slfcst: A Region-of-Interest (ROI) File for Diffusion MRI Analysis
In gdimap: Generalized Diffusion Magnetic Resonance Imaging
Description
Format
Details
References
Description
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.
Format
The file ‘slfcst.nii.gz’ is in gzipped NIfTI format.
The R-package oro.nifti is required to read NIfTI files.
Details
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.
References
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.
gdimap documentation built on May 2, 2019, 8:52 a.m.
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Description Format Details References
Description
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.
Format
The file ‘slfcst.nii.gz’ is in gzipped NIfTI format. The R-package oro.nifti is required to read NIfTI files.
Details
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.
References
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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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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