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fslr (version 2.24.1)

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

500

Version

2.24.1

License

GPL-3

Maintainer

Last Published

August 5th, 2019

Functions in fslr (2.24.1)

cal.max-methods

Extract Image cal.max attribute

aux.file-methods

Extract Image aux.file attribute

descrip-methods

Extract Image descrip attribute

applytopup - calling FSL applytopup

Extract Image bitpix attribute

Determine of Q and S forms are consistent

cal.min-methods

Extract Image cal.min attribute

datatype-methods

Extract Image datatype attribute

data_type-methods

Extract Image data_type attribute

Eddy Current Correction

face_removal_mask

Face Removal Mask

Calculate Dice Coefficient of 2 Binary images

FSL Anatomical Processing Script

Enforce Either Qform or Sform is set

Logical AND with Images using FSL

Wrapper for getForms with filename

fnirt_with_affine

Register using FNIRT, but doing Affine Registration as well

FSL Change file type

Find FSL Version

fnirt_with_affine_apply

Applies FLIRT then FNIRT transformations

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

Absolute Value Image using FSL

Get FSL's Data Directory

fslchfiletype.help

fslchfiletype help

Binarize Image using FSL

FSL Command Wrapper

Log Transform Image using FSL

Get FSL's Directory

Dilate image using FSL

Edge Strength Image using FSL

Image Center of Gravity (FSL)

Fill image holes

Arc Cosine Transform Image using FSL

Use FSL's Brain Extraction Tool (BET)

Help for FSL BET

Index Image using FSL

FSL Copy Geometry

Replace NaNs in Image using FSL

Wrapper for getting fsl help

Erode image using FSL

Register using FLIRT

DTI Fitting Procedure from FSL

fsl_applywarp.help

FSL applywarp help

Eddy Current Correction

Apply Warp from FNIRT

Split images using FSL

Modulus Remainder of 2 Images using FSL

fslsmooth_in_mask

Smooth Image Within a Mask Only

fsl_biascorrect

FSL Bias Correct

Quick Tabulation for logical images

Apply Warp from FLIRT

Divide Images using FSL

Arc Tangent Transform Image using FSL

Exponentiate Image using FSL

Get FSL's Standard Data Directory

Scale Affine Matrix using avscale

Extract Image dim_ attribute

Register using FNIRT

fslreorient2std.help

fslreorient2std help

Get min/max of an image

Mask NaNs in Image using FSL

Multiply Images using FSL

Fill image holes with dilation then erosion

FSL Robust Field of View

FSL Motion Correction

Determine FSL output type

Determine extension of image based on FSLOUTPUTTYPE

Subtract Images using FSL

Merge images using FSL

Smoothness Estimation using smoothest

Get NIfTI header using FSL

Mask image using FSL

Perform OR/Union operation on Images using FSL

Reciprocal Image using FSL

Get range of an image

fslrobustfov.help

FSL Robust Field of View Help

Binarized Inverse Image using FSL

Add Images using FSL

Cosine Transform Image using FSL

mid_sagittal_align

Mid-Sagittal Plane Alignment

qform_code-methods

Extract Image qform_code attribute

Construct MNI Filename

Add Random Uniform Noise Image using FSL

Image Mean Entropy

Add Random Standard Gaussian Noise Image using FSL

Get FSL's Standard Data Directory

Arc Sine Transform Image using FSL

Gaussian smooth image using FSL

Square Image using FSL

FSL Volume in mL (or cubic centimeters)

Sine Transform Image using FSL

Image Standard Deviation

FSL Swap Dimensions

fslswapdim.help

fslswapdim help

Read FSL Transformation

Get Q and S Forms of orientation matrix

FSL Orientation Wrappers

Parse FSL Header

Register EPI images to Structural image

Wrapper for FSL Get Orientation

intent_name-methods

Extract Image intent_name attribute

get_quickshear_mask

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

slice_start-methods

Extract Image slice_start attribute

Get value from FSL header

qform,character-method

Extract NIfTI 3D Image Orientation

Square Root Image using FSL

Extract Image pixdim attribute

intent_p1-methods

Extract Image intent_p1 attribute

Probabilistic diffusion tractography with multiple fibre orientations

run_first_all.help

Run FIRST All Help

scl_inter-methods

Extract Image scl_inter attribute

FSL SUSAN noise reduction

intent_p3-methods

Extract Image intent_p3 attribute

intent_p2-methods

Extract Image intent_p2 attribute

Run MELODIC ICA

Create command declaring FSLDIR

Tangent Transform Image using FSL

Perform XOR/Exclusive Or operation on Images using FSL

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

Parse output from avscale

Read NIfTI file reoriented to RPI

Reorient an Image to RPI orientation

Convert a Transformation

reverse_rpi_orient

Reverse Reorientation an Image to RPI orientation

toffset-methods

Extract Image toffset attribute

Extract Image magic attribute

slice_duration-methods

Extract Image slice_duration attribute

fslreorient2std

FSL Orient to MNI

slice_end-methods

Extract Image slice_end attribute

topup - calling FSL topup

FSL Slice Timing Correction

Subsample image by factor of 2

Threshold an image

vox_offset-methods

Extract Image vox_offset attribute

Open image in FSLView

Logical check if FSL is accessible

Read MNI Filename

intent_code-methods

Extract Image intent_code attribute

scl_slope-methods

Extract Image scl_slope attribute

sform_code-methods

Extract Image sform_code attribute

sizeof_hdr-methods

Extract Image sizeof_hdr attribute

slice_code-methods

Extract Image slice_code attribute