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fslr (version 1.3)

Wrapper functions for FSL (FMRIB Software Library) from Functional MRI of the Brain (FMRIB)

Description

Wrapper functions that interface with FSL (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/), a powerful and commonly-used neuroimaging software, using system commands. The goal is to be able to interface with FSL completely in R, where you pass R nifti objects and the function executes an FSL command and returns an R nifti object if desired.

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Version

Install

install.packages('fslr')

Monthly Downloads

433

Version

1.3

License

GPL-2

Maintainer

John Muschelli

Last Published

November 4th, 2014

Functions in fslr (1.3)

Set Max/Min for nifti object by range of data

Image Center of Gravity (FSL)

Use FSL's Brain Extraction Tool (BET)

Creates onefile specification

Help for FSL BET

nifti image windower

Run MELODIC ICA

fslreorient2std

FSL Orient to MNI

Wrapper for getForms with filename

Check if filename is character or nifti object

Determine of Q and S forms are consistent

Apply Warp from FNIRT

Parse FSL Header

Change Data type for img

fnirt_with_affine

Register using FNIRT, but doing Affine Registration as well

Fill image holes

Check if nifti image or read in

Get FSL's Directory

Threshold an image

FSL SUSAN noise reduction

Gaussian smooth image using FSL

Erode image using FSL

Mask image using FSL

Binarize Image using FSL

Mask nifti Image

Get NIfTI header using FSL

Resets image parameters for a copied nifti object

fslreorient2std.help

fslreorient2std help

Get Q and S Forms of orientation matrix

Drop Image Dimension

Register using FLIRT

Merge images using FSL

Orthographic Display, added options

Determine extension of image based on FSLOUTPUTTYPE

FSL Swap Dimensions

Determine FSL output type

Get value from FSL header

Logical check if FSL is accessible

Gets Voxel Dimensions

Create temporary nii.gz file for FSL

Grab nii file stubname

Register using FNIRT

fsl_applywarp.help

FSL applywarp help

Image Center of Gravity

fsl_biascorrect

FSL Bias Correct

Open image in FSLView

FSL Command Wrapper

Get Z-score over a margin of an img

Window image based on quantiles of Image

Subsample image by factor of 2

Wrapper for getting fsl help

Change intercept to 0 and slope to 1

fslswapdim.help

fslswapdim help

Get range of an image

Make new nifti from array

fnirt_with_affine_apply

Apply Warp from FLIRT

Create command declaring FSLDIR