data_brain_mask: Example of Mask File Used in Diffusion MRI Processing

Description Format Details References See Also


The ‘data_brain_mask.nii.gz’ dataset defines the mask used in the diffusion MRI analysis for ‘data.nii.gz’.


The file ‘data_brain_mask.nii.gz’ is in gzipped NIfTI format. The R-package oro.nifti is required to read NIfTI files. This file may be obtained from ‘data.nii.gz’ by applying FSL/BET pre-processing tools.


For reasons of limited CRAN storage space, a trimmed down data set with just 4 coronal slices was selected. Coronal slices (29:32) were extracted from the original data set.

The mask used here is an all-brain mask; it just removes non-brain regions, as the result of applying a brain extraction tool to the ‘data.nii.gz’ dataset. However, other masks may be defined to select regions of interest (ROIs).


Yeh, F.-C., Wedeen, V. J., and Tseng, W.-Y. I. Generalized q-Sampling Imaging. IEEE Transactions on Medical Imaging 29, 9 (2010), 1626–1635.

Jenkinson, M., Beckmann, C. F., Behrens, T. E., Woolrich, M. W., and Smith, S. M. Fsl. NeuroImage 62, 2 (2012), 782-790.

NITRC repository,

See Also

data, data.bval, data.bvec, data_V1, data_V2, data_gfa, btable

gdimap documentation built on May 29, 2017, 11:03 p.m.