Type:	Package
Title:	Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')
Version:	2.25.3
Maintainer:	John Muschelli <muschellij2@gmail.com>
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.
Imports:	methods, R.utils, graphics, grDevices, stats, utils
Depends:	oro.nifti (≥ 0.5.0), neurobase (≥ 1.32.0), R (≥ 3.2.0)
License:	GPL-3
VignetteBuilder:	knitr
Suggests:	knitr, rmarkdown, covr
BugReports:	https://github.com/muschellij2/fslr/issues
SystemRequirements:	FSL
Encoding:	UTF-8
RoxygenNote:	7.3.1
NeedsCompilation:	no
Packaged:	2024-05-09 19:19:02 UTC; johnmuschelli
Author:	John Muschelli [aut, cre]
Repository:	CRAN
Date/Publication:	2024-05-10 04:20:02 UTC

applytopup - calling FSL applytopup

Description

A tool for applying and correcting estimated susceptibility induced distortions

Usage

applytopup(
  infile,
  datain,
  index,
  topup_files,
  out = NULL,
  method = c("lsr", "jac"),
  interp = c("spline", "trilinear"),
  verbose = TRUE
)

apply_topup(...)

fsl_applytopup(...)

Arguments

Extract Image aux.file attribute

Description

aux_file method for character types

Usage

## S4 method for signature 'character'
aux.file(object)

Arguments

Extract Image bitpix attribute

Description

bitpix method for character types

Usage

## S4 method for signature 'character'
bitpix(object)

Arguments

Extract Image cal.max attribute

Description

cal_max method for character types

Usage

## S4 method for signature 'character'
cal.max(object)

Arguments

Extract Image cal.min attribute

Description

cal_min method for character types

Usage

## S4 method for signature 'character'
cal.min(object)

Arguments

Wrapper for getForms with filename

Description

Checking the q/s-forms for a header

Usage

check_file(file, ...)

Arguments

Value

result of checkout

Examples

library(fslr)
if (have.fsl()){
 mnifile = mni_fname("2")
 check_file(mnifile)
} 

Determine of Q and S forms are consistent

Description

This function determines if the determinants of the sform and qform have the same sign

Usage

checkout(hd)

Arguments

Value

logical indicating if sform and qform consistent

Examples

if (have.fsl()){
 mnifile = file.path(fsldir(), "data", "standard", 
   "MNI152_T1_2mm.nii.gz")
 forms = getForms(mnifile)
 checkout(forms)
} 

Extract Image data_type attribute

Description

data_type method for character types

Usage

## S4 method for signature 'character'
data_type(object)

Arguments

Extract Image datatype attribute

Description

datatype method for character types

Usage

## S4 method for signature 'character'
datatype(object)

Arguments

Extract Image descrip attribute

Description

descrip method for character types

Usage

## S4 method for signature 'character'
descrip(object)

Arguments

Extract Image dim_ attribute

Description

dim_ method for class character

Usage

## S4 method for signature 'character'
dim_(object)

Arguments

Download FSL

Description

Download FSL Tarball

Usage

download_fsl(
  os = c("macosx", "redhat5", "redhat6", "centos5", "centos6", "debian", "ubuntu"),
  outdir = tempdir(),
  overwrite = TRUE,
  ...
)

Arguments

Value

Filename of destination file

DTI Fitting Procedure from FSL

Description

Calls dtifit from FSL

Usage

dtifit(
  infile,
  bvecs,
  bvals,
  mask = NULL,
  outprefix = NULL,
  opts = "",
  bet.opts = "",
  verbose = TRUE,
  sse = FALSE,
  save_tensor = FALSE,
  grad_image = NULL
)

Arguments

Value

Vector of character filenames of output. See Note

Note

On successful completion of the command, the following files will be output, which are: mask - the mask used in the analysis outprefix_V1 - 1st eigenvector outprefix_V2 - 2nd eigenvector outprefix_V3 - 3rd eigenvector outprefix_L1 - 1st eigenvalue outprefix_L2 - 2nd eigenvalue outprefix_L3 - 3rd eigenvalue outprefix_MD - mean diffusivity outprefix_FA - fractional anisotropy outprefix_MO - mode of the anisotropy (oblate ~ -1; isotropic ~ 0; prolate ~ 1) outprefix_S0 - raw T2 signal with no diffusion weighting optional output If sse = TRUE, then the additional file will be present: outprefix_sse - Sum of squared error If save_tensor = TRUE, then the additional file will be present: outprefix_tensor - tensor as a 4D file in this order: Dxx,Dxy,Dxz,Dyy,Dyz,Dzz

Eddy Current Correction

Description

This function calls eddy from FSL for DTI Processing

Usage

eddy(
  infile,
  mask,
  acq_file,
  index_file,
  bvecs,
  bvals,
  topup = NULL,
  outfile = NULL,
  retimg = TRUE,
  opts = "",
  verbose = TRUE,
  eddy_cmd = c("eddy", "eddy_openmp", "eddy_cuda"),
  ...
)

Arguments

Value

Result from system command currently

Eddy Current Correction

Description

This function calls eddy_correct from FSL for DTI Processing

Usage

eddy_correct(infile, outfile = NULL, retimg = TRUE, reference_no = 0, ...)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Enforce Either Qform or Sform is set

Description

Enforce Either Qform or Sform is set

Usage

enforce_form(file, ...)

Arguments

Value

A character filename

Examples

if (have_fsl()) {
res = enforce_form(mni_fname())
}

Face Removal Mask

Description

Face Removal Mask

Usage

face_removal_mask(
  file,
  template = mni_fname(mm = "1"),
  face_mask = mni_face_fname(mm = "1"),
  outfile = NULL,
  dof = 12,
  cost = "mutualinfo",
  retimg = FALSE
)

deface_image(file, ...)

Arguments

Value

An image or filename depending on retimg

Examples

if (have_fsl()) {
   file = "~/Downloads/sample_T1_input.nii.gz"
   if (file.exists(file)) {
       mask = face_removal_mask(file = file,
         template = NULL, face_mask = NULL)
       image = fslmask(file, mask)
   }
}

FSL FAST

Description

This function calls fast from FSL

Usage

fast(
  file,
  outfile = NULL,
  bias_correct = TRUE,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  type = c("T1", "T2", "PD"),
  out_type = c("seg", "mixeltype", "pve_0", "pve_1", "pve_2", "pveseg"),
  verbose = TRUE,
  all_images = FALSE,
  ...
)

fast_all(..., all_images = TRUE)

fast_nobias_all(..., bias_correct = FALSE, all_images = FALSE)

fsl_fast(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslfast(...)

fsl_fast_nobias(
  ...,
  bias_correct = FALSE,
  outfile = tempfile(fileext = ".nii.gz"),
  retimg = FALSE
)

fast_nobias(..., bias_correct = FALSE)

fslfast_nobias(..., bias_correct = FALSE)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

FAST help

Description

This function calls fast's help

Usage

fast.help()

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fast.help()
}

Register using FLIRT

Description

This function calls flirt to register infile to reffile and either saves the image or returns an object of class nifti, along with the transformation matrix omat

Usage

flirt(
  infile,
  reffile,
  omat = NULL,
  dof = 6,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

character or logical depending on intern

FLIRT help

Description

This function calls flirt's help

Usage

flirt.help()

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 flirt.help()
} 

Apply Warp from FLIRT

Description

This function applies a matrix from flirt to other images

Usage

flirt_apply(
  infile,
  reffile,
  initmat,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

character or logical depending on intern

Register using FNIRT

Description

This function calls fnirt to register infile to reffile and either saves the image or returns an object of class nifti

Usage

fnirt(
  infile,
  reffile,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

character or logical depending on intern

FNIRT help

Description

This function calls fnirt's help

Usage

fnirt.help()

Value

Prints help output and returns output as character vector

Register using FNIRT, but doing Affine Registration as well

Description

This function calls fnirt to register infile to reffile and either saves the image or returns an object of class nifti, but does the affine registration first

Usage

fnirt_with_affine(
  infile,
  reffile,
  flirt.omat = NULL,
  flirt.outfile = NULL,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  flirt.opts = "",
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

character or logical depending on intern

Applies FLIRT then FNIRT transformations

Description

Applies an affine transformation with FLIRT then the warp image with FNIRT

Usage

fnirt_with_affine_apply(
  infile,
  reffile,
  flirt.omat = NULL,
  flirt.outfile = NULL,
  fnirt.warpfile = NULL,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  flirt.opts = "",
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

character or logical depending on intern

See Also

fnirt_with_affine

Absolute Value Image using FSL

Description

This function calls fslmaths -abs. The R functions wraps fslmaths

Usage

fsl_abs(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslabs(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Arc Cosine Transform Image using FSL

Description

This function calls fslmaths -acos. The R functions wraps fslmaths

Usage

fsl_acos(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslacos(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Add Images using FSL

Description

This function calls fslmaths -add. The R functions wraps fslmaths

Usage

fsl_add(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fsladd(
  file,
  file2,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

FSL Anatomical Processing Script

Description

This function calls fsl_anat from FSL

Usage

fsl_anat(
  file,
  modality = c("T1", "T2", "PD"),
  outdir = NULL,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

Result from system command, depends if intern is TRUE or FALSE.

fsl_anat help

Description

This function calls fsl_anat's help

Usage

fsl_anat.help()

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fsl_anat.help()
}

Apply Warp from FNIRT

Description

This function applies a coefficient map from fnirt to other images

Usage

fsl_applywarp(
  infile,
  reffile,
  warpfile,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

character or logical depending on intern

FSL applywarp help

Description

This function calls applywarp's help

Usage

fsl_applywarp.help()

Value

Prints help output and returns output as character vector

Arc Sine Transform Image using FSL

Description

This function calls fslmaths -asin. The R functions wraps fslmaths

Usage

fsl_asin(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslasin(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Arc Tangent Transform Image using FSL

Description

This function calls fslmaths -atan. The R functions wraps fslmaths

Usage

fsl_atan(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslatan(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Get FSL's Standard Data Directory

Description

Finds the FSLDIR from system environment or getOption("fsl.path") and pastes on “data/standard”

Usage

fsl_atlas_dir()

Value

Character path

Scale Affine Matrix using avscale

Description

This function calls avscale to get individual matrices for FSL

Usage

fsl_avscale(file, volume = NULL, parsed = TRUE, verbose = TRUE)

avscale(...)

Arguments

Value

Character of information from avscale

Use FSL's Brain Extraction Tool (BET)

Description

This function calls bet to extract a brain from an image, usually for skull stripping.

Usage

fsl_bet(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslbet(
  infile,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  betcmd = c("bet2", "bet"),
  verbose = TRUE,
  ...
)

Arguments

Value

character or logical depending on intern

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

FSL Bias Correct

Description

This function wraps a call to fast that performs bias correction

Usage

fsl_biascorrect(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  remove.seg = TRUE,
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Binarize Image using FSL

Description

This function calls fslmaths -bin. The R functions wraps fslmaths

Usage

fsl_bin(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslbin(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Examples

  set.seed(5)
dims = rep(10, 3)
arr = array(rnorm(prod(dims)), dim = dims)
nim = oro.nifti::nifti(arr)
if (have.fsl()){
 fslbin(nim)
 fsl_bin(nim)
 }

Quick Tabulation for logical images

Description

Creates a 2 by 2 table for

Usage

fsl_bin_tab(x, y, dnames = c("x", "y"), verbose = FALSE)

Arguments

Value

table of x vs y

Note

fsl_bin will be run to make these images binary before running

Binarized Inverse Image using FSL

Description

This function calls fslmaths -binv. The R functions wraps fslmaths

Usage

fsl_binv(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslbinv(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

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

Description

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

Usage

fsl_cluster(
  file,
  threshold,
  retimg = FALSE,
  reorient = FALSE,
  opts = "",
  cope_image = NULL,
  pthresh = NULL,
  peakdist = 0,
  volume = FALSE,
  smooth_est = NULL,
  voxel_resel = NULL,
  fractional = FALSE,
  connectivity = 26,
  mm = FALSE,
  find_minima = FALSE,
  standard_image = NULL,
  verbose = TRUE,
  ...
)

fslcluster(..., retimg = TRUE)

read_cluster_table(file)

Arguments

Value

A list of filenames of outputs and tables:

• opvals filename for image output of log pvals

• oindex filename for output of cluster index (in size order)

• othresh filename for output of thresholded image

• olmax filename for output of local maxima text file

• olmaxim filename for output of local maxima volume

• osize filename for output of size image

• omax filename for output of max image

• omean filename for output of mean image

Examples

if (have_fsl()) { 
file = mni_fname(brain = TRUE, mask = FALSE)
threshold = 6000
clus = fsl_cluster(file, threshold)
}

Cosine Transform Image using FSL

Description

This function calls fslmaths -cos. The R functions wraps fslmaths

Usage

fsl_cos(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslcos(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Get FSL's Data Directory

Description

Finds the FSLDIR from system environment or getOption("fsl.path") and pastes on “data”

Usage

fsl_data_dir()

Value

Character path

Tool to deface a structural T1w image.

Description

Tool to deface a structural T1w image.

Usage

fsl_deface(
  file,
  outfile = NULL,
  retimg = TRUE,
  opts = "",
  deface_cropped = FALSE,
  bet_fractional_intensity = NULL,
  bias_correct = FALSE,
  shift_xyz = NULL,
  cog_xyz = NULL,
  reorient = FALSE,
  intern = FALSE,
  verbose = TRUE,
  ...
)

Arguments

Examples

if (have_fsl()) {
  file = mni_fname(mm = 1, brain = FALSE)
  out = fsl_deface(file, retimg = FALSE)
}

Calculate Dice Coefficient of 2 Binary images

Description

Creates a 2 by 2 table for

Usage

fsl_dice(x, y, ...)

Arguments

Value

Single number of the dice coefficient

Dilate image using FSL

Description

This function calls fslmaths -ero after inverting the image to dilate an image with either the default FSL kernel or the kernel specified in kopts. The function either saves the image or returns an object of class nifti.

Usage

fsl_dilate(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fsldilate(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  kopts = "",
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

Result from system command, depends if intern is TRUE or FALSE. If retimg is TRUE, then the image will be returned.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Examples

if (have.fsl()){
system.time({
dims = c(50, 50, 20)
x = array(rnorm(prod(dims)), dim = dims) 
img = nifti(x, dim= dims, 
datatype = convert.datatype()$FLOAT32, cal.min = min(x), 
cal.max = max(x), pixdim = rep(1, 4))
mask = img > .5
dilated = fsldilate(mask, kopts = "-kernel boxv 5", retimg=TRUE)
})
}    

Divide Images using FSL

Description

This function calls fslmaths -div. The R functions wraps fslmaths

Usage

fsl_div(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fsldiv(
  file,
  file2,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Edge Strength Image using FSL

Description

This function calls fslmaths -edge. The R functions wraps fslmaths

Usage

fsl_edge(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fsledge(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Erode image using FSL

Description

This function calls fslmaths -ero to erode an image with either the default FSL kernel or the kernel specified in kopts. The function either saves the image or returns an object of class nifti.

Usage

fsl_erode(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslerode(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  kopts = "",
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

Result from system command, depends if intern is TRUE or FALSE. If retimg is TRUE, then the image will be returned.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Examples

if (have.fsl()){
system.time({
dims = c(50, 50, 20)
x = array(rnorm(prod(dims)), dim = dims) 
img = nifti(x, dim= dims, 
datatype = convert.datatype()$FLOAT32, cal.min = min(x), 
cal.max = max(x), pixdim = rep(1, 4))
mask = img > .5
eroded = fslerode(mask, kopts = "-kernel boxv 5", retimg=TRUE)
})
}    

Exponentiate Image using FSL

Description

This function calls fslmaths -exp. The R functions wraps fslmaths

Usage

fsl_exp(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslexp(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Fill image holes

Description

This function calls fslmaths -fillh to fill in image holes and either saves the image or returns an object of class nifti

Usage

fsl_fill(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslfill(
  file,
  outfile = NULL,
  bin = TRUE,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  verbose = TRUE,
  ...
)

Arguments

Value

character or logical depending on intern

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Examples

if (have.fsl()){
system.time({
dims = c(50, 50, 20)
x = array(rnorm(prod(dims)), dim = dims) 
img = nifti(x, dim= dims, 
datatype = convert.datatype()$FLOAT32, cal.min = min(x), 
cal.max = max(x), pixdim = rep(1, 4))
mask = img > .5
eroded = fslerode(mask, kopts = "-kernel boxv 5", retimg=TRUE)
filled = fslfill(eroded, retimg= TRUE)
})
}  

Index Image using FSL

Description

This function calls fslmaths -index. The R functions wraps fslmaths

Usage

fsl_index(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslindex(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Log Transform Image using FSL

Description

This function calls fslmaths -log. The R functions wraps fslmaths

Usage

fsl_log(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fsllog(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Mask image using FSL

Description

This function calls fslmaths -mas to mask an image from an image mask and either saves the image or returns an object of class nifti

Usage

fsl_mask(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslmask(
  file,
  mask,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Examples

if (have.fsl()){
system.time({
x = array(rnorm(1e5), dim = c(100, 100, 10))
img = nifti(x, dim= c(100, 100, 10), 
datatype = convert.datatype()$FLOAT32, cal.min = min(x), 
cal.max = max(x), pixdim = rep(1, 4))
mask = img > .5
masked = fslmask(img, mask = mask, retimg=TRUE)
})
} 

FSL Maths

Description

This function calls fslmaths

Usage

fsl_maths(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslmaths(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Merge images using FSL

Description

This function calls fslmerge to merge files on some dimension and either saves the image or returns an object of class nifti

Usage

fsl_merge(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslmerge(
  infiles,
  direction = c("x", "y", "z", "t", "a"),
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  verbose = TRUE,
  ...
)

Arguments

Value

character or logical depending on intern

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Multiply Images using FSL

Description

This function calls fslmaths -mul. The R functions wraps fslmaths

Usage

fsl_mul(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslmul(
  file,
  file2,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Replace NaNs in Image using FSL

Description

This function calls fslmaths -nan. The R functions wraps fslmaths

Usage

fsl_nan(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslnan(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Mask NaNs in Image using FSL

Description

This function calls fslmaths -nanm. The R functions wraps fslmaths

Usage

fsl_nanm(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslnanm(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Add Random Uniform Noise Image using FSL

Description

This function calls fslmaths -rand. The R functions wraps fslmaths

Usage

fsl_rand(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslrand(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Add Random Standard Gaussian Noise Image using FSL

Description

This function calls fslmaths -randn. The R functions wraps fslmaths

Usage

fsl_randn(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslrandn(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Reciprocal Image using FSL

Description

This function calls fslmaths -recip. The R functions wraps fslmaths

Usage

fsl_recip(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslrecip(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Modulus Remainder of 2 Images using FSL

Description

This function calls fslmaths -rem. The R functions wraps fslmaths

Usage

fsl_rem(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslrem(
  file,
  file2,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Resample an Image to Specific Voxel Size

Description

Resample an Image to Specific Voxel Size

Usage

fsl_resample(
  file,
  voxel_size,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  opts = NULL,
  verbose = TRUE
)

Arguments

Value

If retimg then object of class nifti. Otherwise, the output file.

Examples

if (have_fsl()) {
file = mni_fname(mm = 1, brain = TRUE)
est2 = fsl_resample(file = file, voxel_size = 1, retimg = FALSE)
pixdim(est2)
est = fsl_resample(file = file, voxel_size = 1)
pixdim(est)
}

Gaussian smooth image using FSL

Description

This function calls fslmaths -s to smooth an image and either saves the image or returns an object of class nifti

Usage

fsl_smooth(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslsmooth(
  file,
  sigma = 10,
  mask = NULL,
  smooth_mask = TRUE,
  smoothed_mask = NULL,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  verbose = TRUE,
  ...
)

Arguments

Value

Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Examples

if (have.fsl()){
system.time({
dims = c(50, 50, 20)
x = array(rnorm(prod(dims)), dim = dims)
img = nifti(x, dim= dims, 
datatype = convert.datatype()$FLOAT32, cal.min = min(x), 
cal.max = max(x), pixdim = rep(1, 4))
s.img = fslsmooth(img, retimg=TRUE)
})
}

Smoothness Estimation using smoothest

Description

Smoothness Estimation using smoothest

Usage

fsl_smoothest(
  file,
  residual_image,
  z_image,
  dof = NULL,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

An output of smoothness estimate

Examples

if (have_fsl()) {
file = mni_fname(mm = 2, brain = TRUE, mask = TRUE)
img = mni_img(mm = 2, brain = TRUE, mask = FALSE)
mask = mni_img(mm = 2, brain = TRUE, mask = TRUE)
img = zscore_img(img = img, mask = mask)
est = fsl_smoothest(file = file, z_image = img)
}

Square Image using FSL

Description

This function calls fslmaths -sqr. The R functions wraps fslmaths

Usage

fsl_sqr(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslsqr(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Square Root Image using FSL

Description

This function calls fslmaths -sqrt. The R functions wraps fslmaths

Usage

fsl_sqrt(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslsqrt(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Get FSL's Standard Data Directory

Description

Finds the FSLDIR from system environment or getOption("fsl.path") and pastes on “data/standard”

Usage

fsl_std_dir()

fsl_std_file(file = NULL)

Arguments

Value

Character path

Subtract Images using FSL

Description

This function calls fslmaths -sub. The R functions wraps fslmaths

Usage

fsl_sub(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslsub(
  file,
  file2,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Subsample image by factor of 2

Description

This function calls fslmaths -subsamp2 to subsample an image and either saves the image or returns an object of class nifti

Usage

fsl_sub2(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslsub2(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  verbose = TRUE,
  ...
)

Arguments

Value

character or logical depending on intern

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Examples

if (have.fsl()){
system.time({
x = array(rnorm(1e6), dim = c(100, 100, 100))
img = nifti(x, dim= c(100, 100, 100), 
datatype = convert.datatype()$FLOAT32, cal.min = min(x), 
cal.max = max(x), pixdim = rep(1, 4))
subsamp = fslsub2(img, retimg=TRUE)
print(voxdim(subsamp))
})
} 

FSL Swap Dimensions

Description

This function calls fslswapdim

Usage

fsl_swapdim(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslswapdim(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  a = "x",
  b = "y",
  c = "z",
  verbose = TRUE,
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Tangent Transform Image using FSL

Description

This function calls fslmaths -tan. The R functions wraps fslmaths

Usage

fsl_tan(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fsltan(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Threshold an image

Description

This function calls fslmaths -thr -uthr to threshold an image and either saves the image or returns an object of class nifti

Usage

fsl_thresh(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslthresh(
  file,
  outfile = NULL,
  thresh = 0,
  uthresh = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

character or logical depending on intern

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Examples

if (have.fsl()){
system.time({
x = array(rnorm(1e6), dim = c(100, 100, 100))
img = nifti(x, dim= c(100, 100, 100), 
datatype = convert.datatype()$FLOAT32, cal.min = min(x), 
cal.max = max(x), pixdim = rep(1, 4))
thresh = fslthresh(img, thresh=0, uthresh = 2, retimg=TRUE)
})
} 

FSL Timeseries Plot using 'fsl_tsplot' (not 'tsplot')

Description

FSL Timeseries Plot using 'fsl_tsplot' (not 'tsplot')

Usage

fsl_tsplot(
  infile,
  outfile = tempfile(fileext = ".png"),
  plot_title = NULL,
  legend = NULL,
  labels = NULL,
  ymin = NULL,
  ymax = NULL,
  xlabel = NULL,
  ylabel = NULL,
  height = NULL,
  width = NULL,
  precision = NULL,
  unit = NULL,
  scientific_notation = FALSE,
  start_position = NULL,
  end_position = NULL,
  ...
)

fsl_tsplot.help()

Arguments

Value

Name of PNG file

Find FSL Version

Description

Finds the FSL version from FSLDIR/etc/fslversion

Usage

fsl_version(full = FALSE)

fslversion()

fsl_version_gt5()

Arguments

Value

If the version file does not exist, it will throw a warning, but it will return an empty string. Otherwise it will be a string of the version.

Note

This will use fsldir() to get the directory

Examples

if (have_fsl()) {
 fslversion()
 fsl_version()
}

fslabs Help

Description

This function calls fslmaths's help, as fslabs is a wrapper for fslmaths

Usage

fslabs.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslabs.help() 
}

fslacos Help

Description

This function calls fslmaths's help, as fslacos is a wrapper for fslmaths

Usage

fslacos.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslacos.help() 
}

fsladd Help

Description

This function calls fslmaths's help, as fsladd is a wrapper for fslmaths

Usage

fsladd.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fsladd.help() 
}

Logical AND with Images using FSL

Description

This function multiplies two images using fslmul) after binarizing the images (using fslbin

Usage

fsland(file, file2, ...)

fsl_and(file, file2, ...)

Arguments

Value

If retimg then object of class nifti. Otherwise, result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

fslasin Help

Description

This function calls fslmaths's help, as fslasin is a wrapper for fslmaths

Usage

fslasin.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslasin.help() 
}

fslatan Help

Description

This function calls fslmaths's help, as fslatan is a wrapper for fslmaths

Usage

fslatan.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslatan.help() 
}

Help for FSL BET

Description

This function calls bet's help

Usage

fslbet.help(betcmd = c("bet2", "bet"))

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslbet.help()
 fslbet.help("bet")
}  

fslbin Help

Description

This function calls fslmaths's help, as fslbin is a wrapper for fslmaths

Usage

fslbin.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslbin.help() 
}

fslbinv Help

Description

This function calls fslmaths's help, as fslbinv is a wrapper for fslmaths

Usage

fslbinv.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslbinv.help() 
}

FSL Change file type

Description

This function calls fslchfiletype

Usage

fslchfiletype(
  file,
  filetype = "NIFTI_GZ",
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  verbose = TRUE,
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

fslchfiletype help

Description

This function calls fslchfiletype's help

Usage

fslchfiletype.help()

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslchfiletype.help()
}  

FSL Command Wrapper

Description

This function calls fsl command passed to func

Usage

fslcmd(
  func,
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  samefile = FALSE,
  opts_after_outfile = FALSE,
  frontopts = "",
  no.outfile = FALSE,
  trim_front = FALSE,
  run = TRUE,
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Image Center of Gravity (FSL)

Description

Find Center of Gravity of Image from FSL

Usage

fslcog(img, mm = TRUE, verbose = TRUE, ts = FALSE)

Arguments

Value

Vector of length 3 unless ts option invoked

Note

FSL uses a 0-based indexing system, which will give you a different answer compared to cog, but fslcog(img, mm = FALSE) +1 should be relatively close to cog(img)

Examples

if (have.fsl()){
x = array(rnorm(1e6), dim = c(100, 100, 100))
img = nifti(x, dim= c(100, 100, 100), 
datatype = convert.datatype()$FLOAT32, cal.min = min(x), 
cal.max = max(x), pixdim = rep(1, 4))
fslcog(img)
}

fslcos Help

Description

This function calls fslmaths's help, as fslcos is a wrapper for fslmaths

Usage

fslcos.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslcos.help() 
}

FSL Copy Geometry

Description

This function calls fslcpgeom

Usage

fslcpgeom(
  file,
  file_with_header,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

fslcpgeom help

Description

This function calls fslcpgeom's help

Usage

fslcpgeom.help()

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslcpgeom.help()
}  

Get FSL's Directory

Description

Finds the FSLDIR from system environment or getOption("fsl.path") for location of FSL functions and returns it

Usage

fsldir()

fsl_dir()

Value

Character path

fsldiv Help

Description

This function calls fslmaths's help, as fsldiv is a wrapper for fslmaths

Usage

fsldiv.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fsldiv.help() 
}

fsledge Help

Description

This function calls fslmaths's help, as fsledge is a wrapper for fslmaths

Usage

fsledge.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fsledge.help() 
}

Image Mean Entropy

Description

Estimates Mean Entropy of Image from FSL

Usage

fslentropy(img, nonzero = FALSE, verbose = TRUE, ts = FALSE)

Arguments

Value

Vector of unless ts option invoked, then matrix

Note

This uses option -e or -E in fslstats

Register EPI images to Structural image

Description

This function calls epi_reg, designed to register EPI images (typically functional or diffusion) to structural (e.g. T1-weighted) image.

Usage

fslepi_reg(
  epi,
  t1,
  t1_brain,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  fmap = NULL,
  fmap_mag = NULL,
  fmap_mag_brain = NULL,
  echo_spacing = NA,
  phase_enc_dir = c("x", "y", "z", "-x", "-y", "-z"),
  weight = NULL,
  verbose = TRUE,
  opts = "",
  ...
)

fsl_epi_reg(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

epi_reg(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

fslerode Help

Description

This function calls fslmaths's help, as fslerode is a wrapper for fslmaths

Usage

fslerode.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslerode.help() 
}

fslexp Help

Description

This function calls fslmaths's help, as fslexp is a wrapper for fslmaths

Usage

fslexp.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslexp.help() 
}

fslfill Help

Description

This function calls fslmaths's help, as fslfill is a wrapper for fslmaths

Usage

fslfill.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslfill.help() 
}

Fill image holes with dilation then erosion

Description

This function calls fslmaths to dilate an image, then calls it again to erode it.

Usage

fslfill2(
  file,
  outfile = NULL,
  kopts = "",
  remove.ends = TRUE,
  refill = TRUE,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  verbose = TRUE,
  ...
)

Arguments

Value

character or logical depending on intern

Note

This function binarizes the image before running.

FSL Orientation Wrappers

Description

This function calls fslorient -get* and is a simple wrapper of fslorient

Usage

fslgetorient(file, verbose = TRUE)

fslgetsform(file, verbose = TRUE)

fslgetqform(file, verbose = TRUE)

fslgetsformcode(file, verbose = TRUE)

fslgetqformcode(file, verbose = TRUE)

Arguments

Value

Result from system command, output from FSL

Get NIfTI header using FSL

Description

This function calls fslhd to obtain a nifti header

Usage

fslhd(file, opts = "", verbose = TRUE, ...)

Arguments

Value

Character of information from fslhd

Examples

if (have.fsl()){
 mnifile = file.path(fsldir(), "data", "standard", 
   "MNI152_T1_2mm.nii.gz")
 fslhd(mnifile)
}   

FSLhd help

Description

This function calls fslhd's help

Usage

fslhd.help()

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslhd.help()
}   

Parse FSL Header

Description

This function takes in a FSL header and parses the components

Usage

fslhd.parse(hd)

Arguments

Value

data.frame of information from FSL header

Examples

if (have.fsl()){
 mnifile = mni_fname("2")
 hd = fslhd(mnifile)
 fslhd.parse(hd)
}  

Wrapper for getting fsl help

Description

This function takes in the function and returns the help from FSL for that function

Usage

fslhelp(func_name, help.arg = "--help", extra.args = "")

Arguments

Value

Prints help output and returns output as character vector

fslindex Help

Description

This function calls fslmaths's help, as fslindex is a wrapper for fslmaths

Usage

fslindex.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslindex.help() 
}

fsllog Help

Description

This function calls fslmaths's help, as fsllog is a wrapper for fslmaths

Usage

fsllog.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fsllog.help() 
}

fslmask Help

Description

This function calls fslmaths's help, as fslmask is a wrapper for fslmaths

Usage

fslmask.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslmask.help() 
}

FSL Maths Help

Description

This function calls fslmaths's help

Usage

fslmaths.help()

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslmaths.help() 
}

Get min/max of an image

Description

This function calls the range or robust range functions from FSL and then extracts the min/max

Usage

fslmax(file, ...)

fslmin(file, ...)

Arguments

Value

Numeric vector of mins/maxs or just one depending if ts = TRUE

Examples

if (have.fsl()){
 mnifile = file.path(fsldir(), "data", "standard", 
   "MNI152_T1_2mm.nii.gz")
 fslmax(mnifile)
}  

Image Mean

Description

Estimates Mean of Image from FSL

Usage

fslmean(img, nonzero = FALSE, verbose = TRUE, ts = FALSE)

Arguments

Value

Vector of unless ts option invoked, then matrix

Note

This uses option -m or -M in fslstats

FSLMerge help

Description

This function calls fslmerge's help

Usage

fslmerge.help()

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslmerge.help()
}  

fslmul Help

Description

This function calls fslmaths's help, as fslmul is a wrapper for fslmaths

Usage

fslmul.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslmul.help() 
}

fslnan Help

Description

This function calls fslmaths's help, as fslnan is a wrapper for fslmaths

Usage

fslnan.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslnan.help() 
}

fslnanm Help

Description

This function calls fslmaths's help, as fslnanm is a wrapper for fslmaths

Usage

fslnanm.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslnanm.help() 
}

Perform OR/Union operation on Images using FSL

Description

This function calls fslmaths file -add file2 -bin after binarizing file and file2 using fslbin.

Usage

fslor(
  file,
  file2,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  ...
)

fsl_or(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

FSL Orient

Description

This function calls fslorient

Usage

fslorient(
  file,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

fslorient help

Description

This function calls fslorient's help

Usage

fslorient.help()

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslorient.help()
} 

Wrapper for FSL Get Orientation

Description

This function calls fslorient -getorient and is a simple wrapper of fslorient

Usage

fslorienter(file, opts = "", verbose = TRUE)

Arguments

Value

Result from system command, output from FSL

fslrand Help

Description

This function calls fslmaths's help, as fslrand is a wrapper for fslmaths

Usage

fslrand.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslrand.help() 
}

fslrandn Help

Description

This function calls fslmaths's help, as fslrandn is a wrapper for fslmaths

Usage

fslrandn.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslrandn.help() 
}

Get range of an image

Description

This function calls fslstats -R to get the range of an image or fslstats -r to get the robust range

Usage

fslrange(file, robust = FALSE, verbose = TRUE, ts = FALSE, ...)

Arguments

Value

numeric vector of length 2

Examples

if (have.fsl()){
 mnifile = file.path(fsldir(), "data", "standard", 
   "MNI152_T1_2mm.nii.gz")
 fslrange(mnifile)
}  

fslrecip Help

Description

This function calls fslmaths's help, as fslrecip is a wrapper for fslmaths

Usage

fslrecip.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslrecip.help() 
}

fslrem Help

Description

This function calls fslmaths's help, as fslrem is a wrapper for fslmaths

Usage

fslrem.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslrem.help() 
}

FSL Orient to MNI

Description

This function calls fslreorient2std

Usage

fslreorient2std(
  file,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  verbose = TRUE,
  opts = "",
  ...
)

fslreorient2std_mat(
  file,
  matfile = tempfile(fileext = ".mat"),
  verbose = TRUE,
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

fslreorient2std help

Description

This function calls fslreorient2std's help

Usage

fslreorient2std.help()

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslreorient2std.help()
}  

FSL Robust Field of View

Description

This function calls robustfov to automatically crop the image

Usage

fslrobustfov(
  file,
  brain_size = NULL,
  mat_name = NULL,
  roi_name = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  verbose = TRUE,
  ...
)

fsl_robustfov(retimg = FALSE, ...)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

FSL Robust Field of View Help

Description

This function calls robustfov help

Usage

fslrobustfov.help()

FSL ROI

Description

This function calls fslroi

Usage

fslroi(
  file,
  xmin = 0,
  xsize = -1,
  ymin = 0,
  ysize = -1,
  zmin = 0,
  zsize = -1,
  tmin = NULL,
  tsize = NULL,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  verbose = TRUE,
  ...
)

fsl_roi(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslroi_time(file, tmin = NULL, tsize = NULL, ...)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension.

Image Standard Deviation

Description

Estimates Standard Deviation of Image from FSL

Usage

fslsd(img, nonzero = FALSE, verbose = TRUE, ts = FALSE)

Arguments

Value

Vector of unless ts option invoked, then matrix

Note

This uses option -s or -S in fslstats

Sine Transform Image using FSL

Description

This function calls fslmaths -sin. The R functions wraps fslmaths

Usage

fslsin(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

fslsin Help

Description

This function calls fslmaths's help, as fslsin is a wrapper for fslmaths

Usage

fslsin.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslsin.help() 
}

FSL Slice Timing Correction

Description

This function calls slicetimer and performs slice timing correction for fMRI data

Usage

fslslicetimer(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  tr = 3,
  direction = "z",
  indexing = c("up", "down"),
  acq_order = c("contiguous", "interleaved"),
  verbose = TRUE,
  ...
)

fsl_slicetimer(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

fslsmooth Help

Description

This function calls fslmaths's help, as fslsmooth is a wrapper for fslmaths

Usage

fslsmooth.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslsmooth.help() 
}

Smooth Image Within a Mask Only

Description

This function smooth an image within a mask and replaces the values of the original image with the smoothed values.

Usage

fslsmooth_in_mask(file, sigma = 10, mask = NULL, ...)

fsl_smooth_in_mask(...)

Arguments

Value

Object of class nifti

Examples

if (have.fsl()){
system.time({
dims = c(50, 50, 20)
x = array(rnorm(prod(dims)), dim = dims)
img = nifti(x, dim= dims, 
datatype = convert.datatype()$FLOAT32, cal.min = min(x), 
cal.max = max(x), pixdim = rep(1, 4))
mask = abs(img ) > 1
s.img = fslsmooth_in_mask(img, mask = mask)
})
}

Split images using FSL

Description

This function calls fslsplit to merge files on some dimension and either saves the image or returns an object of class nifti

Usage

fslsplit(
  infile,
  direction = c("t", "x", "y", "z"),
  output_basename = NULL,
  retimg = TRUE,
  reorient = FALSE,
  verbose = TRUE
)

fsl_split(..., retimg = FALSE)

Arguments

Value

List of output files

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

FSL Split help

Description

This function calls fslsplit's help

Usage

fslsplit.help()

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslsplit.help()
}  

fslsqr Help

Description

This function calls fslmaths's help, as fslsqr is a wrapper for fslmaths

Usage

fslsqr.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslsqr.help() 
}

fslsqrt Help

Description

This function calls fslmaths's help, as fslsqrt is a wrapper for fslmaths

Usage

fslsqrt.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslsqrt.help() 
}

FSL Stats

Description

This function calls fslstats

Usage

fslstats(file, opts = "", verbose = TRUE, ts = FALSE, ...)

Arguments

Value

Result of fslstats command

Examples

if (have.fsl()){
system.time({
x = array(rnorm(1e6), dim = c(100, 100, 100))
img = nifti(x, dim= c(100, 100, 100), 
datatype = convert.datatype()$FLOAT32, cal.min = min(x), 
cal.max = max(x), pixdim = rep(1, 4))
entropy = fslstats(img, opts='-E')
})
}  

FSL Stats Help

Description

This function calls fslstats's help

Usage

fslstats.help()

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslstats.help() 
}

fslsub Help

Description

This function calls fslmaths's help, as fslsub is a wrapper for fslmaths

Usage

fslsub.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslsub.help() 
}

fslsub2 Help

Description

This function calls fslmaths's help, as fslsub2 is a wrapper for fslmaths

Usage

fslsub2.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslsub2.help() 
}

FSL Sum

Description

This function calls fslstats -M -V to get product, aka the approximate sum.

Usage

fslsum(file, opts = "", ts = FALSE, ...)

Arguments

Value

Numeric value

Note

This may be approximate due to rounding

fslswapdim help

Description

This function calls fslswapdim's help

Usage

fslswapdim.help()

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslswapdim.help()
}  

fsltan Help

Description

This function calls fslmaths's help, as fsltan is a wrapper for fslmaths

Usage

fsltan.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fsltan.help() 
}

fslthresh Help

Description

This function calls fslmaths's help, as fslthresh is a wrapper for fslmaths

Usage

fslthresh.help(...)

Arguments

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslthresh.help() 
}

Get value from FSL header

Description

This function calls fslval to obtain a nifti header

Usage

fslval(file, keyword = "", verbose = TRUE, ...)

Arguments

Value

Character of information from fslhd field specified in keyword

Examples

if (have.fsl()){
 mnifile = file.path(fsldir(), "data", "standard", 
   "MNI152_T1_2mm.nii.gz")
 fslval(mnifile, keyword = "dim1")
}  

fslval help

Description

This function calls fslval's help

Usage

fslval.help()

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 fslval.help()
} 

Open image in FSLView

Description

This function calls fslview to view an image in the FSL viewer

Usage

fslview(file, intern = TRUE, opts = "", verbose = TRUE, ...)

fsleyes(file, intern = TRUE, opts = "", verbose = TRUE, ...)

Arguments

Value

character or logical depending on intern

Note

As of FSL version 5.0.10, this is deprecated: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/WhatsNew

FSLView help

Description

This function calls fslview's help

Usage

fslview.help()

Value

Prints help output and returns output as character vector

Examples

library(fslr)
if (have.fsl()){
  print(fsl_version())
  in_ci <- function() {
   nzchar(Sys.getenv("CI"))
  }
 if (!in_ci()) {
   fslview.help()
 }
}   

FSL Volume in mL (or cubic centimeters)

Description

This function wraps fslsum and voxdim

Usage

fslvol(file, ...)

Arguments

Value

Numeric value of volume in mL

Note

This may be approximate due to rounding

Image Volume

Description

Estimates Volume of Image from FSL

Usage

fslvolume(img, nonzero = FALSE, verbose = TRUE, ts = FALSE)

Arguments

Value

Vector of unless ts option invoked, then matrix

Note

This uses option -v or -V in fslstats

Perform XOR/Exclusive Or operation on Images using FSL

Description

This function calls fslmaths file -add file2 -bin after binarizing file and file2 using fslbin and then uses fsl_thresh to threshold any values greater than 1 back to zero.

Usage

fslxor(
  file,
  file2,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  ...
)

fsl_xor(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

Arguments

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Create command declaring FSLDIR

Description

Finds the FSLDIR from system environment or getOption("fsl.path") for location of FSL functions

Usage

get.fsl(add_bin = TRUE)

get_fsl(add_bin = TRUE)

Arguments

Value

NULL if FSL in path, or bash code for setting up FSL DIR

Note

This will use Sys.getenv("FSLDIR") before getOption("fsl.path"). If the directory is not found for FSL in Sys.getenv("FSLDIR") and getOption("fsl.path"), it will try the default directory /usr/local/fsl.

Determine FSL output type

Description

Finds the FSLOUTPUTTYPE from system environment or getOption("fsl.outputtype") for output type (nii.gz, nii, ANALYZE,etc)

Usage

get.fsloutput()

Value

FSLOUTPUTTYPE, such as NIFTI_GZ. If none found, uses NIFTI_GZ as default

Determine extension of image based on FSLOUTPUTTYPE

Description

Runs get.fsloutput() to extract FSLOUTPUTTYPE and then gets corresponding extension (such as .nii.gz)

Usage

get.imgext()

Value

Extension for output type

Get Q and S Forms of orientation matrix

Description

This function obtains the s and q forms of an image transformation matrix

Usage

getForms(file, verbose = FALSE, ...)

Arguments

Value

list with elements of sform and qform and their respective codes

Examples

if (have.fsl()){
 mnifile = mni_fname("2")
 getForms(mnifile)
}   

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

Description

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

Usage

get_quickshear_mask(brain_mask, buffer = 10, verbose = TRUE)

quickshear_deface_image(
  file,
  brain_mask = NULL,
  buffer = 10,
  verbose = TRUE,
  ...
)

Arguments

Value

A binary image of the non-face areas

Note

adapted from https://github.com/nipy/quickshear/blob/master/quickshear.py

Examples

if (have_fsl()) {
   file = "~/Downloads/sample_T1_input.nii.gz"
   if (file.exists(file)) {
       res = quickshear_deface_image(file)
       brain_mask = fslbet(file) > 0
       mask = get_quickshear_mask(brain_mask)
       image = fslmask(file, mask)
   }
}

Logical check if FSL is accessible

Description

Uses get.fsl to check if FSLDIR is accessible or the option fsl.path is set and returns logical

Usage

have.fsl(...)

have_fsl(...)

Arguments

Value

Logical TRUE is FSL is accessible, FALSE if not

Examples

have.fsl()

Extract Image intent_code attribute

Description

intent_code method for character types

Usage

## S4 method for signature 'character'
intent_code(object)

Arguments

Extract Image intent_name attribute

Description

intent_name method for character types

Usage

## S4 method for signature 'character'
intent_name(object)

Arguments

Extract Image intent_p1 attribute

Description

intent_p1 method for character types

Usage

## S4 method for signature 'character'
intent_p1(object)

Arguments

Extract Image intent_p2 attribute

Description

intent_p2 method for character types

Usage

## S4 method for signature 'character'
intent_p2(object)

Arguments

Extract Image intent_p3 attribute

Description

intent_p3 method for character types

Usage

## S4 method for signature 'character'
intent_p3(object)

Arguments

Convert a Transformation

Description

Convert a Transformation

Usage

invert_xfm(inmat, omat = tempfile(fileext = ".mat"), verbose = TRUE)

concat_xfm(inmat, inmat2, omat = tempfile(fileext = ".mat"), verbose = TRUE)

fixscaleskew_xfm(
  inmat,
  inmat2,
  omat = tempfile(fileext = ".mat"),
  verbose = TRUE
)

Arguments

Value

A filename of the output matrix file

Examples

if (have_fsl()) {
img = mni_fname()
mat = fslreorient2std_mat(img)
inverted = invert_xfm(mat)
readLines(inverted)
catted = concat_xfm(mat, mat)
readLines(catted)
fixed = fixscaleskew_xfm(mat, mat)
readLines(fixed)

}

Extract Image magic attribute

Description

magic method for character types

Usage

## S4 method for signature 'character'
magic(object)

Arguments

FSL Motion Correction

Description

This function calls mcflirt

Usage

mcflirt(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

If retimg then object of class nifti. Otherwise, it will have additional attributes in the additional_files field.

MCFLIRT help

Description

This function calls mcflirt's help

Usage

mcflirt.help()

Value

Prints help output and returns output as character vector

Examples

library(fslr)
if (have.fsl()){
 mcflirt.help()
} 

Run MELODIC ICA

Description

This function calls melodic

Usage

melodic(
  file,
  outdir = dirname(file),
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

Value

character or logical depending on intern

MELODIC help

Description

This function calls melodic's help

Usage

melodic.help()

Value

Prints help output and returns output as character vector

Examples

if (have.fsl()){
 melodic.help()
} 

Mid-Sagittal Plane Alignment

Description

This function takes in an image, flips the image over the left/right plane, registers that flipped image to the original image, then applies the half transformation

Usage

mid_sagittal_align(
  file,
  outfile = NULL,
  retimg = TRUE,
  opts = "",
  translation = TRUE,
  force_rpi = TRUE,
  verbose = TRUE
)

Arguments

Value

Filename of output or nifti depending on retimg

Construct MNI Filename

Description

Finds the standard data directory for FSL and pastes together the string for an MNI template image

Usage

mni_fname(mm = c("1", "0.5", "2"), brain = FALSE, linear = FALSE, mask = FALSE)

mni_face_fname(mm = c("1", "0.5", "2"))

Arguments

Value

Character path of filename, warning if that file does not exist

Read MNI Filename

Description

Simple wrapper for reading in the MNI image constructed from mni_fname

Usage

mni_img(...)

Arguments

Value

Object of class nifti

MRI Defacer

Description

MRI Defacer

Usage

mridefacer(file, ..., verbose = TRUE)

get_mridefacer_mask(
  file,
  brain_mask = NULL,
  bet_opts = "-f 0.5",
  search_radius = 90,
  opts = NULL,
  template_brain = NULL,
  template_brain_weight = NULL,
  template_biometric_mask = NULL,
  verbose = TRUE
)

Arguments

Value

A character filename of the output image

Note

Adapted from https://github.com/mih/mridefacer

Examples

if (have_fsl()) {
file = "~/Downloads/sample_T1_input.nii.gz"
if (file.exists(file)) {
    res = mridefacer(file)
}
}

Parse output from avscale

Description

This function parses the output from fsl_avscale into something more manageable

Usage

parse_avscale(av_out)

Arguments

Value

List of output values

Extract Image pixdim attribute

Description

Gets pixdim from a character

Usage

## S4 method for signature 'character'
pixdim(object)

Arguments

Probabilistic diffusion tractography with multiple fibre orientations

Description

This function wraps probtrackx from FSL

Usage

probtrackx(
  samples = "merged",
  mask,
  seed,
  outdir = "fdt_paths",
  verbose = TRUE,
  mode = NULL,
  targetmasks = NULL,
  mask2 = NULL,
  waypoints = NULL,
  network = FALSE,
  mesh = NULL,
  seedref = NULL,
  dir = FALSE,
  forcedir = FALSE,
  opd = FALSE,
  pd = FALSE,
  os2t = FALSE,
  avoid = NULL,
  stop = NULL,
  xfm = NULL,
  invxfm = NULL,
  nsamples = 5000,
  nsteps = 2000,
  distthresh = 0,
  cthr = 0.2,
  fibthresh = 0.01,
  sampvox = FALSE,
  steplength = 0.5,
  loopcheck = FALSE,
  usef = FALSE,
  randfib = c(0, 1, 2, 3),
  fibst = 1,
  modeuler = FALSE,
  rseed = NULL,
  s2tastext = FALSE,
  opts = ""
)

Arguments

Value

A filename of the output file

Extract NIfTI 3D Image Orientation

Description

Gets q/s-forms from a character

Usage

## S4 method for signature 'character'
qform(object)

## S4 method for signature 'character'
sform(object)

Arguments

Extract Image qform_code attribute

Description

qform_code method for character types

Usage

## S4 method for signature 'character'
qform_code(object)

Arguments

Read FSL Transformation

Description

Read FSL Transformation

Usage

read_xfm(file)

Arguments

Value

A numeric matrix of numeric class

Read NIfTI file reoriented to RPI

Description

This function calls the readnii function after calling rpi_orient_file to force RPI orientation.

Usage

readrpi(file, ..., verbose = TRUE)

Arguments

Examples

if (have.fsl()){
print(fsl_version())
in_ci <- function() {
 nzchar(Sys.getenv("CI"))
 }
 if (in_ci()) {
 destfile = tempfile(fileext = ".nii.gz")
 url = paste0("https://ndownloader.figshare.com/", 
 "files/18068546")
 old_url = paste0("https://github.com/muschellij2/", 
 "Neurohacking/files/3454385/113-01-MPRAGE2.nii.gz")
 dl = tryCatch(download.file(url,
 destfile = destfile))
 if (inherits(dl, "try-error") || dl != 0) {
 dl = download.file(old_url, destfile = destfile)
 }
 res = readrpi(destfile)
 }
 }   

Reverse Reorientation an Image to RPI orientation

Description

This function uses fslswapdim to reorient an image

Usage

reverse_rpi_orient(
  file,
  convention = c("NEUROLOGICAL", "RADIOLOGICAL"),
  orientation,
  verbose = TRUE
)

reverse_rpi_orient_file(
  file,
  convention = c("NEUROLOGICAL", "RADIOLOGICAL"),
  orientation,
  verbose = TRUE
)

Arguments

Value

Object of class nifti

Reorient an Image to RPI orientation

Description

This function uses fslswapdim to reorient an image

Usage

rpi_orient(file, verbose = TRUE)

rpi_orient_file(file, verbose = TRUE)

is_rpi(file, verbose = FALSE)

is.rpi(file, verbose = FALSE)

Arguments

Value

List of 3 elements

• img: Reoriented image of class nifti

• convention: Convention (Neurological/Radiological) of original image

• orientation: Original image orientations

Note

'orient_rpi' and 'orient_rpi_file' uses 'RNifti' to ensure the reading orientation

Examples

lr_fname = system.file( "nifti", "mniLR.nii.gz", package = "oro.nifti")
img = readnii(lr_fname)

rl_fname = system.file( "nifti", "mniRL.nii.gz", package = "oro.nifti")
rl_img = readnii(rl_fname)
stopifnot(all(rl_img[nrow(rl_img):1,,] == img))

## Not run: 
if (have_fsl()) {


reor = rpi_orient(rl_fname)
rev = reverse_rpi_orient(reor$img, convention = reor$convention,
orientation = reor$orientation)
stopifnot(all(rev == rl_img))
}

## End(Not run)


reor = orient_rpi(rl_fname)
stopifnot(all(img == reor$img))

rev = reverse_orient_rpi(reor$img, convention = reor$convention,
orientation = reor$orientation)
stopifnot(all(rev == rl_img))

Run FIRST All

Description

Wrapper for run_first_all from FSL for FIRST analysis segmentation of subcortical structures

Usage

run_first_all(
  img,
  oprefix = tempfile(),
  brain_extracted = FALSE,
  structures = NULL,
  affine = NULL,
  opts = "",
  verbose = TRUE
)

Arguments