Package oasis details

Multiple Sclerosis Lesion Segmentation using Magnetic Resonance Imaging (MRI)

Trains and makes predictions from the OASIS method, described in detail in the paper "OASIS is Automated Statistical Inference for Segmentation, with applications to multiple sclerosis lesion segmentation in MRI" . OASIS is a method for multiple sclerosis (MS) lesion segmentation on structural magnetic resonance image (MRI) studies. OASIS creates probability maps of lesion presence using the FLAIR, T2, T1, and PD structural MRI volumes. This packages allows for training of the OASIS model and prediction of OASIS probability maps from a trained model with user supplied studies that have a gold standard lesion segmentation masks. The package will also create OASIS probability maps for MRI studies using the OASIS model from the OASIS paper if no gold standard lesion segmentation masks are available.

Maintainer: Elizabeth M. Sweeney < elizabethmargaretsweeney at gmail.com >

 
From within R, enter citation('oasis')


Sweeney EM, Shinohara RT, Shiee N, Mateen FJ, Chudgar AA, Cuzzocreo JL,
Calabresi PA, Pham DL, Reich DS, Crainiceanu CM (2013). "OASIS is
Automated Statistical Inference for Segmentation, with applications to
multiple sclerosis lesion segmentation in MRI." _NeuroImage: clinical_,
*2*, 402-413.

A BibTeX entry for LaTeX users is

@Article{sweeney2013oasis,
title = {OASIS is Automated Statistical Inference for Segmentation, with applications to multiple sclerosis lesion segmentation in MRI},
author = {Elizabeth M Sweeney and Russell T Shinohara and Navid Shiee and Farrah J Mateen and Avni A Chudgar and Jennifer L Cuzzocreo and Peter A Calabresi and Dzung L Pham and Daniel S Reich and Ciprian M Crainiceanu},
journal = {NeuroImage: clinical},
volume = {2},
pages = {402--413},
year = {2013},
publisher = {Elsevier},
}

 

If you have any problems with this package you can open a new issue or check the already existing ones here.

 
 
To install this package, start R and enter:

source("https://neuroconductor.org/neurocLite.R")

# Default Install
neuro_install('oasis')

# from GitHub
neuro_install('oasis', release = "stable", release_repo = "github")
neuro_install('oasis', release = "current", release_repo = "github")

More detailed installation instructions can be found here.

 

Initially submitted on October 3 2018 1:23PM
Last updated on October 3 2018 1:23PM
Package type standard
Source GitHub https://github.com/emsweene/oasis GitHub
Neuroconductor GitHub https://github.com/neuroconductor/oasis GitHub
DependsR (2.10)
Importsneurobase, fslr (2.13), methods, stats, parallel, oro.nifti, mmand
Suggestshttr, covr, ROCR
Reverse Importsmimosa (3.0.1)