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fslr (version 2.25.3)

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

Description

Wrapper functions that interface with 'FSL' , 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

413

Version

2.25.3

License

GPL-3

Maintainer

Last Published

May 10th, 2024

Functions in fslr (2.25.3)

dtifit

DTI Fitting Procedure from FSL
face_removal_mask

Face Removal Mask
eddy_correct

Eddy Current Correction
enforce_form

Enforce Either Qform or Sform is set
fnirt_with_affine

Register using FNIRT, but doing Affine Registration as well
fnirt

Register using FNIRT
fnirt.help

FNIRT help
fnirt_with_affine_apply

Applies FLIRT then FNIRT transformations
fast.help

FAST help
fsl_applywarp

Apply Warp from FNIRT
fsl_cluster

Form clusters, report information about clusters and/or perform cluster-based inference. Wrapper for cluster
fsl_dice

Calculate Dice Coefficient of 2 Binary images
fsl_anat

FSL Anatomical Processing Script
fsl_applywarp.help

FSL applywarp help
fsl_data_dir

Get FSL's Data Directory
flirt

Register using FLIRT
fsl_deface

Tool to deface a structural T1w image.
flirt.help

FLIRT help
fsl_anat.help

fsl_anat help
fsl_avscale

Scale Affine Matrix using avscale
fsladd.help

fsladd Help
fsl_std_dir

Get FSL's Standard Data Directory
fsl_atlas_dir

Get FSL's Standard Data Directory
fsl_tsplot

FSL Timeseries Plot using `fsl_tsplot` (not `tsplot`)
fslasin.help

fslasin Help
fsland

Logical AND with Images using FSL
flirt_apply

Apply Warp from FLIRT
fsl_bin

Binarize Image using FSL
fsl_asin

Arc Sine Transform Image using FSL
fslabs.help

fslabs Help
fsl_binv

Binarized Inverse Image using FSL
fsl_acos

Arc Cosine Transform Image using FSL
fslcmd

FSL Command Wrapper
fsl_biascorrect

FSL Bias Correct
fslbinv.help

fslbinv Help
fsl_resample

Resample an Image to Specific Voxel Size
fslcpgeom

FSL Copy Geometry
fsl_smoothest

Smoothness Estimation using smoothest
fsl_edge

Edge Strength Image using FSL
fsledge.help

fsledge Help
fslcpgeom.help

fslcpgeom help
fslatan.help

fslatan Help
fsl_atan

Arc Tangent Transform Image using FSL
fsl_bin_tab

Quick Tabulation for logical images
fsl_version

Find FSL Version
fsl_div

Divide Images using FSL
fsl_abs

Absolute Value Image using FSL
fslcog

Image Center of Gravity (FSL)
fsl_index

Index Image using FSL
fslhelp

Wrapper for getting fsl help
fsldiv.help

fsldiv Help
fsl_add

Add Images using FSL
fslentropy

Image Mean Entropy
fslacos.help

fslacos Help
fsl_dilate

Dilate image using FSL
fsl_erode

Erode image using FSL
fsl_bet

Use FSL's Brain Extraction Tool (BET)
fslbet.help

Help for FSL BET
fsldir

Get FSL's Directory
fslchfiletype

FSL Change file type
fslhd

Get NIfTI header using FSL
fslfill2

Fill image holes with dilation then erosion
fslbin.help

fslbin Help
fslchfiletype.help

fslchfiletype help
fslmax

Get min/max of an image
fslepi_reg

Register EPI images to Structural image
fsl_fill

Fill image holes
fslfill.help

fslfill Help
fslcos.help

fslcos Help
fslindex.help

fslindex Help
fsl_cos

Cosine Transform Image using FSL
fsl_exp

Exponentiate Image using FSL
fslgetorient

FSL Orientation Wrappers
fslhd.parse

Parse FSL Header
fslrecip.help

fslrecip Help
fslmask.help

fslmask Help
fslexp.help

fslexp Help
fslmean

Image Mean
fslorienter

Wrapper for FSL Get Orientation
fslsqr.help

fslsqr Help
fsl_rem

Modulus Remainder of 2 Images using FSL
fslerode.help

fslerode Help
fslhd.help

FSLhd help
fslmaths.help

FSL Maths Help
fslsd

Image Standard Deviation
fsl_rand

Add Random Uniform Noise Image using FSL
fslrand.help

fslrand Help
fsl_merge

Merge images using FSL
fslsplit.help

FSL Split help
fsl_sqr

Square Image using FSL
fsl_mul

Multiply Images using FSL
fsl_sqrt

Square Root Image using FSL
fslval

Get value from FSL header
fsl_maths

FSL Maths
fslthresh.help

fslthresh Help
fslsin

Sine Transform Image using FSL
fsl_thresh

Threshold an image
fslmerge.help

FSLMerge help
fslorient

FSL Orient
fslrandn.help

fslrandn Help
fslor

Perform OR/Union operation on Images using FSL
fslorient.help

fslorient help
fsl_randn

Add Random Standard Gaussian Noise Image using FSL
fslslicetimer

FSL Slice Timing Correction
fslrange

Get range of an image
fsllog.help

fsllog Help
fslnanm.help

fslnanm Help
fslsmooth.help

fslsmooth Help
fslmul.help

fslmul Help
fsl_nan

Replace NaNs in Image using FSL
fslsin.help

fslsin Help
fsl_log

Log Transform Image using FSL
fsl_mask

Mask image using FSL
fsl_smooth

Gaussian smooth image using FSL
fsl_recip

Reciprocal Image using FSL
fslstats.help

FSL Stats Help
fsl_sub

Subtract Images using FSL
fsltan.help

fsltan Help
fslval.help

fslval help
fsl_nanm

Mask NaNs in Image using FSL
fslsmooth_in_mask

Smooth Image Within a Mask Only
fslrobustfov.help

FSL Robust Field of View Help
fsl_tan

Tangent Transform Image using FSL
get.imgext

Determine extension of image based on FSLOUTPUTTYPE
fslnan.help

fslnan Help
get.fsloutput

Determine FSL output type
fslroi

FSL ROI
fslrem.help

fslrem Help
intent_p2-methods

Extract Image intent_p2 attribute
fslxor

Perform XOR/Exclusive Or operation on Images using FSL
intent_p3-methods

Extract Image intent_p3 attribute
fsl_swapdim

FSL Swap Dimensions
fslsplit

Split images using FSL
fslswapdim.help

fslswapdim help
qform,character-method

Extract NIfTI 3D Image Orientation
pixdim-methods

Extract Image pixdim attribute
sizeof_hdr-methods

Extract Image sizeof_hdr attribute
slice_code-methods

Extract Image slice_code attribute
fslsub.help

fslsub Help
probtrackx

Probabilistic diffusion tractography with multiple fibre orientations
parse_avscale

Parse output from avscale
fsl_sub2

Subsample image by factor of 2
get.fsl

Create command declaring FSLDIR
getForms

Get Q and S Forms of orientation matrix
get_quickshear_mask

Face Removal Mask using "Quickshear Defacing for Neuroimages" (Schimke et al. 2011)
fslview.help

FSLView help
have.fsl

Logical check if FSL is accessible
rpi_orient

Reorient an Image to RPI orientation
invert_xfm

Convert a Transformation
magic-methods

Extract Image magic attribute
fslview

Open image in FSLView
melodic

Run MELODIC ICA
intent_code-methods

Extract Image intent_code attribute
mcflirt.help

MCFLIRT help
run_first_all

Run FIRST All
fslreorient2std

FSL Orient to MNI
reverse_rpi_orient

Reverse Reorientation an Image to RPI orientation
scl_slope-methods

Extract Image scl_slope attribute
fslreorient2std.help

fslreorient2std help
mcflirt

FSL Motion Correction
read_xfm

Read FSL Transformation
susan

FSL SUSAN noise reduction
mid_sagittal_align

Mid-Sagittal Plane Alignment
readrpi

Read NIfTI file reoriented to RPI
slice_end-methods

Extract Image slice_end attribute
slice_duration-methods

Extract Image slice_duration attribute
qform_code-methods

Extract Image qform_code attribute
melodic.help

MELODIC help
slice_start-methods

Extract Image slice_start attribute
mni_fname

Construct MNI Filename
run_first_all.help

Run FIRST All Help
sform_code-methods

Extract Image sform_code attribute
vox_offset-methods

Extract Image vox_offset attribute
fslstats

FSL Stats
fslsum

FSL Sum
topup

topup - calling FSL topup
fslrobustfov

FSL Robust Field of View
intent_name-methods

Extract Image intent_name attribute
scl_inter-methods

Extract Image scl_inter attribute
mni_img

Read MNI Filename
mridefacer

MRI Defacer
fslvol

FSL Volume in mL (or cubic centimeters)
fslsub2.help

fslsub2 Help
fslsqrt.help

fslsqrt Help
fslvolume

Image Volume
intent_p1-methods

Extract Image intent_p1 attribute
toffset-methods

Extract Image toffset attribute
susan.help

FSL SUSAN Help
xfibres

Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques with Crossing Fibers
cal.min-methods

Extract Image cal.min attribute
aux.file-methods

Extract Image aux.file attribute
applytopup

applytopup - calling FSL applytopup
descrip-methods

Extract Image descrip attribute
checkout

Determine of Q and S forms are consistent
cal.max-methods

Extract Image cal.max attribute
datatype-methods

Extract Image datatype attribute
check_file

Wrapper for getForms with filename
data_type-methods

Extract Image data_type attribute
bitpix-methods

Extract Image bitpix attribute
fast

FSL FAST
download_fsl

Download FSL
dim_-methods

Extract Image dim_ attribute
eddy

Eddy Current Correction