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fslr: Connecting the FSL Software with R

John Muschelli, Elizabeth Sweeney, Martin Lindquist, Ciprian Crainiceanu
2015 The R Journal  
We present the package fslr, a set of R functions that interface with FSL (FMRIB Software Library), a commonly-used open-source software package for processing and analyzing neuroimaging data.  ...  pipelines based on FSL functionality while interfacing with the functionality provided by R.  ...  Interfacing R with existing, powerful software provides users with thoroughly-tested software and an additional community of users, which would not be available if the functions were rewritten in R. fslr  ... 
pmid:27330830 pmcid:PMC4911193 fatcat:l2y2vu2umrb5fgxds2puxwvt2i

fslr: Connecting the FSL Software with R

John Muschelli, Elizabeth Sweeney, Martin Lindquist, Ciprian Crainiceanu
unpublished
We present the package fslr, a set of R functions that interface with FSL (FMRIB Software Library), a commonly-used open-source software package for processing and analyzing neuroimaging data.  ...  pipelines based on FSL functionality while interfacing with the functionality provided by R.  ...  Interfacing R with existing, powerful software provides users with thoroughly-tested software and an additional community of users, which would not be available if the functions were rewritten in R. fslr  ... 
fatcat:3l4klinzcvdv7ir7ts3v6gz2xe

freesurfer: Connecting the Freesurfer software with R

John Muschelli, Elizabeth Sweeney, Ciprian M. Crainiceanu
2018 F1000Research  
We present the package freesurfer, a set of R functions that interface with Freesurfer, a commonly-used open-source software package for processing and analyzing structural neuroimaging data, specifically  ...  The freesurfer package performs operations on nifti image objects in R using command-line functions from Freesurfer, and returns R objects back to the user. freesurfer allows users to process neuroanatomical  ...  Acknowledgements This paper was generated using the rticles package 21 .  ... 
doi:10.12688/f1000research.14361.1 pmid:30057753 pmcid:PMC6051196 fatcat:mdlc2wkyqraxnldwk7fkeli4ia

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

Adrian Gherman, John Muschelli, Brian Caffo, Ciprian Crainiceanu
2020 Frontiers in Neuroinformatics  
This provides a lingua franca for the large community of R analysts to interface with multiple XNAT-based publicly available neuroimaging repositories.  ...  The program has similar capabilities with PyXNAT and XNATpy, which were developed for Python users. Rxnat was developed to address the increased popularity of R among neuroimaging researchers.  ...  BC and CC oversaw the project, wrote the additional 10%, polished the manuscript, and managed the project. All authors contributed to the article and approved the submitted version.  ... 
doi:10.3389/fninf.2020.572068 pmid:33240070 pmcid:PMC7680896 fatcat:652nqa4fzbfhbfak6vy7uefyui

Neuromaps: structural and functional interpretation of brain maps [article]

Ross D Markello, Justine Y Hansen, Zhen-Qi Liu, Vincent Bazinet, Golia Shafiei, Laura Estefany Suarez, Nadia Blostein, Jakob Seidlitz, Sylvain Baillet, Theodore D Satterthwaite, Mallar Chakravarty, Armin Raznahan (+1 others)
2022 biorxiv/medrxiv   pre-print
By combining open-access data with transparent functionality for standardizing and comparing brain maps, the neuromaps software package provides a systematic workflow for comprehensive structural and functional  ...  Here we introduce the neuromaps toolbox, an open-access software package for accessing, transforming, and analyzing structural and functional brain annotations.  ...  ACKNOWLEDGEMENTS This research was undertaken thanks in part to funding from the Canada First Research Excellence Fund, awarded to McGill University for the Healthy Brains for  ... 
doi:10.1101/2022.01.06.475081 fatcat:2pkrudv2vjhoxno45hazpx24cq

Neuroconductor: an R platform for medical imaging analysis

2017 Biostatistics  
The goals of the project are to: (i) provide a centralized repository of R software dedicated to image analysis, (ii) disseminate software updates quickly, (iii) train a large, diverse community of scientists  ...  Based on the programming language R (https://www.r-project.org/), Neuroconductor starts with 51 inter-operable packages that cover multiple areas of imaging including visualization, data processing and  ...  It uses a single CT scan as input, processes the data using FSL [40] , called through fslr in R [32] , and creates a segmentation of the hemorrhagic stroke based on a pre-trained supervised machine learning  ... 
doi:10.1093/biostatistics/kxx068 pmid:29325029 pmcid:PMC6409417 fatcat:5ewfkspqj5eezgyzdungvc3coi

An Improved Algorithm of White Matter Hyperintensity Detection in Elderly Adults

T Ding, AD Cohen, EE O'Connor, HT Karim, A Crainiceanu, J Muschelli, O Lopez, WE Klunk, HJ Aizenstein, R Krafty, CM Crainiceanu, DL Tudorascu
2019 NeuroImage: Clinical  
Automated segmentation of the aging brain raises significant challenges because of the prevalence, extent, and heterogeneity of white matter hyperintensities.  ...  OASIS-AD is a major refinement of OASIS that takes into account the specific challenges raised by white matter hyperintensities in Alzheimer's disease.  ...  Acknowledgement This work was supported by the following National Institutes of Health/NIA grants: R01 AG063752, P30 AG066468, RF1 AG025516, P01 AG025204, R01 AG034852, R01 GM113243.  ... 
doi:10.1016/j.nicl.2019.102151 pmid:31927502 pmcid:PMC6957792 fatcat:2pqe3mbl4vaxxkuygxmuuwumwa

ciftify: A framework for surface-based analysis of legacy MR acquisitions [article]

Erin W Dickie, Alan Anticevic, Dawn E Smith, Timothy S Coalson, Mathuvanthi Manogaran, Navona Calarco, Joseph D Viviano, Matthew F Glasser, David C Van Essen, Aristotle N Voineskos
2018 bioRxiv   pre-print
To simplify usage for new data, the workflow has been bundled with fMRIPrep following the BIDS-app framework.  ...  Within this framework, any functional dataset with an accompanying (i.e. T1w) anatomical data can be analyzed in CIFTI format.  ...  {hemisphere}.sphere.reg.reg_LR.native.surf.gii -> registration sphere (fsnative to fsLR via FreeSurfer registration) spheres for resampling from freesurfer to HCP's "fsaverageL R" fsLR32k MNI fsLR32k derivatives  ... 
doi:10.1101/484428 fatcat:gimi5xcgxvba5hialwnn4dyxky

Recommendations for Processing Head CT Data

John Muschelli
2019 Frontiers in Neuroinformatics  
Currently, there is only one image processing pipeline for head CT, which focuses mainly on head CT data with lesions.  ...  We describe going from raw DICOM data to a spatially normalized brain within CT presenting a full example with code.  ...  ACKNOWLEDGMENTS This work has been supported by the R01NS060910 and 5U01NS080824 grants from the National Institute of Neurological Disorders and Stroke at the National Institutes of Health (NINDS/NIH)  ... 
doi:10.3389/fninf.2019.00061 pmid:31551745 pmcid:PMC6738271 fatcat:lnbjkk6qvnfahbn5qdd4akzleq

Referee report. For: freesurfer: Connecting the Freesurfer software with R [version 1; referees: 2 approved]

Pierre Lafaye De Micheaux
2018
We present the package , a set of R functions that interface with freesurfer Freesurfer, a commonly-used open-source software package for processing and analyzing structural neuroimaging data, specifically  ...  The package performs operations on nifti freesurfer image objects in R using command-line functions from Freesurfer, and returns R objects back to the user. allows users to process freesurfer neuroanatomical  ...  Acknowledgements This paper was generated using the rticles package 21 .  ... 
doi:10.5256/f1000research.15624.r35180 fatcat:26jopeb4dfa63mfkvv36wiidwa

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

Matthew Sharrock, W. Andrew Mould, Hasan Ali, Meghan Hildreth, Daniel F Hanley, John Muschelli
2020 medRxiv   pre-print
This is the first publicly available neural network model for segmentation of ICH, the only model evaluated with the presence of both IVH and SDH and the only model validated in the workflow of a series  ...  Using an automated pipeline and 2D and 3D deep neural networks, we show that we can quickly and accurately estimate ICH volume with high agreement with timeconsuming manual segmentation.  ...  In R, the ichseg package was used (https://github.com/muschellij2/ichseg), using the fslr package (Muschelli et al. 2015a ) to call functions from the FSL (Jenkinson et al. 2012 ) neuroimaging software  ... 
doi:10.1101/2020.03.05.20031823 fatcat:dhsjofqanfd4pebkkd57grbtae

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

John Muschelli, Elizabeth M. Sweeney, Natalie L. Ullman, Paul Vespa, Daniel F. Hanley, Ciprian M. Crainiceanu
2017 NeuroImage: Clinical  
We provide an R package and a webpage for implementing and testing the proposed approach.  ...  In practical terms the difference between the random forest and the logistic regression is quite small.  ...  Chris Rorden was also extremely helpful in adapting his dcm2nii software to some issues specific to CT scans and the data for the population moment images. Sources of Funding The  ... 
doi:10.1016/j.nicl.2017.02.007 pmid:28275541 pmcid:PMC5328741 fatcat:nc7sgduxjfbdfln6mknl7mr7py

Spatial Topography of Individual-Specific Cortical Networks Predicts Human Cognition, Personality and Emotion [article]

Ru Kong, Jingwei Li, Csaba Orban, Mert Rory Sabuncu, Hesheng Liu, Alexander Schaefer, Nanbo Sun, Xi-Nian Zuo, Avram Holmes, Simon B. Eickhoff, B.T. Thomas Yeo
2017 bioRxiv   pre-print
Compared with other approaches, MS-HBM parcellations generalized better to new rs-fMRI and task-fMRI data from the same subjects.  ...  phenotypes based on connectivity strength.  ...  ; Smith et al., 2004) , (iii) motion correction using rigid body translation and rotation with the FSL package.  ... 
doi:10.1101/213041 fatcat:tirpj3trb5b65heyvrerffvkpa

Image Segmentation, Registration and Characterization in R with SimpleITK

Richard Beare, Bradley Lowekamp, Ziv Yaniv
2018 Journal of Statistical Software  
In this article we describe the SimpleITK R package. SimpleITK is a simplified interface to the insight segmentation and registration toolkit (ITK).  ...  SimpleITK provides packages for many interpreter environments, including R.  ...  Acknowledgments This work was supported by the Intramural Research Program of the U.S.  ... 
doi:10.18637/jss.v086.i08 pmid:30288153 pmcid:PMC6168008 fatcat:namgrlek7ncgvazbwwdv5skwpi

Fully Automated Detection of Paramagnetic Rims in Multiple Sclerosis Lesions on 3T Susceptibility-Based MR Imaging [article]

Carolyn Lou, Pascal Sati, Martina Absinta, Kelly Clark, Jordan D Dworkin, Alessandra M Valcarcel, Matthew K Schindler, Daniel S Reich, Elizabeth M Sweeney, Russell T Shinohara
2020 bioRxiv   pre-print
Results: The number of PRLs per subject identified via our automated lesion labelling method was highly correlated with the gold standard count of PRLs per subject, r = 0.91 (95% CI [0.79, 0.97]).  ...  Methods: T1-weighted, T2-FLAIR, and T2*-phase MRI of the brain were collected at 3T for 19 subjects with MS.  ...  T1, FLAIR, and phase 146 images were then preprocessed using the fslr R package (28), an R wrapper for the FSL software 147 (29,30). Images were visualized with ITK-SNAP (31).  ... 
doi:10.1101/2020.08.31.276238 fatcat:hyq3f7jsk5gljpfhlomfge6pcq
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