Function reference • fslr

All functions
`applytopup()` `apply_topup()` `fsl_applytopup()`	applytopup - calling FSL applytopup
`aux.file(<character>)`	Extract Image aux.file attribute
`bitpix(<character>)`	Extract Image bitpix attribute
`cal.max(<character>)`	Extract Image cal.max attribute
`cal.min(<character>)`	Extract Image cal.min attribute
`check_file()`	Wrapper for getForms with filename
`checkout()`	Determine of Q and S forms are consistent
`data_type(<character>)`	Extract Image data_type attribute
`datatype(<character>)`	Extract Image datatype attribute
`descrip(<character>)`	Extract Image descrip attribute
`dim_(<character>)`	Extract Image dim_ attribute
`download_fsl()`	Download FSL
`dtifit()`	DTI Fitting Procedure from FSL
`eddy()`	Eddy Current Correction
`eddy_correct()`	Eddy Current Correction
`enforce_form()`	Enforce Either Qform or Sform is set
`face_removal_mask()` `deface_image()`	Face Removal Mask
`fast()` `fast_all()` `fast_nobias_all()` `fsl_fast()` `fslfast()` `fsl_fast_nobias()` `fast_nobias()` `fslfast_nobias()`	FSL FAST
`fast.help()`	FAST help
`flirt()`	Register using FLIRT
`flirt.help()`	FLIRT help
`flirt_apply()`	Apply Warp from FLIRT
`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
`fsl_anat()`	FSL Anatomical Processing Script
`fsl_anat.help()`	fsl_anat help
`fsl_applywarp()`	Apply Warp from FNIRT
`fsl_applywarp.help()`	FSL applywarp help
`fsl_atlas_dir()`	Get FSL's Standard Data Directory
`fsl_avscale()` `avscale()`	Scale Affine Matrix using `avscale`
`fsl_biascorrect()`	FSL Bias Correct
`fsl_bin_tab()`	Quick Tabulation for logical images
`fsl_cluster()` `fslcluster()` `read_cluster_table()`	Form clusters, report information about clusters and/or perform cluster-based inference. Wrapper for `cluster`
`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_resample()`	Resample an Image to Specific Voxel Size
`fsl_smoothest()`	Smoothness Estimation using `smoothest`
`fsl_std_dir()` `fsl_std_file()`	Get FSL's Standard Data Directory
`fsl_tsplot()` `fsl_tsplot.help()`	FSL Timeseries Plot using `fsl_tsplot` (not `tsplot`)
`fsl_version()` `fslversion()` `fsl_version_gt5()`	Find FSL Version
`fsl_abs()` `fslabs()`	Absolute Value Image using FSL
`fslabs.help()`	fslabs Help
`fsl_acos()` `fslacos()`	Arc Cosine Transform Image using FSL
`fslacos.help()`	fslacos Help
`fsl_add()` `fsladd()`	Add Images using FSL
`fsladd.help()`	fsladd Help
`fsland()` `fsl_and()`	Logical AND with Images using FSL
`fsl_asin()` `fslasin()`	Arc Sine Transform Image using FSL
`fslasin.help()`	fslasin Help
`fsl_atan()` `fslatan()`	Arc Tangent Transform Image using FSL
`fslatan.help()`	fslatan Help
`fsl_bet()` `fslbet()`	Use FSL's Brain Extraction Tool (BET)
`fslbet.help()`	Help for FSL BET
`fsl_bin()` `fslbin()`	Binarize Image using FSL
`fslbin.help()`	fslbin Help
`fsl_binv()` `fslbinv()`	Binarized Inverse Image using FSL
`fslbinv.help()`	fslbinv Help
`fslchfiletype()`	FSL Change file type
`fslchfiletype.help()`	fslchfiletype help
`fslcmd()`	FSL Command Wrapper
`fslcog()`	Image Center of Gravity (FSL)
`fsl_cos()` `fslcos()`	Cosine Transform Image using FSL
`fslcos.help()`	fslcos Help
`fslcpgeom()`	FSL Copy Geometry
`fslcpgeom.help()`	fslcpgeom help
`fsl_dilate()` `fsldilate()`	Dilate image using FSL
`fsldir()` `fsl_dir()`	Get FSL's Directory
`fsl_div()` `fsldiv()`	Divide Images using FSL
`fsldiv.help()`	fsldiv Help
`fsl_edge()` `fsledge()`	Edge Strength Image using FSL
`fsledge.help()`	fsledge Help
`fslentropy()`	Image Mean Entropy
`fslepi_reg()` `fsl_epi_reg()` `epi_reg()`	Register EPI images to Structural image
`fsl_erode()` `fslerode()`	Erode image using FSL
`fslerode.help()`	fslerode Help
`fsl_exp()` `fslexp()`	Exponentiate Image using FSL
`fslexp.help()`	fslexp Help
`fsl_fill()` `fslfill()`	Fill image holes
`fslfill.help()`	fslfill Help
`fslfill2()`	Fill image holes with dilation then erosion
`fslhd()`	Get NIfTI header using FSL
`fslhd.help()`	FSLhd help
`fslhd.parse()`	Parse FSL Header
`fslhelp()`	Wrapper for getting fsl help
`fsl_index()` `fslindex()`	Index Image using FSL
`fslindex.help()`	fslindex Help
`fsl_log()` `fsllog()`	Log Transform Image using FSL
`fsllog.help()`	fsllog Help
`fsl_mask()` `fslmask()`	Mask image using FSL
`fslmask.help()`	fslmask Help
`fsl_maths()` `fslmaths()`	FSL Maths
`fslmaths.help()`	FSL Maths Help
`fslmean()`	Image Mean
`fsl_merge()` `fslmerge()`	Merge images using FSL
`fslmerge.help()`	FSLMerge help
`fslmax()` `fslmin()`	Get min/max of an image
`fsl_mul()` `fslmul()`	Multiply Images using FSL
`fslmul.help()`	fslmul Help
`fsl_nan()` `fslnan()`	Replace NaNs in Image using FSL
`fslnan.help()`	fslnan Help
`fsl_nanm()` `fslnanm()`	Mask NaNs in Image using FSL
`fslnanm.help()`	fslnanm Help
`fslor()` `fsl_or()`	Perform OR/Union operation on Images using FSL
`fslorient()`	FSL Orient
`fslorient.help()`	fslorient help
`fslgetorient()` `fslgetsform()` `fslgetqform()` `fslgetsformcode()` `fslgetqformcode()`	FSL Orientation Wrappers
`fslorienter()`	Wrapper for FSL Get Orientation
`fsl_rand()` `fslrand()`	Add Random Uniform Noise Image using FSL
`fslrand.help()`	fslrand Help
`fsl_randn()` `fslrandn()`	Add Random Standard Gaussian Noise Image using FSL
`fslrandn.help()`	fslrandn Help
`fslrange()`	Get range of an image
`fsl_recip()` `fslrecip()`	Reciprocal Image using FSL
`fslrecip.help()`	fslrecip Help
`fsl_rem()` `fslrem()`	Modulus Remainder of 2 Images using FSL
`fslrem.help()`	fslrem Help
`fslreorient2std()` `fslreorient2std_mat()`	FSL Orient to MNI
`fslreorient2std.help()`	fslreorient2std help
`fslrobustfov()` `fsl_robustfov()`	FSL Robust Field of View
`fslrobustfov.help()`	FSL Robust Field of View Help
`fslroi()` `fsl_roi()` `fslroi_time()`	FSL ROI
`fslsd()`	Image Standard Deviation
`fslsin()`	Sine Transform Image using FSL
`fslsin.help()`	fslsin Help
`fslslicetimer()` `fsl_slicetimer()`	FSL Slice Timing Correction
`fsl_smooth()` `fslsmooth()`	Gaussian smooth image using FSL
`fslsmooth.help()`	fslsmooth Help
`fslsmooth_in_mask()` `fsl_smooth_in_mask()`	Smooth Image Within a Mask Only
`fslsplit()` `fsl_split()`	Split images using FSL
`fslsplit.help()`	FSL Split help
`fsl_sqr()` `fslsqr()`	Square Image using FSL
`fslsqr.help()`	fslsqr Help
`fsl_sqrt()` `fslsqrt()`	Square Root Image using FSL
`fslsqrt.help()`	fslsqrt Help
`fslstats()`	FSL Stats
`fslstats.help()`	FSL Stats Help
`fsl_sub()` `fslsub()`	Subtract Images using FSL
`fslsub.help()`	fslsub Help
`fsl_sub2()` `fslsub2()`	Subsample image by factor of 2
`fslsub2.help()`	fslsub2 Help
`fslsum()`	FSL Sum
`fsl_swapdim()` `fslswapdim()`	FSL Swap Dimensions
`fslswapdim.help()`	fslswapdim help
`fsl_tan()` `fsltan()`	Tangent Transform Image using FSL
`fsltan.help()`	fsltan Help
`fsl_thresh()` `fslthresh()`	Threshold an image
`fslthresh.help()`	fslthresh Help
`fslval()`	Get value from FSL header
`fslval.help()`	fslval help
`fslview()` `fsleyes()`	Open image in FSLView
`fslview.help()`	FSLView help
`fslvol()`	FSL Volume in mL (or cubic centimeters)
`fslvolume()`	Image Volume
`fslxor()` `fsl_xor()`	Perform XOR/Exclusive Or operation on Images using FSL
`get.fsl()` `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_quickshear_mask()` `quickshear_deface_image()`	Face Removal Mask using "Quickshear Defacing for Neuroimages" (Schimke et al. 2011)
`have.fsl()` `have_fsl()`	Logical check if FSL is accessible
`intent_code(<character>)`	Extract Image intent_code attribute
`intent_name(<character>)`	Extract Image intent_name attribute
`intent_p1(<character>)`	Extract Image intent_p1 attribute
`intent_p2(<character>)`	Extract Image intent_p2 attribute
`intent_p3(<character>)`	Extract Image intent_p3 attribute
`invert_xfm()` `concat_xfm()` `fixscaleskew_xfm()`	Convert a Transformation
`magic(<character>)`	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_fname()` `mni_face_fname()`	Construct MNI Filename
`mni_img()`	Read MNI Filename
`mridefacer()` `get_mridefacer_mask()`	MRI Defacer
`qform(<character>)` `sform(<character>)`	Extract NIfTI 3D Image Orientation
`parse_avscale()`	Parse output from `avscale`
`pixdim(<character>)`	Extract Image pixdim attribute
`probtrackx()`	Probabilistic diffusion tractography with multiple fibre orientations
`qform_code(<character>)`	Extract Image qform_code attribute
`read_xfm()`	Read FSL Transformation
`readrpi()`	Read NIfTI file reoriented to RPI
`reverse_rpi_orient()` `reverse_rpi_orient_file()`	Reverse Reorientation an Image to RPI orientation
`rpi_orient()` `rpi_orient_file()` `is_rpi()` `is.rpi()`	Reorient an Image to RPI orientation
`run_first_all()`	Run FIRST All
`run_first_all.help()`	Run FIRST All Help
`scl_inter(<character>)`	Extract Image scl_inter attribute
`scl_slope(<character>)`	Extract Image scl_slope attribute
`sform_code(<character>)`	Extract Image sform_code attribute
`sizeof_hdr(<character>)`	Extract Image sizeof_hdr attribute
`slice_code(<character>)`	Extract Image slice_code attribute
`slice_duration(<character>)`	Extract Image slice_duration attribute
`slice_end(<character>)`	Extract Image slice_end attribute
`slice_start(<character>)`	Extract Image slice_start attribute
`susan()`	FSL SUSAN noise reduction
`susan.help()`	FSL SUSAN Help
`toffset(<character>)`	Extract Image toffset attribute
`topup()` `fsl_topup()`	topup - calling FSL topup
`vox_offset(<character>)`	Extract Image vox_offset attribute
`xfibres()`	Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques with Crossing Fibers

Reference

All functions