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fslr (version 1.4.4)

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

554

Version

1.4.4

License

GPL-3

Maintainer

John Muschelli

Last Published

May 21st, 2015

Functions in fslr (1.4.4)

cal.min-methods

Extract Image cal.min attribute

FSL Swap Dimensions

Apply Warp from FLIRT

Binarized Inverse Image using FSL

Check output filename

fnirt_with_affine_apply

Applies FLIRT then FNIRT transformations

Log Transform Image using FSL

dropEmptyImageDimensions

Drop Empty Image Dimensions

checknii-methods

Force object to filename with .nii extension

Change Data type for img

checkimg-methods

Force object to filename with .nii extension

Merge images using FSL

data_type-methods

Extract Image data_type attribute

Double Orthographic Display

Image Center of Gravity

Add a colorbar to an ortho2 object

intent_p3-methods

Extract Image intent_p3 attribute

Arc Sine Transform Image using FSL

cal.max-methods

Extract Image cal.max attribute

Determine of Q and S forms are consistent

FSL Volume in mL (or cubic centimeters)

Arc Tangent Transform Image using FSL

fslreorient2std.help

fslreorient2std help

Logical check if FSL is accessible

Dilate image using FSL

Mask image using FSL

FSL Change file type

Wrapper for getForms with filename

Square Image using FSL

Get Image file extension

descrip-methods

Extract Image descrip attribute

Edge Strength Image using FSL

Grab nii file stubname

fsl_applywarp.help

FSL applywarp help

aux.file-methods

Extract Image aux.file attribute

Reciprocal Image using FSL

fsl_biascorrect

FSL Bias Correct

Register using FNIRT

Determine extension of image based on FSLOUTPUTTYPE

Get FSL's Directory

FSL Command Wrapper

Threshold an image

fslswapdim.help

fslswapdim help

Fill image holes with dilation then erosion

FSL Copy Geometry

Replace NaNs in Image using FSL

copyNIfTIHeader

Copy NIfTI Header to an array

Divide Images using FSL

Apply Warp from FNIRT

Binarize Image using FSL

Parse FSL Header

Extract Image dim_ attribute

Arc Cosine Transform Image using FSL

fslchfiletype.help

fslchfiletype help

Exponentiate Image using FSL

Index Image using FSL

intent_name-methods

Extract Image intent_name attribute

Resets image parameters for a copied nifti object

Fill image holes

Sine Transform Image using FSL

Cosine Transform Image using FSL

fnirt_with_affine

Register using FNIRT, but doing Affine Registration as well

Help for FSL BET

Use FSL's Brain Extraction Tool (BET)

Subsample image by factor of 2

Image Center of Gravity (FSL)

Absolute Value Image using FSL

Determine FSL output type

intent_code-methods

Extract Image intent_code attribute

slice_duration-methods

Extract Image slice_duration attribute

fslreorient2std

FSL Orient to MNI

Wrapper for getting fsl help

datatype-methods

Extract Image datatype attribute

Get NIfTI header using FSL

Register using FLIRT

Extract Image bitpix attribute

slice_start-methods

Extract Image slice_start attribute

FSL SUSAN noise reduction

Image Center of Gravity Wrapper

scl_slope-methods

Extract Image scl_slope attribute

Window image based on quantiles of Image

Multiply Images using FSL

Make new nifti from array

Get value from FSL header

Create command declaring FSLDIR

Add Random Standard Guassian Noise Image using FSL

Orthographic Display, added options

sform_code-methods

Extract Image sform_code attribute

Mask nifti Image

nifti image windower

qform_code-methods

Extract Image qform_code attribute

Get Z-score over a margin of an img

Modulus Remainder of 2 Images using FSL

Add Random Uniform Noise Image using FSL

Square Root Image using FSL

slice_end-methods

Extract Image slice_end attribute

toffset-methods

Extract Image toffset attribute

Get Q and S Forms of orientation matrix

Subtract Images using FSL

slice_code-methods

Extract Image slice_code attribute

Mask NaNs in Image using FSL

Open image in FSLView

qform,character-method

Extract NIfTI 3D Image Orientation

Create temporary nii.gz file for FSL

sizeof_hdr-methods

Extract Image sizeof_hdr attribute

intent_p1-methods

Extract Image intent_p1 attribute

Extract Image magic attribute

Tangent Transform Image using FSL

Gaussian smooth image using FSL

vox_offset-methods

Extract Image vox_offset attribute

check_nifti-methods

Check if nifti image or read in a nifti image

FSL Anatomical Processing Script

Run MELODIC ICA

Add Images using FSL

Extract Image pixdim attribute

Erode image using FSL

Get range of an image

intent_p2-methods

Extract Image intent_p2 attribute

scl_inter-methods

Extract Image scl_inter attribute