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

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

## Documentation for package ‘fslr’ version 2.27.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

A B C D E F G H I M P Q R S T V X

## -- A --

applytopup | applytopup - calling FSL applytopup
apply_mid_sagittal_align | Mid-Sagittal Plane Alignment
apply_topup | applytopup - calling FSL applytopup
aux.file-method | Extract Image aux.file attribute
aux.file-methods | Extract Image aux.file attribute
avscale | Scale Affine Matrix using 'avscale'

## -- B --

bedpostx | Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques with Crossing Fibers
bitpix-method | Extract Image bitpix attribute
bitpix-methods | Extract Image bitpix attribute

## -- C --

cal.max-method | Extract Image cal.max attribute
cal.max-methods | Extract Image cal.max attribute
cal.min-method | Extract Image cal.min attribute
cal.min-methods | Extract Image cal.min attribute
checkout | Determine of Q and S forms are consistent
check_file | Wrapper for getForms with filename
concat_xfm | Convert a Transformation

## -- D --

datatype-method | Extract Image datatype attribute
datatype-methods | Extract Image datatype attribute
data_type-method | Extract Image data_type attribute
data_type-methods | Extract Image data_type attribute
deface_image | Face Removal Mask
descrip-method | Extract Image descrip attribute
descrip-methods | Extract Image descrip attribute
dim_-method | Extract Image dim_ attribute
dim_-methods | Extract Image dim_ attribute
download_fsl | Download FSL
dtifit | DTI Fitting Procedure from FSL

## -- E --

eddy | Eddy Current Correction
eddy_correct | Eddy Current Correction
enforce_form | Enforce Either Qform or Sform is set
epi_reg | Register EPI images to Structural image

## -- F --

face_removal_mask | Face Removal Mask
fast | FSL FAST
fast.help | FAST help
fast_all | FSL FAST
fast_nobias | FSL FAST
fast_nobias_all | FSL FAST
fixscaleskew_xfm | Convert a Transformation
flirt | Register using FLIRT
flirt.help | FLIRT help
flirt_apply | Apply Warp from FLIRT
flirt_apply.help | FLIRT help
fnirt | Register using FNIRT
fnirt.help | FNIRT help
fnirt_with_affine | Register using FNIRT, but doing Affine Registration as well
fnirt_with_affine_apply | Applies FLIRT then FNIRT transformations
fslabs | Absolute Value Image using FSL
fslabs.help | fslabs Help
fslacos | Arc Cosine Transform Image using FSL
fslacos.help | fslacos Help
fsladd | Add Images using FSL
fsladd.help | fsladd Help
fsland | Logical AND with Images using FSL
fslasin | Arc Sine Transform Image using FSL
fslasin.help | fslasin Help
fslatan | Arc Tangent Transform Image using FSL
fslatan.help | fslatan Help
fslbet | Use FSL's Brain Extraction Tool (BET)
fslbet.help | Help for FSL BET
fslbin | Binarize Image using FSL
fslbin.help | fslbin Help
fslbinv | Binarized Inverse Image using FSL
fslbinv.help | fslbinv Help
fslchfiletype | FSL Change file type
fslchfiletype.help | fslchfiletype help
fslcluster | Form clusters, report information about clusters and/or perform cluster-based inference. Wrapper for 'cluster'
fslcmd | FSL Command Wrapper
fslcog | Image Center of Gravity (FSL)
fslcos | Cosine Transform Image using FSL
fslcos.help | fslcos Help
fslcpgeom | FSL Copy Geometry
fslcpgeom.help | fslcpgeom help
fsldilate | Dilate image using FSL
fsldir | Get FSL's Directory
fsldiv | Divide Images using FSL
fsldiv.help | fsldiv Help
fsledge | Edge Strength Image using FSL
fsledge.help | fsledge Help
fslentropy | Image Mean Entropy
fslentropy.help | FSL Stats Help
fslepi_reg | Register EPI images to Structural image
fslerode | Erode image using FSL
fslerode.help | fslerode Help
fslexp | Exponentiate Image using FSL
fslexp.help | fslexp Help
fsleyes | Open image in FSLView
fslfast | FSL FAST
fslfast_nobias | FSL FAST
fslfill | Fill image holes
fslfill.help | fslfill Help
fslfill2 | Fill image holes with dilation then erosion
fslgetorient | FSL Orientation Wrappers
fslgetqform | FSL Orientation Wrappers
fslgetqformcode | FSL Orientation Wrappers
fslgetsform | FSL Orientation Wrappers
fslgetsformcode | FSL Orientation Wrappers
fslhd | Get NIfTI header using FSL
fslhd.help | FSLhd help
fslhd.parse | Parse FSL Header
fslhelp | Wrapper for getting fsl help
fslindex | Index Image using FSL
fslindex.help | fslindex Help
fsllog | Log Transform Image using FSL
fsllog.help | fsllog Help
fslmask | Mask image using FSL
fslmask.help | fslmask Help
fslmaths | FSL Maths
fslmaths.help | FSL Maths Help
fslmax | Get min/max of an image
fslmean | Image Mean
fslmean.help | FSL Stats Help
fslmerge | Merge images using FSL
fslmerge.help | FSLMerge help
fslmin | Get min/max of an image
fslmul | Multiply Images using FSL
fslmul.help | fslmul Help
fslnan | Replace NaNs in Image using FSL
fslnan.help | fslnan Help
fslnanm | Mask NaNs in Image using FSL
fslnanm.help | fslnanm Help
fslor | Perform OR/Union operation on Images using FSL
fslorient | FSL Orient
fslorient.help | fslorient help
fslorienter | Wrapper for FSL Get Orientation
fslrand | Add Random Uniform Noise Image using FSL
fslrand.help | fslrand Help
fslrandn | Add Random Standard Gaussian Noise Image using FSL
fslrandn.help | fslrandn Help
fslrange | Get range of an image
fslrange.help | FSL Stats Help
fslrecip | Reciprocal Image using FSL
fslrecip.help | fslrecip Help
fslrem | Modulus Remainder of 2 Images using FSL
fslrem.help | fslrem Help
fslreorient2std | FSL Orient to MNI
fslreorient2std.help | fslreorient2std help
fslreorient2std_mat | FSL Orient to MNI
fslrobustfov | FSL Robust Field of View
fslrobustfov.help | FSL Robust Field of View Help
fslroi | FSL ROI
fslroi_time | FSL ROI
fslsd | Image Standard Deviation
fslsd.help | FSL Stats Help
fslsin | Sine Transform Image using FSL
fslsin.help | fslsin Help
fslslicetimer | FSL Slice Timing Correction
fslsmooth | Gaussian smooth image using FSL
fslsmooth.help | fslsmooth Help
fslsmooth_in_mask | Smooth Image Within a Mask Only
fslsplit | Split images using FSL
fslsplit.help | FSL Split help
fslsqr | Square Image using FSL
fslsqr.help | fslsqr Help
fslsqrt | Square Root Image using FSL
fslsqrt.help | fslsqrt Help
fslstats | FSL Stats
fslstats.help | FSL Stats Help
fslsub | Subtract Images using FSL
fslsub.help | fslsub Help
fslsub2 | Subsample image by factor of 2
fslsub2.help | fslsub2 Help
fslsum | FSL Sum
fslswapdim | FSL Swap Dimensions
fslswapdim.help | fslswapdim help
fsltan | Tangent Transform Image using FSL
fsltan.help | fsltan Help
fslthresh | Threshold an image
fslthresh.help | fslthresh Help
fslval | Get value from FSL header
fslval.help | fslval help
fslversion | Find FSL Version
fslview | Open image in FSLView
fslview.help | FSLView help
fslvol | FSL Volume in mL (or cubic centimeters)
fslvolume | Image Volume
fslxor | Perform XOR/Exclusive Or operation on Images using FSL
fsl_abs | Absolute Value Image using FSL
fsl_acos | Arc Cosine Transform Image using FSL
fsl_add | Add Images using FSL
fsl_anat | FSL Anatomical Processing Script
fsl_anat.help | fsl_anat help
fsl_and | Logical AND with Images using FSL
fsl_applytopup | applytopup - calling FSL applytopup
fsl_applywarp | Apply Warp from FNIRT
fsl_applywarp.help | FSL applywarp help
fsl_asin | Arc Sine Transform Image using FSL
fsl_atan | Arc Tangent Transform Image using FSL
fsl_atlas_dir | Get FSL's Standard Data Directory
fsl_avscale | Scale Affine Matrix using 'avscale'
fsl_bet | Use FSL's Brain Extraction Tool (BET)
fsl_biascorrect | FSL Bias Correct
fsl_bin | Binarize Image using FSL
fsl_binv | Binarized Inverse Image using FSL
fsl_bin_tab | Quick Tabulation for logical images
fsl_cluster | Form clusters, report information about clusters and/or perform cluster-based inference. Wrapper for 'cluster'
fsl_cos | Cosine Transform Image 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
fsl_dilate | Dilate image using FSL
fsl_dir | Get FSL's Directory
fsl_div | Divide Images using FSL
fsl_edge | Edge Strength Image using FSL
fsl_epi_reg | Register EPI images to Structural image
fsl_erode | Erode image using FSL
fsl_exp | Exponentiate Image using FSL
fsl_fast | FSL FAST
fsl_fast_nobias | FSL FAST
fsl_fill | Fill image holes
fsl_index | Index Image using FSL
fsl_log | Log Transform Image using FSL
fsl_mask | Mask image using FSL
fsl_maths | FSL Maths
fsl_merge | Merge images using FSL
fsl_mul | Multiply Images using FSL
fsl_nan | Replace NaNs in Image using FSL
fsl_nanm | Mask NaNs in Image using FSL
fsl_or | Perform OR/Union operation on Images using FSL
fsl_rand | Add Random Uniform Noise Image using FSL
fsl_randn | Add Random Standard Gaussian Noise Image using FSL
fsl_recip | Reciprocal Image using FSL
fsl_rem | Modulus Remainder of 2 Images using FSL
fsl_resample | Resample an Image to Specific Voxel Size
fsl_robustfov | FSL Robust Field of View
fsl_roi | FSL ROI
fsl_slicetimer | FSL Slice Timing Correction
fsl_smooth | Gaussian smooth image using FSL
fsl_smoothest | Smoothness Estimation using 'smoothest'
fsl_smooth_in_mask | Smooth Image Within a Mask Only
fsl_split | Split images using FSL
fsl_sqr | Square Image using FSL
fsl_sqrt | Square Root Image using FSL
fsl_std_dir | Get FSL's Standard Data Directory
fsl_std_file | Get FSL's Standard Data Directory
fsl_sub | Subtract Images using FSL
fsl_sub2 | Subsample image by factor of 2
fsl_swapdim | FSL Swap Dimensions
fsl_tan | Tangent Transform Image using FSL
fsl_thresh | Threshold an image
fsl_topup | topup - calling FSL topup
fsl_tsplot | FSL Timeseries Plot using 'fsl_tsplot' (not 'tsplot')
fsl_tsplot.help | FSL Timeseries Plot using 'fsl_tsplot' (not 'tsplot')
fsl_version | Find FSL Version
fsl_version_gt5 | Find FSL Version
fsl_xor | Perform XOR/Exclusive Or operation on Images using FSL

## -- G --

get.fsl | Create command declaring FSLDIR
get.fsloutput | Determine FSL output type
get.imgext | Determine extension of image based on FSLOUTPUTTYPE
getForms | Get Q and S Forms of orientation matrix
get_fsl | Create command declaring FSLDIR
get_mridefacer_mask | MRI Defacer
get_quickshear_mask | Face Removal Mask using "Quickshear Defacing for Neuroimages" (Schimke et al. 2011)

## -- H --

have.fsl | Logical check if FSL is accessible
have_fsl | Logical check if FSL is accessible

## -- I --

intent_code-method | Extract Image intent_code attribute
intent_code-methods | Extract Image intent_code attribute
intent_name-method | Extract Image intent_name attribute
intent_name-methods | Extract Image intent_name attribute
intent_p1-method | Extract Image intent_p1 attribute
intent_p1-methods | Extract Image intent_p1 attribute
intent_p2-method | Extract Image intent_p2 attribute
intent_p2-methods | Extract Image intent_p2 attribute
intent_p3-method | Extract Image intent_p3 attribute
intent_p3-methods | Extract Image intent_p3 attribute
invert_xfm | Convert a Transformation
is.rpi | Reorient an Image to RPI orientation
is_rpi | Reorient an Image to RPI orientation

## -- M --

magic-method | Extract Image magic attribute
magic-methods | Extract Image magic attribute
mcflirt | FSL Motion Correction
mcflirt.help | MCFLIRT help
melodic | Run MELODIC ICA
melodic.help | MELODIC help
mid_sagittal_align | Mid-Sagittal Plane Alignment
mni_face_fname | Construct MNI Filename
mni_fname | Construct MNI Filename
mni_img | Read MNI Filename
mridefacer | MRI Defacer

## -- P --

parse_avscale | Parse output from 'avscale'
pixdim-method | Extract Image pixdim attribute
pixdim-methods | Extract Image pixdim attribute
probtrackx | Probabilistic diffusion tractography with multiple fibre orientations

## -- Q --

qform,character | Extract NIfTI 3D Image Orientation
qform-method | Extract NIfTI 3D Image Orientation
qform_code-method | Extract Image qform_code attribute
qform_code-methods | Extract Image qform_code attribute
quickshear_deface_image | Face Removal Mask using "Quickshear Defacing for Neuroimages" (Schimke et al. 2011)

## -- R --

readrpi | Read NIfTI file reoriented to RPI
read_cluster_table | Form clusters, report information about clusters and/or perform cluster-based inference. Wrapper for 'cluster'
read_xfm | Read FSL Transformation
reverse_rpi_orient | Reverse Reorientation an Image to RPI orientation
reverse_rpi_orient_file | Reverse Reorientation an Image to RPI orientation
rpi_orient | Reorient an Image to RPI orientation
rpi_orient_file | Reorient an Image to RPI orientation
run_first_all | Run FIRST All
run_first_all.help | Run FIRST All Help

## -- S --

scl_inter-method | Extract Image scl_inter attribute
scl_inter-methods | Extract Image scl_inter attribute
scl_slope-method | Extract Image scl_slope attribute
scl_slope-methods | Extract Image scl_slope attribute
sform,character | Extract NIfTI 3D Image Orientation
sform-method | Extract NIfTI 3D Image Orientation
sform_code-method | Extract Image sform_code attribute
sform_code-methods | Extract Image sform_code attribute
sizeof_hdr-method | Extract Image sizeof_hdr attribute
sizeof_hdr-methods | Extract Image sizeof_hdr attribute
slice_code-method | Extract Image slice_code attribute
slice_code-methods | Extract Image slice_code attribute
slice_duration-method | Extract Image slice_duration attribute
slice_duration-methods | Extract Image slice_duration attribute
slice_end-method | Extract Image slice_end attribute
slice_end-methods | Extract Image slice_end attribute
slice_start-method | Extract Image slice_start attribute
slice_start-methods | Extract Image slice_start attribute
susan | FSL SUSAN noise reduction
susan.help | FSL SUSAN Help

## -- T --

toffset-method | Extract Image toffset attribute
toffset-methods | Extract Image toffset attribute
topup | topup - calling FSL topup

## -- V --

vox_offset-method | Extract Image vox_offset attribute
vox_offset-methods | Extract Image vox_offset attribute

## -- X --

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