gdimap (version 0.1-9)

niinorm: Normalization of Principal Diffusion Directions

Description

niinorm normalizes Principal Diffusion Directions (PDDs) in NIfTI files. The unnormalized PDD values produced by gqi.odfvmf retain information about the estimated von Mises-Fisher parameters at each voxel, which are useful in probabilistic tractography. On the other hand, normalized PDD values are useful for visualization and seed mask creation, namely using the ‘FSL/fslview’ tool.

Usage

niinorm(srcdir=tempfile(), filename="data_V1", savedir=tempdir())

Arguments

srcdir

directory where loading files are located (default: tempdir().)

filename

name of the NIfTI file with PDD values to be normalized (default: ‘"data_V1")’.)

savedir

directory for saving processed results (default: tempdir().)

Value

niinorm accepts NIfTI files with incorporated PDD values as produced by gqi.odfvmf, and outputs NIfTI files with normalized PDD values in the unit sphere. The output NIfTI filenames receive the suffix 'n', e.g., ‘data_V1n’ and ‘data_V2n’.

See Also

gqi.odfvmf

Examples

## Not run: 
# ## Example using the PDD files in gdimap
# ## normalize vector data generated by vMF functions
# ## before visualization with FSL/fslview
# fi1 <- "data_V1.nii.gz"
# p <- system.file(file.path("extdata", fi1), package = "gdimap")
# p1 <- strsplit(p,fi1)[[1]][1]
# niinorm(srcdir=p1, filename=fi1, savedir=tempdir())
# fi2 <- "data_V2.nii.gz"
# niinorm(srcdir=p1, filename=fi2, savedir=tempdir())
# ## try fslview if installed
# fo1 <- file.path(tempdir(),"data_V1n.nii.gz")
# fo2 <- file.path(tempdir(),"data_V2n.nii.gz")
# fo3 <- file.path(p1, "data_gfa.nii.gz")
# if(Sys.which("fslview") != "") system(paste("fslview", fo3, fo2, fo1, "&"))
# ## End(Not run)