slfcst: A Region-of-Interest (ROI) File for Diffusion MRI Analysis

Description Format Details References


The ‘slfcst.nii.gz’ is a region-of-interest (ROI) file that was formed by extracting the superior longitudinal fasciculus (SLF) and corticospinal tract (CST) regions from the main data diffusion set ‘data.nii.gz’.

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. Hence, the argument bview="coronal" is used in the examples, and the range of coronal slices is (1:4). User specified complete data sets may be used without restrictions.


The file ‘slfcst.nii.gz’ is in gzipped NIfTI format. The R-package oro.nifti is required to read NIfTI files.


The extracted regions were registered to the DSI data set using the FSL/FLIRT tool. The procedure uses the ‘JHU-ICBM-labels-2mm.nii.gz’ atlas included in the FSL toolbox.

The ROI file ‘slfcst.nii.gz’ depicts brain regions where anatomic white matter fibre crossings are known to exist, forming multiple pathway bundles connected to the cerebral cortex.


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

Whitcher, B., Schmid, V. J., and Thornton, A. Working with the DICOM and NIfTI data standards in R. Journal of Statistical Software 44, 6 (2011), 1-28.

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