OASIS Image Preprocessing

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Description

This function does the required preprocessing for OASIS for the FLAIR, T2, T1, and PD volumes using FSL through fslr. The preprocessing steps are (1) inhomogeneity correct using fsl_biascorrect and (2) rigid registration using flirt to the T1 space.

Usage

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oasis_preproc(flair, t1, t2, pd = NULL, brain_mask = NULL, verbose = TRUE,
  cores = 1)

Arguments

flair

FLAIR volume of class nifti

t1

T1 volume of class nifti

t2

T2 volume of class nifti

pd

PD volume of class nifti

brain_mask

binary mask volume of class nifti

verbose

a logical value for printing diagnostic output

cores

numeric indicating the number of cores to be used (no more than 4 is useful for this software implementation)

Value

Returns a list of objects of class nifti, namely the inhomogeneity corrected FLAIR, T1, T2, and PD registered to the space of the T1 volume.

Examples

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## Not run: 
library(neurobase)
flair <- readnii('path/to/flair', reorient = FALSE)
t1 <- readnii('path/to/t1', reorient = FALSE)
t2 <- readnii('path/to/t2', reorient = FALSE)
pd <- readnii('path/to/pd', reorient = FALSE)
oasis_preprocessed_data <- oasis_preproc(flair, t1, t2, pd)

## End(Not run)