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fslr (version 2.25.2)

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

433

Version

2.25.2

License

GPL-3

Maintainer

John Muschelli

Last Published

August 25th, 2022

Functions in fslr (2.25.2)

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Determine of Q and S forms are consistent
datatype-methods

Extract Image datatype attribute
bitpix-methods

Extract Image bitpix attribute
data_type-methods

Extract Image data_type attribute
cal.min-methods

Extract Image cal.min attribute
cal.max-methods

Extract Image cal.max attribute
applytopup

applytopup - calling FSL applytopup
descrip-methods

Extract Image descrip attribute
check_file

Wrapper for getForms with filename
eddy_correct

Eddy Current Correction
dtifit

DTI Fitting Procedure from FSL
face_removal_mask

Face Removal Mask
fast

FSL FAST
flirt

Register using FLIRT
fsl_anat

FSL Anatomical Processing Script
fast.help

FAST help
fsl_applywarp.help

FSL applywarp help
fnirt

Register using FNIRT
fsl_resample

Resample an Image to Specific Voxel Size
fsl_cluster

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

Scale Affine Matrix using avscale
fsl_applywarp

Apply Warp from FNIRT
fsl_anat.help

fsl_anat help
fsl_atlas_dir

Get FSL's Standard Data Directory
fsl_bin_tab

Quick Tabulation for logical images
fsl_biascorrect

FSL Bias Correct
enforce_form

Enforce Either Qform or Sform is set
aux.file-methods

Extract Image aux.file attribute
fnirt.help

FNIRT help
eddy

Eddy Current Correction
download_fsl

Download FSL
dim_-methods

Extract Image dim_ attribute
flirt.help

FLIRT help
fsl_smoothest

Smoothness Estimation using smoothest
flirt_apply

Apply Warp from FLIRT
fslacos.help

fslacos Help
fsl_acos

Arc Cosine Transform Image using FSL
fslabs.help

fslabs Help
fsl_add

Add Images using FSL
fnirt_with_affine_apply

Applies FLIRT then FNIRT transformations
fsland

Logical AND with Images using FSL
fsl_data_dir

Get FSL's Data Directory
fsl_deface

Tool to deface a structural T1w image.
fsl_dice

Calculate Dice Coefficient of 2 Binary images
fnirt_with_affine

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

fsladd Help
fsl_tsplot

FSL Timeseries Plot using `fsl_tsplot` (not `tsplot`)
fsl_std_dir

Get FSL's Standard Data Directory
fsl_bet

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

Help for FSL BET
fslcos.help

fslcos Help
fsl_binv

Binarized Inverse Image using FSL
fslcpgeom

FSL Copy Geometry
fslbinv.help

fslbinv Help
fsl_cos

Cosine Transform Image using FSL
fsl_atan

Arc Tangent Transform Image using FSL
fsl_abs

Absolute Value Image using FSL
fsl_asin

Arc Sine Transform Image using FSL
fslcmd

FSL Command Wrapper
fsl_version

Find FSL Version
fslcog

Image Center of Gravity (FSL)
fsl_bin

Binarize Image using FSL
fslasin.help

fslasin Help
fsl_erode

Erode image using FSL
fslerode.help

fslerode Help
fsl_edge

Edge Strength Image using FSL
fsl_log

Log Transform Image using FSL
fslindex.help

fslindex Help
fslfill.help

fslfill Help
fsl_fill

Fill image holes
fslbin.help

fslbin Help
fsledge.help

fsledge Help
fslexp.help

fslexp Help
fsl_exp

Exponentiate Image using FSL
fsldir

Get FSL's Directory
fslmask.help

fslmask Help
fsl_dilate

Dilate image using FSL
fsl_maths

FSL Maths
fslentropy

Image Mean Entropy
fslhelp

Wrapper for getting fsl help
fslepi_reg

Register EPI images to Structural image
fsl_div

Divide Images using FSL
fslfill2

Fill image holes with dilation then erosion
fslhd

Get NIfTI header using FSL
fslmaths.help

FSL Maths Help
fsldiv.help

fsldiv Help
fsl_index

Index Image using FSL
fslnanm.help

fslnanm Help
fslmerge.help

FSLMerge help
fslatan.help

fslatan Help
fsl_merge

Merge images using FSL
fslor

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

fslcpgeom help
fslnan.help

fslnan Help
fslhd.help

FSLhd help
fslchfiletype.help

fslchfiletype help
fsllog.help

fsllog Help
fsl_rem

Modulus Remainder of 2 Images using FSL
fslrecip.help

fslrecip Help
fslchfiletype

FSL Change file type
fslgetorient

FSL Orientation Wrappers
fsl_nanm

Mask NaNs in Image using FSL
fslhd.parse

Parse FSL Header
fsl_mask

Mask image using FSL
fsl_rand

Add Random Uniform Noise Image using FSL
fslmean

Image Mean
fslsin.help

fslsin Help
fslsplit

Split images using FSL
fslsmooth_in_mask

Smooth Image Within a Mask Only
fslslicetimer

FSL Slice Timing Correction
fslrange

Get range of an image
fslreorient2std.help

fslreorient2std help
fslmax

Get min/max of an image
fslorient

FSL Orient
fslrobustfov

FSL Robust Field of View
fsl_mul

Multiply Images using FSL
fslrem.help

fslrem Help
fslrand.help

fslrand Help
fslsmooth.help

fslsmooth Help
fsl_recip

Reciprocal Image using FSL
fslsplit.help

FSL Split help
fsl_smooth

Gaussian smooth image using FSL
fslswapdim.help

fslswapdim help
fslreorient2std

FSL Orient to MNI
fsl_swapdim

FSL Swap Dimensions
fslval

Get value from FSL header
fslsum

FSL Sum
fsl_sqr

Square Image using FSL
fslsub2.help

fslsub2 Help
fslorienter

Wrapper for FSL Get Orientation
fslsqrt.help

fslsqrt Help
fslthresh.help

fslthresh Help
fslview

Open image in FSLView
fslview.help

FSLView help
get.fsloutput

Determine FSL output type
get.imgext

Determine extension of image based on FSLOUTPUTTYPE
fsl_thresh

Threshold an image
invert_xfm

Convert a Transformation
magic-methods

Extract Image magic attribute
fslrobustfov.help

FSL Robust Field of View Help
fslroi

FSL ROI
fsl_nan

Replace NaNs in Image using FSL
fslstats.help

FSL Stats Help
fslval.help

fslval help
fslmul.help

fslmul Help
fsl_tan

Tangent Transform Image using FSL
mni_img

Read MNI Filename
fslorient.help

fslorient help
fslstats

FSL Stats
have.fsl

Logical check if FSL is accessible
getForms

Get Q and S Forms of orientation matrix
get_quickshear_mask

Face Removal Mask using "Quickshear Defacing for Neuroimages" (Schimke et al. 2011)
intent_code-methods

Extract Image intent_code attribute
fsl_sqrt

Square Root Image using FSL
mid_sagittal_align

Mid-Sagittal Plane Alignment
fsl_randn

Add Random Standard Gaussian Noise Image using FSL
mni_fname

Construct MNI Filename
mridefacer

MRI Defacer
fsl_sub

Subtract Images using FSL
fslxor

Perform XOR/Exclusive Or operation on Images using FSL
fsltan.help

fsltan Help
intent_p3-methods

Extract Image intent_p3 attribute
intent_p2-methods

Extract Image intent_p2 attribute
get.fsl

Create command declaring FSLDIR
qform,character-method

Extract NIfTI 3D Image Orientation
parse_avscale

Parse output from avscale
mcflirt

FSL Motion Correction
mcflirt.help

MCFLIRT help
fslsd

Image Standard Deviation
fslvol

FSL Volume in mL (or cubic centimeters)
fsl_sub2

Subsample image by factor of 2
fslsqr.help

fslsqr Help
fslsub.help

fslsub Help
melodic.help

MELODIC help
fslvolume

Image Volume
readrpi

Read NIfTI file reoriented to RPI
intent_p1-methods

Extract Image intent_p1 attribute
melodic

Run MELODIC ICA
probtrackx

Probabilistic diffusion tractography with multiple fibre orientations
pixdim-methods

Extract Image pixdim attribute
read_xfm

Read FSL Transformation
rpi_orient

Reorient an Image to RPI orientation
slice_duration-methods

Extract Image slice_duration attribute
scl_slope-methods

Extract Image scl_slope attribute
fslsin

Sine Transform Image using FSL
fslrandn.help

fslrandn Help
susan.help

FSL SUSAN Help
intent_name-methods

Extract Image intent_name attribute
reverse_rpi_orient

Reverse Reorientation an Image to RPI orientation
qform_code-methods

Extract Image qform_code attribute
slice_end-methods

Extract Image slice_end attribute
scl_inter-methods

Extract Image scl_inter attribute
run_first_all.help

Run FIRST All Help
slice_start-methods

Extract Image slice_start attribute
sform_code-methods

Extract Image sform_code attribute
run_first_all

Run FIRST All
susan

FSL SUSAN noise reduction
xfibres

Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques with Crossing Fibers
sizeof_hdr-methods

Extract Image sizeof_hdr attribute
toffset-methods

Extract Image toffset attribute
slice_code-methods

Extract Image slice_code attribute
topup

topup - calling FSL topup
vox_offset-methods

Extract Image vox_offset attribute