John Muschelli III

2023

ModelArray: An R package for statistical analysis of fixel-wise data

Zhao, C., Tapera, T. M., Bagautdinova, J., Bourque, J., Covitz, S., Gur, R. E., Gur, R. C., Larsen, B., Mehta, K., Meisler, S. L., Murtha, K., Muschelli, J., Roalf, D. R., Sydnor, V. J., Valcarcel, A. M., Shinohara, R. T., Cieslak, M. & Satterthwaite, T. D., May 1 2023, In: NeuroImage. 271, 120037.

Research output: Contribution to journal › Article › peer-review

Open Access

Open-source Tools for Training Resources–OTTR

Savonen, C., Wright, C., Hoffman, A. M., Muschelli, J., Cox, K., Tan, F. J. & Leek, J. T., 2023, In: Journal of Statistics and Data Science Education. 31, 1, p. 57-65 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2022

Bayesian deep learning outperforms clinical trial estimators of intracerebral and intraventricular hemorrhage volume

Sharrock, M. F., Mould, W. A., Hildreth, M., Ryu, E. P., Walborn, N., Awad, I. A., Hanley, D. F. & Muschelli, J., Sep 1 2022, In: Journal of Neuroimaging. 32, 5, p. 968-976 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

ciftiTools: A package for reading, writing, visualizing, and manipulating CIFTI files in R

Pham, D. D., Muschelli, J. & Mejia, A. F., Apr 15 2022, In: NeuroImage. 250, 118877.

Research output: Contribution to journal › Article › peer-review

Open Access

Comparison of Accelerometry-Based Measures of Physical Activity: Retrospective Observational Data Analysis Study

Karas, M., Muschelli, J., Leroux, A., Urbanek, J. K., Wanigatunga, A. A., Bai, J., Crainiceanu, C. M. & Schrack, J. A., Jul 1 2022, In: JMIR mHealth and uHealth. 10, 7, e38077.

Research output: Contribution to journal › Article › peer-review

Open Access

Curating the Evidence About COVID-19 for Frontline Public Health and Clinical Care: The Novel Coronavirus Research Compendium

the Novel Coronavirus Research Compendium Team, Mar 2022, In: Public health reports. 137, 2, p. 197-202 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Genome-wide association studies of 27 accelerometry-derived physical activity measurements identified novel loci and genetic mechanisms

Qi, G., Dutta, D., Leroux, A., Ray, D., Muschelli, J., Crainiceanu, C. & Chatterjee, N., Mar 2022, In: Genetic epidemiology. 46, 2, p. 122-138 17 p.

Research output: Contribution to journal › Article › peer-review

Predictive performance of selected breath volatile organic carbon compounds in stage 1 lung cancer

Smirnova, E., Mallow, C., Muschelli, J., Shao, Y., Thiboutot, J., Lam, A., Rule, A. M., Crainiceanu, C. & Yarmus, L., Jun 2022, In: Translational Lung Cancer Research. 11, 6, p. 1009-1018 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2021

3D Deep Neural Network Segmentation of Intracerebral Hemorrhage: Development and Validation for Clinical Trials

Sharrock, M. F., Mould, W. A., Ali, H., Hildreth, M., Awad, I. A., Hanley, D. F. & Muschelli, J., Jul 2021, In: Neuroinformatics. 19, 3, p. 403-415 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

A multi-scanner neuroimaging data harmonization using RAVEL and ComBat

Eshaghzadeh Torbati, M., Minhas, D. S., Ahmad, G., O'Connor, E. E., Muschelli, J., Laymon, C. M., Yang, Z., Cohen, A. D., Aizenstein, H. J., Klunk, W. E., Christian, B. T., Hwang, S. J., Crainiceanu, C. M. & Tudorascu, D. L., Dec 15 2021, In: NeuroImage. 245, 118703.

Research output: Contribution to journal › Article › peer-review

Open Access

Clinical Characterization and Prediction of Clinical Severity of SARS-CoV-2 Infection among US Adults Using Data from the US National COVID Cohort Collaborative

Bennett, T. D., Moffitt, R. A., Hajagos, J. G., Amor, B., Anand, A., Bissell, M. M., Bradwell, K. R., Bremer, C., Byrd, J. B., Denham, A., DeWitt, P. E., Gabriel, D., Garibaldi, B. T., Girvin, A. T., Guinney, J., Hill, E. L., Hong, S. S., Jimenez, H., Kavuluru, R. & Kostka, K. & 25 others, Lehmann, H. P., Levitt, E., Mallipattu, S. K., Manna, A., McMurry, J. A., Morris, M., Muschelli, J., Neumann, A. J., Palchuk, M. B., Pfaff, E. R., Qian, Z., Qureshi, N., Russell, S., Spratt, H., Walden, A., Williams, A. E., Wooldridge, J. T., Yoo, Y. J., Zhang, X. T., Zhu, R. L., Austin, C. P., Saltz, J. H., Gersing, K. R., Haendel, M. A. & Chute, C. G., Jul 13 2021, In: JAMA Network Open. 4, 7, p. E2116901

Research output: Contribution to journal › Article › peer-review

Open Access

Development of severe COVID-19 adaptive risk predictor (SCARP), a calculator to predict severe disease or death in Hospitalized patients with COVID-19

Wongvibulsin, S., Garibaldi, B. T., Antar, A. A. R., Wen, J., Wang, M. C., Gupta, A., Bollinger, R., Xu, Y., Wang, K., Betz, J. F., Muschelli, J., Bandeen-Roche, K., Zeger, S. L. & Robinson, M. L., Jun 1 2021, In: Annals of internal medicine. 174, 6, p. 777-785 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Diurnal physical activity patterns across ages in a large uk based cohort: The uk biobank study

Wrobel, J., Muschelli, J. & Leroux, A., Feb 2 2021, In: Sensors. 21, 4, p. 1-14 14 p., 1545.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Interpreting blood GLUcose data with R package iglu

Broll, S., Urbanek, J., Buchanan, D., Chun, E., Muschelli, J., Punjabi, N. M. & Gaynanova, I., Apr 2021, In: PloS one. 16, 4 April, e0248560.

Research output: Contribution to journal › Article › peer-review

Open Access

Moderated t-tests for group-level fMRI analysis

Wang, G., Muschelli, J. & Lindquist, M. A., Aug 15 2021, In: NeuroImage. 237, 118141.

Research output: Contribution to journal › Article › peer-review

Open Access

Outcome-Stratified Analysis of Biomarker Trajectories for Patients Infected with Severe Acute Respiratory Syndrome Coronavirus 2

Bowring, M. G., Wang, Z., Xu, Y., Betz, J., Muschelli, J., Garibaldi, B. T. & Zeger, S. L., Oct 1 2021, In: American journal of epidemiology. 190, 10, p. 2094-2106 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Quantifying the Predictive Performance of Objectively Measured Physical Activity on Mortality in the UK Biobank

Leroux, A., Xu, S., Kundu, P., Muschelli, J., Smirnova, E., Chatterjee, N. & Crainiceanu, C., Aug 1 2021, In: Journals of Gerontology - Series A Biological Sciences and Medical Sciences. 76, 8, p. 1486-1494 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Sex and Gender Differences in Testing, Hospital Admission, Clinical Presentation, and Drivers of Severe Outcomes from COVID-19

Scully, E. P., Schumock, G., Fu, M., Massaccesi, G., Muschelli, J., Betz, J., Klein, E. Y., West, N. E., Robinson, M., Garibaldi, B. T., Bandeen-Roche, K., Zeger, S., Klein, S. L. & Gupta, A., Sep 1 2021, In: Open Forum Infectious Diseases. 8, 9, ofab448.

Research output: Contribution to journal › Article › peer-review

Open Access

The ANTsX ecosystem for quantitative biological and medical imaging

Tustison, N. J., Cook, P. A., Holbrook, A. J., Johnson, H. J., Muschelli, J., Devenyi, G. A., Duda, J. T., Das, S. R., Cullen, N. C., Gillen, D. L., Yassa, M. A., Stone, J. R., Gee, J. C. & Avants, B. B., Apr 27 2021, In: Scientific reports. 11, 1, p. 9068 1 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2020

An improved algorithm of white matter hyperintensity detection in elderly adults

Ding, T., Cohen, A. D., O'Connor, E. E., Karim, H. T., Crainiceanu, A., Muschelli, J., Lopez, O., Klunk, W. E., Aizenstein, H. J., Krafty, R., Crainiceanu, C. M. & Tudorascu, D. L., 2020, In: NeuroImage: Clinical. 25, 102151.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

ari: The Automated R Instructor

Kross, S., Leek, J. T. & Muschelli, J., 2020, In: R Journal. 12, 1, p. 258-265 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Postcardiac arrest neurological prognostication with quantitative regional cerebral densitometry

Hannawi, Y., Muschelli, J., Mulder, M., Sharrock, M., Storm, C., Leithner, C., Crainiceanu, C. M. & Stevens, R. D., Sep 2020, In: Resuscitation. 154, p. 101-109 9 p.

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Relationship of White Matter Lesions with Intracerebral Hemorrhage Expansion and Functional Outcome: MISTIE II and CLEAR III

For the MISTIE and CLEAR Investigators, Oct 1 2020, In: Neurocritical care. 33, 2, p. 516-524 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Rxnat: An Open-Source R Package for XNAT-Based Repositories

Gherman, A., Muschelli, J., Caffo, B. & Crainiceanu, C., Nov 9 2020, In: Frontiers in Neuroinformatics. 14, 572068.

Research output: Contribution to journal › Article › peer-review

Open Access

TAPAS: A Thresholding Approach for Probability Map Automatic Segmentation in Multiple Sclerosis

Valcarcel, A. M., Muschelli, J., Pham, D. L., Martin, M. L., Yushkevich, P., Brandstadter, R., Patterson, K. R., Schindler, M. K., Calabresi, P. A., Bakshi, R. & Shinohara, R. T., 2020, In: NeuroImage: Clinical. 27, 102256.

Research output: Contribution to journal › Article › peer-review

Open Access

Template Creation for High-Resolution Computed Tomography Scans of the Lung in R Software

Ryan, S. M., Vestal, B., Maier, L. A., Carlson, N. E. & Muschelli, J., Aug 2020, In: Academic radiology. 27, 8, p. e204-e215

Research output: Contribution to journal › Article › peer-review

Open Access

“The doctor said formula would help me”: Health sector influences on use of infant formula in peri-urban Lima, Peru

Rothstein, J. D., Caulfield, L. E., Broaddus-Shea, E. T., Muschelli, J., Gilman, R. H. & Winch, P. J., Jan 2020, In: Social Science and Medicine. 244, 112324.

Research output: Contribution to journal › Article › peer-review

Open Access

8 Scopus citations

2019

crsra: A learning analytics tool for understanding student behaviour in massive open online courses

Hadavand, A., Muschelli, J. & Leek, J., Aug 5 2019, In: Journal of Learning Analytics. 6, 2, p. 140-152 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

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. & Crainiceanu, C. M., Apr 1 2019, In: Biostatistics. 20, 2, p. 218-239 22 p.

Research output: Contribution to journal › Article › peer-review

Open Access

18 Scopus citations

Recommendations for Processing Head CT Data

Muschelli, J., Sep 4 2019, In: Frontiers in Neuroinformatics. 13, 61.

Research output: Contribution to journal › Article › peer-review

Open Access

6 Scopus citations

2018

A dual modeling approach to automatic segmentation of cerebral T2 hyperintensities and T1 black holes in multiple sclerosis

Valcarcel, A. M., Linn, K. A., Khalid, F., Vandekar, S. N., Tauhid, S., Satterthwaite, T. D., Muschelli, J., Martin, M. L., Bakshi, R. & Shinohara, R. T., Jan 1 2018, In: NeuroImage: Clinical. 20, p. 1211-1221 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Feasibility of Coping Effectiveness Training for Caregivers of Children with Autism Spectrum Disorder: a Genetic Counseling Intervention

Haakonsen Smith, C., Turbitt, E., Muschelli, J., Leonard, L., Lewis, K. L., Freedman, B., Muratori, M. & Biesecker, B. B., Feb 1 2018, In: Journal of Genetic Counseling. 27, 1, p. 252-262 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Freesurfer: Connecting the Freesurfer software with R.

Muschelli, J., Sweeney, E. & Crainiceanu, C. M., 2018, In: F1000Research. 7, 599.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

MIMoSA: An Automated Method for Intermodal Segmentation Analysis of Multiple Sclerosis Brain Lesions

Valcarcel, A. M., Linn, K. A., Vandekar, S. N., Satterthwaite, T. D., Muschelli, J., Calabresi, P. A., Pham, D. L., Martin, M. L. & Shinohara, R. T., Jul 1 2018, In: Journal of Neuroimaging. 28, 4, p. 389-398 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

22 Scopus citations

Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure

Commowick, O., Istace, A., Kain, M., Laurent, B., Leray, F., Simon, M., Pop, S. C., Girard, P., Améli, R., Ferré, J. C., Kerbrat, A., Tourdias, T., Cervenansky, F., Glatard, T., Beaumont, J., Doyle, S., Forbes, F., Knight, J., Khademi, A. & Mahbod, A. & 25 others, Wang, C., McKinley, R., Wagner, F., Muschelli, J., Sweeney, E., Roura, E., Lladó, X., Santos, M. M., Santos, W. P., Silva-Filho, A. G., Tomas-Fernandez, X., Urien, H., Bloch, I., Valverde, S., Cabezas, M., Vera-Olmos, F. J., Malpica, N., Guttmann, C., Vukusic, S., Edan, G., Dojat, M., Styner, M., Warfield, S. K., Cotton, F. & Barillot, C., Dec 1 2018, In: Scientific reports. 8, 1, 13650.

Research output: Contribution to journal › Article › peer-review

Open Access

51 Scopus citations

Radiomic subtyping improves disease stratification beyond key molecular, clinical, and standard imaging characteristics in patients with glioblastoma

Kickingereder, P., Neuberger, U., Bonekamp, D., Piechotta, P. L., Götz, M., Wick, A., Sill, M., Kratz, A., Shinohara, R. T., Jones, D. T. W., Radbruch, A., Muschelli, J., Unterberg, A., Debus, J., Schlemmer, H. P., Herold-Mende, C., Pfister, S., Von Deimling, A., Wick, W. & Capper, D. & 2 others, Maier-Hein, K. H. & Bendszus, M., May 18 2018, In: Neuro-oncology. 20, 6, p. 848-857 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

76 Scopus citations

2017

ISLES 2015 - A public evaluation benchmark for ischemic stroke lesion segmentation from multispectral MRI

Maier, O., Menze, B. H., von der Gablentz, J., Häni, L., Heinrich, M. P., Liebrand, M., Winzeck, S., Basit, A., Bentley, P., Chen, L., Christiaens, D., Dutil, F., Egger, K., Feng, C., Glocker, B., Götz, M., Haeck, T., Halme, H. L., Havaei, M. & Iftekharuddin, K. M. & 29 others, Jodoin, P. M., Kamnitsas, K., Kellner, E., Korvenoja, A., Larochelle, H., Ledig, C., Lee, J. H., Maes, F., Mahmood, Q., Maier-Hein, K. H., McKinley, R., Muschelli, J., Pal, C., Pei, L., Rangarajan, J. R., Reza, S. M. S., Robben, D., Rueckert, D., Salli, E., Suetens, P., Wang, C. W., Wilms, M., Kirschke, J. S., Krämer, U. M., Münte, T. F., Schramm, P., Wiest, R., Handels, H. & Reyes, M., Jan 1 2017, In: Medical image analysis. 35, p. 250-269 20 p.

Research output: Contribution to journal › Article › peer-review

Open Access

204 Scopus citations

PItcHPERFeCT: Primary Intracranial Hemorrhage Probability Estimation using Random Forests on CT

Muschelli, J., Sweeney, E. M., Ullman, N. L., Vespa, P., Hanley, D. F. & Crainiceanu, C. M., 2017, In: NeuroImage: Clinical. 14, p. 379-390 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

22 Scopus citations

Thrombolytic removal of intraventricular haemorrhage in treatment of severe stroke: results of the randomised, multicentre, multiregion, placebo-controlled CLEAR III trial

CLEAR III Investigators, Feb 11 2017, In: The Lancet. 389, 10069, p. 603-611 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

175 Scopus citations

2016

Large-scale radiomic profiling of recurrent glioblastoma identifies an imaging predictor for stratifying anti-angiogenic treatment response

Kickingereder, P., Götz, M., Muschelli, J., Wick, A., Neuberger, U., Shinohara, R. T., Sill, M., Nowosielski, M., Schlemmer, H. P., Radbruch, A., Wick, W., Bendszus, M., Maier-Hein, K. H. & Bonekamp, D., Dec 1 2016, In: Clinical Cancer Research. 22, 23, p. 5765-5771 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

139 Scopus citations

Preventive care delivery to young children with sickle cell disease

Bundy, D. G., Muschelli, J., Clemens, G. D., Strous, J. J., Thompson, R. E., Casella, J. F. & Miller, M. R., 2016, In: Journal of Pediatric Hematology/Oncology. 38, 4, p. 294-300 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

7 Scopus citations

Relating multi-sequence longitudinal intensity profiles and clinical covariates in incident multiple sclerosis lesions

Sweeney, E. M., Shinohara, R. T., Dewey, B. E., Schindler, M. K., Muschelli, J., Reich, D. S., Crainiceanu, C. M. & Eloyan, A., 2016, In: NeuroImage: Clinical. 10, p. 1-17 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

10 Scopus citations

Removing inter-subject technical variability in magnetic resonance imaging studies

The Alzheimer's Disease Neuroimaging Initiative, May 15 2016, In: NeuroImage. 132, p. 198-212 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

38 Scopus citations

Reproducibility and bias in healthy brain segmentation: Comparison of two popular neuroimaging platforms

Tudorascu, D. L., Karim, H. T., Maronge, J. M., Alhilali, L., Fakhran, S., Aizenstein, H. J., Muschelli, J. & Crainiceanu, C. M., 2016, In: Frontiers in Neuroscience. 10, NOV, 503.

Research output: Contribution to journal › Article › peer-review

Open Access

11 Scopus citations

Safety and efficacy of minimally invasive surgery plus alteplase in intracerebral haemorrhage evacuation (MISTIE): a randomised, controlled, open-label, phase 2 trial

Hanley, D. F., Thompson, R. E., Muschelli, J., Rosenblum, M., McBee, N., Lane, K., Bistran-Hall, A. J., Mayo, S. W., Keyl, P., Gandhi, D., Morgan, T. C., Ullman, N., Mould, W. A., Carhuapoma, J. R., Kase, C., Ziai, W., Thompson, C. B., Yenokyan, G., Huang, E. & Broaddus, W. C. & 14 others, Graham, R. S., Aldrich, E. F., Dodd, R., Wijman, C., Caron, J. L., Huang, J., Camarata, P., Mendelow, A. D., Gregson, B., Janis, S., Vespa, P., Martin, N., Awad, I. & Zuccarello, M., Nov 1 2016, In: The Lancet Neurology. 15, 12, p. 1228-1237 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

165 Scopus citations

2015

Accuracy of the ABC/2 Score for Intracerebral Hemorrhage: Systematic Review and Analysis of MISTIE, CLEAR-IVH, and CLEAR III

Webb, A. J. S., Ullman, N. L., Morgan, T. C., Muschelli, J., Kornbluth, J., Awad, I. A., Mayo, S., Rosenblum, M., Ziai, W., Zuccarrello, M., Aldrich, F., John, S., Harnof, S., Lopez, G., Broaddus, W. C., Wijman, C., Vespa, P., Bullock, R., Haines, S. J. & Cruz-Flores, S. & 4 others, Tuhrim, S., Hill, M. D., Narayan, R. & Hanley, D. F., Sep 28 2015, In: Stroke. 46, 9, p. 2470-2476 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

72 Scopus citations

Fslr: Connecting the FSL software with R

Muschelli, J., Sweeney, E., Lindquist, M. & Crainiceanu, C., 2015, In: R Journal. 7, 1, p. 163-175 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

16 Scopus citations

Motor overflow in children with attention-deficit/hyperactivity disorder is associated with decreased extent of neural activation in the motor cortex

Gaddis, A., Rosch, K. S., Dirlikov, B., Crocetti, D., MacNeil, L., Barber, A. D., Muschelli, J., Caffo, B., Pekar, J. J. & Mostofsky, S. H., 2015, In: Psychiatry Research - Neuroimaging. 233, 3, p. 488-495 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

21 Scopus citations

Neural Correlates of Visuomotor Learning in Autism

Sharer, E., Crocetti, D., Muschelli, J., Barber, A. D., Nebel, M. B., Caffo, B. S., Pekar, J. J. & Mostofsky, S. H., Dec 1 2015, In: Journal of child neurology. 30, 14, p. 1877-1886 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

16 Scopus citations

Quantitative Intracerebral Hemorrhage Localization

Muschelli, J., Ullman, N. L., Sweeney, E. M., Eloyan, A., Martin, N., Vespa, P., Hanley, D. F. & Crainiceanu, C. M., Nov 1 2015, In: Stroke. 46, 11, p. 3270-3273 4 p.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

John Muschelli III

Research output

Search results