Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 fslr: Connecting the FSL Software with R.

Literature DB >> 27330830

fslr: Connecting the FSL Software with R.

John Muschelli¹, Elizabeth Sweeney², Martin Lindquist³, Ciprian Crainiceanu⁴.

Abstract

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. The fslr package performs operations on 'nifti' image objects in R using command-line functions from FSL, and returns R objects back to the user. fslr allows users to develop image processing and analysis pipelines based on FSL functionality while interfacing with the functionality provided by R. We present an example of the analysis of structural magnetic resonance images, which demonstrates how R users can leverage the functionality of FSL without switching to shell commands.

Entities: Chemical Disease Gene Species

Year: 2015 PMID： 27330830 PMCID： PMC4911193

Source DB: PubMed Journal: R J ISSN： 2073-4859 Impact factor: 3.984

19 in total

1. A global optimisation method for robust affine registration of brain images.

Authors: M Jenkinson; S Smith
Journal: Med Image Anal Date: 2001-06 Impact factor: 8.545

2. Improved optimization for the robust and accurate linear registration and motion correction of brain images.

Authors: Mark Jenkinson; Peter Bannister; Michael Brady; Stephen Smith
Journal: Neuroimage Date: 2002-10 Impact factor: 6.556

3. Multi-atlas skull-stripping.

Authors: Jimit Doshi; Guray Erus; Yangming Ou; Bilwaj Gaonkar; Christos Davatzikos
Journal: Acad Radiol Date: 2013-12 Impact factor: 3.173

4. A nonparametric method for automatic correction of intensity nonuniformity in MRI data.

Authors: J G Sled; A P Zijdenbos; A C Evans
Journal: IEEE Trans Med Imaging Date: 1998-02 Impact factor: 10.048

Review 5. The secret lives of experiments: methods reporting in the fMRI literature.

Authors: Joshua Carp
Journal: Neuroimage Date: 2012-07-10 Impact factor: 6.556

Review 6. FreeSurfer.

Authors: Bruce Fischl
Journal: Neuroimage Date: 2012-01-10 Impact factor: 6.556

7. N4ITK: improved N3 bias correction.

Authors: Nicholas J Tustison; Brian B Avants; Philip A Cook; Yuanjie Zheng; Alexander Egan; Paul A Yushkevich; James C Gee
Journal: IEEE Trans Med Imaging Date: 2010-04-08 Impact factor: 10.048

8. Automatic lesion incidence estimation and detection in multiple sclerosis using multisequence longitudinal MRI.

Authors: E M Sweeney; R T Shinohara; C D Shea; D S Reich; C M Crainiceanu
Journal: AJNR Am J Neuroradiol Date: 2012-07-05 Impact factor: 3.825

9. Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python.

Authors: Krzysztof Gorgolewski; Christopher D Burns; Cindee Madison; Dav Clark; Yaroslav O Halchenko; Michael L Waskom; Satrajit S Ghosh
Journal: Front Neuroinform Date: 2011-08-22 Impact factor: 4.081

Review 10. FSL.

Authors: Mark Jenkinson; Christian F Beckmann; Timothy E J Behrens; Mark W Woolrich; Stephen M Smith
Journal: Neuroimage Date: 2011-09-16 Impact factor: 6.556

17 in total

1. Removing inter-subject technical variability in magnetic resonance imaging studies.

Authors: Jean-Philippe Fortin; Elizabeth M Sweeney; John Muschelli; Ciprian M Crainiceanu; Russell T Shinohara
Journal: Neuroimage Date: 2016-02-23 Impact factor: 6.556

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

Authors: Alessandra M Valcarcel; Kristin A Linn; Simon N Vandekar; Theodore D Satterthwaite; John Muschelli; Peter A Calabresi; Dzung L Pham; Melissa Lynne Martin; Russell T Shinohara
Journal: J Neuroimaging Date: 2018-03-08 Impact factor: 2.486

3. Harmonization of multi-site diffusion tensor imaging data.

Authors: Jean-Philippe Fortin; Drew Parker; Birkan Tunç; Takanori Watanabe; Mark A Elliott; Kosha Ruparel; David R Roalf; Theodore D Satterthwaite; Ruben C Gur; Raquel E Gur; Robert T Schultz; Ragini Verma; Russell T Shinohara
Journal: Neuroimage Date: 2017-08-18 Impact factor: 6.556

fslr: Connecting the FSL Software with R.

1. A global optimisation method for robust affine registration of brain images.

2. Improved optimization for the robust and accurate linear registration and motion correction of brain images.

3. Multi-atlas skull-stripping.

4. A nonparametric method for automatic correction of intensity nonuniformity in MRI data.

Review 5. The secret lives of experiments: methods reporting in the fMRI literature.

Review 6. FreeSurfer.

7. N4ITK: improved N3 bias correction.

8. Automatic lesion incidence estimation and detection in multiple sclerosis using multisequence longitudinal MRI.

9. Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python.

Review 10. FSL.

1. Removing inter-subject technical variability in magnetic resonance imaging studies.

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

3. Harmonization of multi-site diffusion tensor imaging data.

4. Neuroconductor: an R platform for medical imaging analysis.

5. MULTI-DOMAIN LEARNING BY META-LEARNING: TAKING OPTIMAL STEPS IN MULTI-DOMAIN LOSS LANDSCAPES BY INNER-LOOP LEARNING.

6. Functional Magnetic Resonance Imaging Studies in Sexual Medicine: A Primer.

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

8. Identification of Two Distinct Working Memory-Related Brain Networks in Healthy Young Adults.

9. freesurfer: Connecting the Freesurfer software with R.

10. 3D Deep Neural Network Segmentation of Intracerebral Hemorrhage: Development and Validation for Clinical Trials.