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Ari: The Automated R Instructor [article]

Sean Kross, Jeffrey T. Leek, John Muschelli
2020 arXiv   pre-print
., 2016) and have interfaces in R (Edmondson, 2019; Muschelli, 2019a; Leeper, 2017) .  ...  Currently in ari, synthesis of the the audio can be rendered using any of these services through the text2speech package (Muschelli, 2019b) .  ... 
arXiv:2007.13477v2 fatcat:snlqxwot2be4bkvvm3quv2jq7i

Recommendations for Processing Head CT Data

John Muschelli
2019 Frontiers in Neuroinformatics  
R package (Muschelli, 2019) .  ...  Interfaces exist, such as the dcm2niir (Muschelli, 2018) package in R and nipype Python module (Gorgolewski et al., 2011) .  ...  Copyright © 2019 Muschelli. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).  ... 
doi:10.3389/fninf.2019.00061 pmid:31551745 pmcid:PMC6738271 fatcat:lnbjkk6qvnfahbn5qdd4akzleq

freesurfer: Connecting the Freesurfer software with R

John Muschelli, Elizabeth Sweeney, Ciprian M. Crainiceanu
2018 F1000Research  
neurobase is not loaded): > neurobase::ortho2(ss, mask = ss) > mask = ss >0 I then retried the previous instruction now we have the mask: > nu_masked = nu_correct(file = reoriented_img, mask = mask) Muschelli  ... 
doi:10.12688/f1000research.14361.1 pmid:30057753 pmcid:PMC6051196 fatcat:mdlc2wkyqraxnldwk7fkeli4ia

Moderated t-tests for group-level fMRI analysis

Guoqing Wang, John Muschelli, Martin A. Lindquist
2021 NeuroImage  
John Muschelli: Formal analysis, Software, Writing -review & editing. Martin A. Lindquist: Conceptualization, Methodology, Writing -review & editing, Supervision, Funding acquisition.  ... 
doi:10.1016/j.neuroimage.2021.118141 pmid:33962000 fatcat:4e5cdax76ndjhgabqdl5uiowsa

ari: The Automated R Instructor

Sean Kross, Jeffrey,T. Leek, John Muschelli
2020 The R Journal  
., 2016) and have interfaces in R (Edmondson, 2019; Muschelli, 2019a; Leeper, 2017) .  ...  Currently in ari, synthesis of the the audio can be rendered using any of these services through the text2speech package (Muschelli, 2019b) .  ... 
doi:10.32614/rj-2020-023 fatcat:rjeybpkhxbfbfdyjqf6nmisg6y

Interpreting blood GLUcose data with R package iglu [article]

Steven Broll, Jacek Urbanek, David Buchanan, Elizabeth Chun, John Muschelli, Naresh Punjabi, Irina Gaynanova
2020 bioRxiv   pre-print
This work was supported by the National Institutes of Health [HL11716, HL146709]; and an agreement from the Johns Hopkins University [80045538 to I.G.].  ...  Acknowledgements The authors are thankful to Marielle Hicban, Mary Martin, Nhan Nguyen, Pratik Patel and John Schwenck for assisting in writing several metric functions in version 2.0.0 of iglu package  ... 
doi:10.1101/2020.09.28.310482 fatcat:r4q42lhsibhwbmchxe3wyahswa

Open-source Tools for Training Resources – OTTR [article]

Candace Savonen, Carrie Wright, Ava M. Hoffman, John Muschelli, Katherine Cox, Frederick J. Tan, Jeffrey T. Leek
2022 arXiv   pre-print
Data science and informatics tools are developing at a blistering rate, but their users often lack the educational background or resources to efficiently apply the methods to their research. Training resources often deprecate because their maintenance is not prioritized by funding, giving teams little time to devote to such endeavors. Our group has developed Open-source Tools for Training Resources (OTTR) to offer greater efficiency and flexibility for creating and maintaining online course
more » ... ent. OTTR empowers creators to customize their work and allows for a simple workflow to publish using multiple platforms. OTTR allows content creators to publish material to multiple massive online learner communities using familiar rendering mechanics. OTTR allows the incorporation of pedagogical practices like formative and summative assessments in the form of multiple choice questions and fill in the blank problems that are automatically graded. No local installation of any software is required to begin creating content with OTTR. Thus far, 15 courses have been created with OTTR repository template. By using the OTTR system, the maintenance workload for updating these courses across platforms has been drastically reduced.
arXiv:2203.07083v1 fatcat:wcedmv7xlvdpbeb62e5d2abbmi

fslr: Connecting the FSL Software with R

John Muschelli, Elizabeth Sweeney, Martin Lindquist, Ciprian Crainiceanu
2015 The R Journal  
Muschelli et al. Page 15 R J. Author manuscript; available in PMC 2016 June 16. Muschelli et al. Page 16 R J. Author manuscript; available in PMC 2016 June 16.  ... 
pmid:27330830 pmcid:PMC4911193 fatcat:l2y2vu2umrb5fgxds2puxwvt2i

A Publicly Available, High Resolution, Unbiased CT Brain Template [chapter]

John Muschelli
2020 Communications in Computer and Information Science  
All data was converted from DICOM files to NIfTI (Neuroimaging Informatics Technology Initiative) using dcm2niix (Li et al. 2016 ) using the dcm2niir package (Muschelli 2018) .  ...  For all images, the head was skull-stripped so that only brain tissue and cerebrospinal fluid (CSF) spaces were kept, using a previously validated method (Muschelli et al. 2015) using the brain extraction  ... 
doi:10.1007/978-3-030-50153-2_27 fatcat:uxukwccghrhafbksbpgvxfzr5a

Quantitative Intracerebral Hemorrhage Localization

John Muschelli, Natalie L. Ullman, Elizabeth M. Sweeney, Ani Eloyan, Neil Martin, Paul Vespa, Daniel F. Hanley, Ciprian M. Crainiceanu
2015 Stroke  
Disclosures Johns Hopkins University holds a use patent for intraventricular tissue plasminogen activator.  ... 
doi:10.1161/strokeaha.115.010369 pmid:26451031 pmcid:PMC4624463 fatcat:zsrxumt5krg2lcndytq32ntndm

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

Adrian Gherman, John Muschelli, Brian Caffo, Ciprian Crainiceanu
2020 Frontiers in Neuroinformatics  
Another effort is Neuroconductor, which is a domain specific R repository for image analysis (Muschelli et al., 2018) .  ...  t1 <-readrpi(T1_image[1]) The neck removal step is implemented using the remove_neck function from the extrantsr (Muschelli, 2019) package.  ... 
doi:10.3389/fninf.2020.572068 pmid:33240070 pmcid:PMC7680896 fatcat:652nqa4fzbfhbfak6vy7uefyui

Removing inter-subject technical variability in magnetic resonance imaging studies

Jean-Philippe Fortin, Elizabeth M. Sweeney, John Muschelli, Ciprian M. Crainiceanu, Russell T. Shinohara
2016 NeuroImage  
., 2015] and WhiteStripe [Shinohara and Muschelli, 2015] . We applied the N4 inhomogeneity correction algorithm [Tustison et al., 2010] to each image.  ...  Comparison to intensity normalization methods We compare RAVEL to two intensity normalization procedures without scan effect correction: White Stripe, as implemented in Shinohara and Muschelli [2015]  ... 
doi:10.1016/j.neuroimage.2016.02.036 pmid:26923370 pmcid:PMC5540379 fatcat:hn5rciikdraxvckficpqjj4g7a

ROC and AUC with a Binary Predictor: a Potentially Misleading Metric [article]

John Muschelli
2019 arXiv   pre-print
In analysis of binary outcomes, the receiver operator characteristic (ROC) curve is heavily used to show the performance of a model or algorithm. The ROC curve is informative about the performance over a series of thresholds and can be summarized by the area under the curve (AUC), a single number. When a predictor is categorical, the ROC curve has only as many thresholds as the one less than number of categories; when the predictor is binary there is only one threshold. As the AUC may be used
more » ... decision-making processes on determining the best model, it important to discuss how it agrees with the intuition from the ROC curve. We discuss how the interpolation of the curve between thresholds with binary predictors can largely change the AUC. Overall, we believe a linear interpolation from the ROC curve with binary predictors, which is most commonly done in software, corresponding to the estimated AUC. We believe these ROC curves and AUC can lead to misleading results. We compare R, Python, Stata, and SAS software implementations.
arXiv:1903.04881v1 fatcat:x3cei2qgffhebavyi3mxe2whle

brainR: Interactive 3 and 4D Images of High Resolution Neuroimage Data

John Muschelli, Elizabeth Sweeney, Ciprian Crainiceanu
2014 The R Journal  
Muschelli et al. Page 11 R J. Author manuscript; available in PMC 2016 June 16.  ... 
pmid:27330829 pmcid:PMC4911196 fatcat:duvbhr7itjazbaa25l4v5qj45m

Ventricular Catheter Location and the Clearance of Intraventricular Hemorrhage

Jennifer Jaffe, Eric Melnychuk, John Muschelli, Wendy Ziai, Timothy Morgan, Daniel F. Hanley, Issam A. Awad
2012 Neurosurgery  
Background-There is no consensus regarding optimal position of external ventricular drain (EVD) with regard to clearance of intraventricular hemorrhage (IVH). Objective-To assess the hypothesis that EVD laterality may influence the clearance of blood from the ventricular system, with and without administration of thrombolytic agent. Methods-The EVD location was assessed in 100 patients in two CLEAR Phase II trials assessing the safety, and dose optimization of thrombolysis through the EVD to
more » ... elerate the clearance of obstructive IVH. Laterality of catheter was correlated with clearance rates. Results-Clearance of IVH over the first 3 days was significantly greater when thrombolytic was administered as compared to placebo, regardless of catheter laterality (p < 0.005, CI −14.0, −4.14 for contralateral EVD and CI −24.7, −5.44 for ipsilateral EVD, respectively). When thrombolytic was administered, there was a trend of more rapid clearance of total IVH through an EVD placed on the side of dominant intraventricular blood as compared to an EVD on the side with lesser blood (P = 0.09; CI −9.62, 0.69). This was not true when placebo was administered. Clearance of 3 rd and 4 th ventricular blood was unrelated to EVD laterality. Conclusion-It is possible that placement of EVD may be optimized to enhance the clearance of total IVH if lytic agents are used. Catheters on either side can clear the 3 rd and 4 th ventricles with equal efficiency.
doi:10.1227/neu.0b013e31823f6571 pmid:22067423 pmcid:PMC3719169 fatcat:g224fmyi5vb73g5ekje2mik7he
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