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fslr (version 1.9.2.1)

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 objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'FSL' command and returns an R object of class 'nifti' if desired.

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Version

Install

install.packages('fslr')

Monthly Downloads

433

Version

1.9.2.1

License

GPL-3

Maintainer

John Muschelli

Last Published

September 6th, 2016

Functions in fslr (1.9.2.1)

cal.max-methods

Extract Image cal.max attribute
check_nifti-methods

Check if nifti image or read in a nifti image
breaker

Find Breaks for nifti Image Ploting
bitpix-methods

Extract Image bitpix attribute
applyEmptyImageDimensions

Apply Subsetting from Empty Image Dimensions
check_mask_fail

Check Mask is Binary, Fail otherwise
cal.min-methods

Extract Image cal.min attribute
check_mask

Check Mask is Binary
check_file

Wrapper for getForms with filename
aux.file-methods

Extract Image aux.file attribute
checkniigz-methods

Force object to filename with .nii.gz extension
cog

Image Center of Gravity
checknii-methods

Force object to filename with .nii extension
copyNIfTIHeader

Copy NIfTI Header to an array
colorbar

Add a colorbar to an ortho2 object
checkout

Determine of Q and S forms are consistent
checkimg-methods

Force object to filename
datatype-methods

Extract Image datatype attribute
data_type-methods

Extract Image data_type attribute
check_outfile

Check output filename
descrip-methods

Extract Image descrip attribute
dtifit

DTI Fitting Procedure from FSL
fast.help

FAST help
fast

FSL FAST
double_ortho

Double Orthographic Display
dim_-methods

Extract Image dim_ attribute
dropEmptyImageDimensions

Drop Empty Image Dimensions
download_fsl

Download FSL
eddy_correct

Eddy Current Correction
file_imgext

Get Image file extension
fsl_anat.help

fsl_anat help
flirt

Register using FLIRT
fnirt.help

FNIRT help
fnirt_with_affine

Register using FNIRT, but doing Affine Registration as well
flirt.help

FLIRT help
flirt_apply

Apply Warp from FLIRT
fnirt

Register using FNIRT
finite_img-methods

Finite Image
fnirt_with_affine_apply

Applies FLIRT then FNIRT transformations
fsl_data_dir

Get FSL's Data Directory
fsl_anat

FSL Anatomical Processing Script
fsl_biascorrect

FSL Bias Correct
fsl_applywarp.help

FSL applywarp help
fsl_applywarp

Apply Warp from FNIRT
fsl_atlas_dir

Get FSL's Standard Data Directory
fslabs.help

fslabs Help
fsl_std_dir

Get FSL's Standard Data Directory
fsl_slicetimer

FSL Slice Timing Correction
fslabs

Absolute Value Image using FSL
fslacos.help

fslacos Help
fslbet.help

Help for FSL BET
fslacos

Arc Cosine Transform Image using FSL
fslasin.help

fslasin Help
fsladd.help

fsladd Help
fslbet

Use FSL's Brain Extraction Tool (BET)
fsladd

Add Images using FSL
fslasin

Arc Sine Transform Image using FSL
fslatan.help

fslatan Help
datatype

Change Data type for img
fslatan

Arc Tangent Transform Image using FSL
fslbin.help

fslbin Help
fslcpgeom.help

fslcpgeom help
fslbin

Binarize Image using FSL
fslmerge

Merge images using FSL
fslcpgeom

FSL Copy Geometry
fslmul.help

fslmul Help
fslexp

Exponentiate Image using FSL
fslfill.help

fslfill Help
fslbinv.help

fslbinv Help
fslrem

Modulus Remainder of 2 Images using FSL
fslmaths.help

FSL Maths Help
fslbinv

Binarized Inverse Image using FSL
fsldilate

Dilate image using FSL
fsldir

Get FSL's Directory
fslnan.help

fslnan Help
fslmaths

FSL Maths
fslmul

Multiply Images using FSL
fslorienter

Wrapper for FSL Get Orientation
fslrand.help

fslrand Help
fslchfiletype.help

fslchfiletype help
fslerode

Erode image using FSL
fslchfiletype

FSL Change file type
fslexp.help

fslexp Help
fslmask.help

fslmask Help
fslerode.help

fslerode Help
fslcmd

FSL Command Wrapper
fslnan

Replace NaNs in Image using FSL
fslmask

Mask image using FSL
fslcog

Image Center of Gravity (FSL)
fslnanm.help

fslnanm Help
fslfill2

Fill image holes with dilation then erosion
fslfill

Fill image holes
fsldiv

Divide Images using FSL
fslnanm

Mask NaNs in Image using FSL
fslindex

Index Image using FSL
fslindex.help

fslindex Help
fslgetorient

FSL Orientation Wrappers
fslrem.help

fslrem Help
fslreorient2std.help

fslreorient2std help
fsltan

Tangent Transform Image using FSL
fslview

Open image in FSLView
fslvol

FSL Volume in mL (or cubic centimeters)
nii.stub

Grab nii file stubname
qform,character-method

Extract NIfTI 3D Image Orientation
scl_slope-methods

Extract Image scl_slope attribute
sform_code-methods

Extract Image sform_code attribute
rescale_img

Image Rescaler
xfibres

Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques with Crossing Fibers
robust_window

Window image based on quantiles of Image
xyz

Image Center of Gravity Wrapper
zero_pad

Zero pads an image
zlimmer

Find Image z-limits
fslsum

FSL Sum
fslsub2.help

fslsub2 Help
fslsub2

Subsample image by factor of 2
fslsmooth

Gaussian smooth image using FSL
fslsmooth.help

fslsmooth Help
fslentropy

Image Mean Entropy
getEmptyImageDimensions

Get Empty Image Dimensions
fslswapdim.help

fslswapdim help
getForms

Get Q and S Forms of orientation matrix
fsldiv.help

fsldiv Help
melodic.help

MELODIC help
mcflirt

FSL Motion Correction
fslsin

Sine Transform Image using FSL
fslreorient2std

FSL Orient to MNI
fslsin.help

fslsin Help
fslsqr

Square Image using FSL
fslsqr.help

fslsqr Help
fslswapdim

FSL Swap Dimensions
fsltan.help

fsltan Help
have.fsl

Logical check if FSL is accessible
intent_code-methods

Extract Image intent_code attribute
mni_fname

Construct MNI Filename
melodic

Run MELODIC ICA
fslthresh.help

fslthresh Help
intent_p1-methods

Extract Image intent_p1 attribute
intent_name-methods

Extract Image intent_name attribute
slice_start-methods

Extract Image slice_start attribute
susan.help

FSL SUSAN Help
fslcos.help

fslcos Help
fslcos

Cosine Transform Image using FSL
fsledge.help

fsledge Help
fsllog

Log Transform Image using FSL
fslrandn

Add Random Standard Guassian Noise Image using FSL
fslhd

Get NIfTI header using FSL
fsllog.help

fsllog Help
fsledge

Edge Strength Image using FSL
fslhd.help

FSLhd help
fslrange

Get range of an image
fslhd.parse

Parse FSL Header
fslmean

Image Mean
fslhelp

Wrapper for getting fsl help
fslorient

FSL Orient
fslmerge.help

FSLMerge help
fslorient.help

fslorient help
fslrand

Add Random Uniform Noise Image using FSL
fslsplit.help

FSL Split help
fslrandn.help

fslrandn Help
fslsplit

Split images using FSL
mni_img

Read MNI Filename
same_dims

Check if Objects have Same Dimensions
qform_code-methods

Extract Image qform_code attribute
probtrackx

Probabilistic diffusion tractography with multiple fibre orientations
multi_overlay

Create Multi-Image Plot with Overlays
scl_inter-methods

Extract Image scl_inter attribute
toffset-methods

Extract Image toffset attribute
vox_offset-methods

Extract Image vox_offset attribute
fslrecip.help

fslrecip Help
fslrecip

Reciprocal Image using FSL
fslstats.help

FSL Stats Help
intent_p2-methods

Extract Image intent_p2 attribute
fslview.help

FSLView help
fslval

Get value from FSL header
fslstats

FSL Stats
intent_p3-methods

Extract Image intent_p3 attribute
quantile_img

Create Quantile Image
run_first_all.help

Run FIRST All Help
readNIfTI2

readNIfTI with default non-reoirientation
run_first_all

Run FIRST All
fslsub.help

fslsub Help
fslsub

Subtract Images using FSL
mcflirt.help

MCFLIRT help
niftiarr

Make new nifti from array
newnii

Resets image parameters for a copied nifti object
maskEmptyImageDimensions

Make Mask from Empty Image Dimensions
get.imgext

Determine extension of image based on FSLOUTPUTTYPE
get.fsloutput

Determine FSL output type
remake_img

Remake Image from Vector
replace_dropped_dimensions

Remake Dropped Dimensions
fslroi

FSL ROI
fslsqrt

Square Root Image using FSL
fslsqrt.help

fslsqrt Help
fslsd

Image Standard Deviation
fslthresh

Threshold an image
get.fsl

Create command declaring FSLDIR
fslval.help

fslval help
fslvolume

Image Volume
magic-methods

Extract Image magic attribute
mask_img

Mask nifti Image
ortho_diff

Plot differences for Prediction and Gold Standard
parse_img_ext

Parse Image Extensions
ortho2

Orthographic Display, added options
susan

FSL SUSAN noise reduction
slice_code-methods

Extract Image slice_code attribute
pixdim-methods

Extract Image pixdim attribute
sizeof_hdr-methods

Extract Image sizeof_hdr attribute
zscore_img

Get Z-score over a margin of an img
tempimg

Create temporary nii.gz file for FSL
slice_duration-methods

Extract Image slice_duration attribute
slice_end-methods

Extract Image slice_end attribute
window_img

nifti image windower
writeNIfTI2

writeNIfTI with default non-reoirientation