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F1000Res. 2018 May 16;7:599. doi: 10.12688/f1000research.14361.1. eCollection 2018.

freesurfer: Connecting the Freesurfer software with R.

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Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
Flatiron Health, New York, NY, 10010, USA.


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 T1-weighted images. 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 images and provides functionality to convert and read the output of the Freesurfer pipelines more easily, including brain images, brain surfaces, and Freesurfer output tables.


freesurfer; neuroconductor; neuroimaging; r

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