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fslr (version 1.0)

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

1.0

License

GPL-2

Maintainer

John Muschelli

Last Published

June 13th, 2014

Functions in fslr (1.0)

fslmaths.help

FSL Maths Help
melodic

Run MELODIC ICA
fslfill

Fill image holes
fslhelp

Wrapper for getting fsl help
fslmask

Mask image using FSL
zero_trans

Change intercept to 0 and slope to 1
cal_img

Set Max/Min for nifti object by range of data
fslrange

Get range of an image
get.fsl

Get FSL's Location
get.imgext

Determine extension of image based on FSLOUTPUTTYPE
fslhd.help

FSLhd help
melodic.help

MELODIC help
check_file

Wrapper for getForms with filename
fslhd

Get NIfTI header using FSL
fslmerge

Merge images using FSL
fslhd.parse

Parse FSL Header
datatype

Change Data type for img
checkimg

Check if filename is character or nifti object
fslview

Open image in FSLView
have.fsl

Logical check if FSL is accessible
check_nifti

Check if nifti image or read in
fslmerge.help

FSLMerge help
fslsmooth

Gaussian smooth image using FSL
fslthresh

Threshold an image
nii.stub

Grab nii file stubname
flirt

Register using FLIRT
tempimg

Create temporary nii.gz file for FSL
getForms

Get Q and S Forms of orientation matrix
checkout

Determine of Q and S forms are consistent
voxdim

Gets Voxel Dimensions
newnii

Resets image parameters for a copied nifti object
zscore_img

Get Z-score over a margin of an img
fslmaths

FSL Maths
fslsub2

Subsample image by factor of 2
fslstats.help

FSL Stats Help
fslstats

FSL Stats
fslview.help

FSLView help
flirt.help

FLIRT help
fslerode

Erode image using FSL
get.fsloutput

Determine FSL output type
rescale_img

Image Rescaler