applytopup              applytopup - calling FSL applytopup
aux.file-methods        Extract Image aux.file attribute
bitpix-methods          Extract Image bitpix attribute
cal.max-methods         Extract Image cal.max attribute
cal.min-methods         Extract Image cal.min attribute
check_file              Wrapper for getForms with filename
checkout                Determine of Q and S forms are consistent
data_type-methods       Extract Image data_type attribute
datatype-methods        Extract Image datatype attribute
descrip-methods         Extract Image descrip attribute
dim_-methods            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       Face Removal Mask
fast                    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_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_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_bin_tab             Quick Tabulation for logical images
fsl_binv                Binarized Inverse Image using FSL
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_div                 Divide Images using FSL
fsl_edge                Edge Strength Image using FSL
fsl_erode               Erode image using FSL
fsl_exp                 Exponentiate Image using FSL
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_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_smooth              Gaussian smooth image using FSL
fsl_smoothest           Smoothness Estimation using 'smoothest'
fsl_sqr                 Square Image using FSL
fsl_sqrt                Square Root Image using FSL
fsl_std_dir             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_tsplot              FSL Timeseries Plot using 'fsl_tsplot' (not
                        'tsplot')
fsl_version             Find FSL Version
fslabs.help             fslabs Help
fslacos.help            fslacos Help
fsladd.help             fsladd Help
fsland                  Logical AND with Images using FSL
fslasin.help            fslasin Help
fslatan.help            fslatan Help
fslbet.help             Help for FSL BET
fslbin.help             fslbin Help
fslbinv.help            fslbinv Help
fslchfiletype           FSL Change file type
fslchfiletype.help      fslchfiletype help
fslcmd                  FSL Command Wrapper
fslcog                  Image Center of Gravity (FSL)
fslcos.help             fslcos Help
fslcpgeom               FSL Copy Geometry
fslcpgeom.help          fslcpgeom help
fsldir                  Get FSL's Directory
fsldiv.help             fsldiv Help
fsledge.help            fsledge Help
fslentropy              Image Mean Entropy
fslepi_reg              Register EPI images to Structural image
fslerode.help           fslerode Help
fslexp.help             fslexp Help
fslfill.help            fslfill Help
fslfill2                Fill image holes with dilation then erosion
fslgetorient            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.help           fslindex Help
fsllog.help             fsllog Help
fslmask.help            fslmask Help
fslmaths.help           FSL Maths Help
fslmax                  Get min/max of an image
fslmean                 Image Mean
fslmerge.help           FSLMerge help
fslmul.help             fslmul Help
fslnan.help             fslnan Help
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.help            fslrand Help
fslrandn.help           fslrandn Help
fslrange                Get range of an image
fslrecip.help           fslrecip Help
fslrem.help             fslrem Help
fslreorient2std         FSL Orient to MNI
fslreorient2std.help    fslreorient2std help
fslrobustfov            FSL Robust Field of View
fslrobustfov.help       FSL Robust Field of View Help
fslroi                  FSL ROI
fslsd                   Image Standard Deviation
fslsin                  Sine Transform Image using FSL
fslsin.help             fslsin Help
fslslicetimer           FSL Slice Timing Correction
fslsmooth.help          fslsmooth Help
fslsmooth_in_mask       Smooth Image Within a Mask Only
fslsplit                Split images using FSL
fslsplit.help           FSL Split help
fslsqr.help             fslsqr Help
fslsqrt.help            fslsqrt Help
fslstats                FSL Stats
fslstats.help           FSL Stats Help
fslsub.help             fslsub Help
fslsub2.help            fslsub2 Help
fslsum                  FSL Sum
fslswapdim.help         fslswapdim help
fsltan.help             fsltan Help
fslthresh.help          fslthresh Help
fslval                  Get value from FSL header
fslval.help             fslval help
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
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     Face Removal Mask using "Quickshear Defacing
                        for Neuroimages" (Schimke et al. 2011)
have.fsl                Logical check if FSL is accessible
intent_code-methods     Extract Image intent_code attribute
intent_name-methods     Extract Image intent_name attribute
intent_p1-methods       Extract Image intent_p1 attribute
intent_p2-methods       Extract Image intent_p2 attribute
intent_p3-methods       Extract Image intent_p3 attribute
invert_xfm              Convert a Transformation
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_fname               Construct MNI Filename
mni_img                 Read MNI Filename
mridefacer              MRI Defacer
parse_avscale           Parse output from 'avscale'
pixdim-methods          Extract Image pixdim attribute
probtrackx              Probabilistic diffusion tractography with
                        multiple fibre orientations
qform,character-method
                        Extract NIfTI 3D Image Orientation
qform_code-methods      Extract Image qform_code attribute
read_xfm                Read FSL Transformation
readrpi                 Read NIfTI file reoriented to RPI
reverse_rpi_orient      Reverse Reorientation an Image to RPI
                        orientation
rpi_orient              Reorient an Image to RPI orientation
run_first_all           Run FIRST All
run_first_all.help      Run FIRST All Help
scl_inter-methods       Extract Image scl_inter attribute
scl_slope-methods       Extract Image scl_slope attribute
sform_code-methods      Extract Image sform_code attribute
sizeof_hdr-methods      Extract Image sizeof_hdr attribute
slice_code-methods      Extract Image slice_code attribute
slice_duration-methods
                        Extract Image slice_duration attribute
slice_end-methods       Extract Image slice_end attribute
slice_start-methods     Extract Image slice_start attribute
susan                   FSL SUSAN noise reduction
susan.help              FSL SUSAN Help
toffset-methods         Extract Image toffset attribute
topup                   topup - calling FSL topup
vox_offset-methods      Extract Image vox_offset attribute
xfibres                 Bayesian Estimation of Diffusion Parameters
                        Obtained using Sampling Techniques with
                        Crossing Fibers
