbi.2008.4541142

A multi-resolution census algorithm for calculating vortex statistics in turbulent flows
Whitcher, B., Lee, T.C.M., Weiss, J.B., Hoar, T.J. and Nychka, D.W. 2008. A multi-resolution census algorithm for calculating vortex statistics in turbulent flows. Journal of the Royal Statistical Society: Series C (Applied Statistics). 57 (3), pp. 293-312. https://doi.org/10.1111/j.1467-9876.2007.00614.x

Using the wild bootstrap to quantify uncertainty in diffusion tensor imaging
Whitcher, B., Tuch, D.S., Wisco, J.J., Sorensen, A.G. and Wang, L. 2007. Using the wild bootstrap to quantify uncertainty in diffusion tensor imaging. Human Brain Mapping. 29 (3), pp. 346-362. https://doi.org/10.1002/hbm.20395

Statistical group comparison of diffusion tensors via multivariate hypothesis testing
Whitcher, B., Wisco, J.J., Hadjikhani, N. and Tuch, D.S. 2007. Statistical group comparison of diffusion tensors via multivariate hypothesis testing. Magnetic Resonance in Medicine. 57 (6), pp. 1065-1074. https://doi.org/10.1002/mrm.21229

Study-level wavelet cluster analysis and data-driven signal models in pharmacological MRI
Schwarz, A.J., Whitcher, B., Gozzi, A., Reese, T. and Bifone, A. 2007. Study-level wavelet cluster analysis and data-driven signal models in pharmacological MRI. Journal of Neuroscience Methods. 159 (2), pp. 346-360. https://doi.org/10.1016/j.jneumeth.2006.07.017

Resampling methods for improved wavelet-based multiple hypothesis testing of parametric maps in functional MRI
Şendur, L., Suckling, J., Whitcher, B. and Bullmore, E. 2007. Resampling methods for improved wavelet-based multiple hypothesis testing of parametric maps in functional MRI. NeuroImage. 37 (4), pp. 1186-1194. https://doi.org/10.1016/j.neuroimage.2007.05.057

Quantifying heterogeneity in dynamic contrast-enhanced MRI parameter maps
Rose, C.J., Mills, S., O'Connor, J.P.B., Buonaccorsi, G.A., Roberts, C., Watson, Y., Whitcher, B., Jayson, G., Jackson, A. and Parker, G.J.M. 2007. Quantifying heterogeneity in dynamic contrast-enhanced MRI parameter maps. MICCAI 2007: Medical Image Computing and Computer-Assisted Intervention – MICCAI 2007. Brisbane, Australia 29 Oct - 02 Nov 2007 Springer. https://doi.org/10.1007/978-3-540-75759-7_46

Wavelet-based bootstrapping of spatial patterns on a finite lattice
Whitcher, B. 2006. Wavelet-based bootstrapping of spatial patterns on a finite lattice. Computational Statistics & Data Analysis. 50 (9), pp. 2399-2421. https://doi.org/10.1016/j.csda.2004.12.016

Noninvasive brain imaging for experimental medicine in drug discovery and development: Promise and pitfalls
Whitcher, B. and Matthews, P.M. 2006. Noninvasive brain imaging for experimental medicine in drug discovery and development: Promise and pitfalls. International Journal of Pharmaceutical Medicine. 20, pp. 167-175. https://doi.org/10.2165/00124363-200620030-00003

Semi-parametric analysis of dynamic contrast-enhanced MRI using bayesian P-splines
Schmid, V.J., Whitcher, B. and Yang, G.-Z. 2006. Semi-parametric analysis of dynamic contrast-enhanced MRI using bayesian P-splines. MICCAI 2006: Medical Image Computing and Computer-Assisted Intervention – MICCAI 2006. Copenhagen, Denmark 01 - 06 Oct 2006 Springer. https://doi.org/10.1007/11866565_83

Bayesian methods for pharmacokinetic models in dynamic contrast-enhanced magnetic resonance imaging
Schmid, V.J., Whitcher, B., Padhani, A.R., Taylor, N.J. and Yang, G.-Z. 2006. Bayesian methods for pharmacokinetic models in dynamic contrast-enhanced magnetic resonance imaging. IEEE Transactions on Medical Imaging. 25 (12), pp. 1627-1636. https://doi.org/10.1109/tmi.2006.884210

A resilient, low-frequency, small-world human brain functional network with highly connected association cortical hubs
Achard, S., Salvador, R., Whitcher, B., Suckling, J. and Bullmore, E. 2006. A resilient, low-frequency, small-world human brain functional network with highly connected association cortical hubs. Journal of Neuroscience. 26 (1), pp. 63-72. https://doi.org/10.1523/jneurosci.3874-05.2006

Co-deposition of salmeterol and fluticasone propionate by a combination inhaler
Theophilus, A., Moore, A., Prime, D., Rossomanno, S., Whitcher, B. and Chrystyn, H. 2006. Co-deposition of salmeterol and fluticasone propionate by a combination inhaler. International Journal of Pharmaceutics. 313 (1-2), pp. 14-22. https://doi.org/10.1016/j.ijpharm.2006.01.018

Time-varying spectral analysis in neurophysiological time series using Hilbert wavelet pairs
Whitcher, Brandon, Craigmile, Peter F. and Brown, Peter 2005. Time-varying spectral analysis in neurophysiological time series using Hilbert wavelet pairs. Signal Processing. 85 (11), pp. 2065-2081. https://doi.org/10.1016/j.sigpro.2005.07.002

Wavelet-based cluster analysis: Data-driven grouping of voxel time courses with application to perfusion-weighted and pharmacological MRI of the rat brain
Whitcher, B., Schwarz, A.J., Barjat, H., Smart, S.C., Grundy, R.I. and James, M.F. 2005. Wavelet-based cluster analysis: Data-driven grouping of voxel time courses with application to perfusion-weighted and pharmacological MRI of the rat brain. NeuroImage. 24 (2), pp. 281-295. https://doi.org/10.1016/j.neuroimage.2004.08.022

Multiple hypothesis mapping of functional MRI data in orthogonal and complex wavelet domains
Şendur, L., Maxim, V., Whitcher, B. and Bullmore, E. 2005. Multiple hypothesis mapping of functional MRI data in orthogonal and complex wavelet domains. IEEE Transactions on Signal Processing. 53 (9), pp. 3413-3426. https://doi.org/10.1109/tsp.2005.853098

Multiscale systematic risk
Gençay, R., Selçuk, F. and Whitcher, B. 2005. Multiscale systematic risk. Journal of International Money and Finance. 24 (1), pp. 55-70. https://doi.org/10.1016/j.jimonfin.2004.10.003

Statistical analysis of pharmacokinetic models in dynamic contrast-enhanced magnetic resonance imaging.
Schmid, V.J., Whitcher, B.J., Yang, G.Z., Taylor, N.J., Padhani, A.R. and Whitcher, B. 2005. Statistical analysis of pharmacokinetic models in dynamic contrast-enhanced magnetic resonance imaging. MICCAI 2005: Medical Image Computing and Computer-Assisted Intervention – MICCAI 2005. Palm Springs, CA, USA 26 - 29 Oct 2005 Springer. https://doi.org/10.1007/11566489_109

Wavelet-based estimation for seasonal long-memory processes
Whitcher, B. 2004. Wavelet-based estimation for seasonal long-memory processes. Technometrics. 46 (2), pp. 225-238. https://doi.org/10.1198/004017004000000275

Wavelets and functional magnetic resonance imaging of the human brain
Bullmore, E., Fadili, J., Maxim, V., Şendur, L., Whitcher, Brandon, Suckling, J., Brammer, M. and Breakspear, M. 2004. Wavelets and functional magnetic resonance imaging of the human brain. NeuroImage. 23 (1), pp. S234-S249. https://doi.org/10.1016/j.neuroimage.2004.07.012

Identifying and tracking turbulence structures
Storlie, C., Davis, C., Hoar, T., Lee, T., Nychka, D., Weiss, J.B. and Whitcher, Brandon 2004. Identifying and tracking turbulence structures. 38th Asilomar Conference on Signals, Systems and Computers. California, USA 07-10 IEEE . https://doi.org/10.1109/ACSSC.2004.1399449

Systematic risk and timescales
Gençay, R., Selçuk, F. and Whitcher, B. 2003. Systematic risk and timescales. Quantitative Finance. 3 (2), pp. 108-116. https://doi.org/10.1088/1469-7688/3/2/305

A wavelet solution to the spurious regression of fractionally differenced processes
Fan, Y. and Whitcher, B. 2003. A wavelet solution to the spurious regression of fractionally differenced processes. Applied Stochastic Models in Business and Industry. 19 (3). https://doi.org/10.1002/asmb.497

Stochastic Multiresolution Models for Turbulence
Whitcher, Brandon, Weiss, J.B., Nychka, D.W. and Hoar, T.J. 2003. Stochastic Multiresolution Models for Turbulence. in: Recent Advances and Trends in Nonparametric Statistics Elsevier. pp. 497-509

Testing for homogeneity of variance in time series: Long memory, wavelets, and the Nile River
Whitcher, Brandon, Byers, S.D., Guttorp, P. and Percival, D.B. 2002. Testing for homogeneity of variance in time series: Long memory, wavelets, and the Nile River. Water Resources Research. 38 (5), pp. 12-1 - 12-16. https://doi.org/10.1029/2001wr000509

Scaling properties of foreign exchange volatility
Gençay, R., Selçuk, F. and Whitcher, Brandon 2001. Scaling properties of foreign exchange volatility. Physica A: Statistical Mechanics and its Applications. 289 (1-2), pp. 249-266. https://doi.org/10.1016/s0378-4371(00)00456-8

Simulating gaussian stationary processes with unbounded spectra
Whitcher, B. 2001. Simulating gaussian stationary processes with unbounded spectra. Journal of Computational and Graphical Statistics. 10 (1), pp. 112-134. https://doi.org/10.1198/10618600152418674

Differentiating intraday seasonalities through wavelet multi-scaling
Gençay, R., Selçuk, F. and Whitcher, B. 2001. Differentiating intraday seasonalities through wavelet multi-scaling. Physica A: Statistical Mechanics and its Applications. 289 (3-4), pp. 543-556. https://doi.org/10.1016/s0378-4371(00)00463-5

Wavelet estimation of a local long memory parameter
Whitcher, B. and Jensen, M.J. 2000. Wavelet estimation of a local long memory parameter. Exploration Geophysics. 31 (1-2), pp. 94-103. https://doi.org/10.1071/eg00094

Wavelet analysis of covariance with application to atmospheric time series
Whitcher, Brandon, Guttorp, P. and Percival, D.B. 2000. Wavelet analysis of covariance with application to atmospheric time series. Journal of Geophysical Research Atmospheres. 105 (D11), pp. 14941-14962 2000JD900110. https://doi.org/10.1029/2000JD900110

Multiscale detection and location of multiple variance changes in the presence of long memory
Whitcher, Brandon, Guttorp, P. and Percival, D.B. 2000. Multiscale detection and location of multiple variance changes in the presence of long memory. Journal of Statistical Computation and Simulation. 68 (1), pp. 65-87. https://doi.org/10.1080/00949650008812056