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

aux_file-methodsExtract Image aux.file attribute
bitpix-methodsExtract Image bitpix attribute
cal_max-methodsExtract Image cal.max attribute
cal_min-methodsExtract Image cal.min attribute
check_fileWrapper for getForms with filename
checkoutDetermine of Q and S forms are consistent
data_type-methodsExtract Image data_type attribute
datatype-methodsExtract Image datatype attribute
descrip-methodsExtract Image descrip attribute
dim_-methodsExtract Image dim_ attribute
download_fslDownload FSL
dtifitDTI Fitting Procedure from FSL
eddy_correctEddy Current Correction
fast.helpFAST help
flirtRegister using FLIRT
flirt_applyApply Warp from FLIRT
flirt.helpFLIRT help
fnirtRegister using FNIRT
fnirt.helpFNIRT help
fnirt_with_affineRegister using FNIRT, but doing Affine Registration as well
fnirt_with_affine_applyApplies FLIRT then FNIRT transformations
fslabsAbsolute Value Image using FSL
fslabs.helpfslabs Help
fslacosArc Cosine Transform Image using FSL
fslacos.helpfslacos Help
fsladdAdd Images using FSL
fsladd.helpfsladd Help
fsl_anatFSL Anatomical Processing Script
fsl_anat.helpfsl_anat help
fsl_applywarpApply Warp from FNIRT
fsl_applywarp.helpFSL applywarp help
fslasinArc Sine Transform Image using FSL
fslasin.helpfslasin Help
fslatanArc Tangent Transform Image using FSL
fslatan.helpfslatan Help
fsl_atlas_dirGet FSL's Standard Data Directory
fsl_avscaleScale Affine Matrix using 'avscale'
fslbetUse FSL's Brain Extraction Tool (BET)
fslbet.helpHelp for FSL BET
fsl_biascorrectFSL Bias Correct
fslbinBinarize Image using FSL
fslbin.helpfslbin Help
fsl_bin_tabQuick Tabulation for logical images
fslbinvBinarized Inverse Image using FSL
fslbinv.helpfslbinv Help
fslchfiletypeFSL Change file type
fslchfiletype.helpfslchfiletype help
fslcmdFSL Command Wrapper
fslcogImage Center of Gravity (FSL)
fslcosCosine Transform Image using FSL
fslcos.helpfslcos Help
fslcpgeomFSL Copy Geometry
fslcpgeom.helpfslcpgeom help
fsl_data_dirGet FSL's Data Directory
fsl_diceCalculate Dice Coefficient of 2 Binary images
fsldilateDilate image using FSL
fsldirGet FSL's Directory
fsldivDivide Images using FSL
fsldiv.helpfsldiv Help
fsledgeEdge Strength Image using FSL
fsledge.helpfsledge Help
fslentropyImage Mean Entropy
fslerodeErode image using FSL
fslerode.helpfslerode Help
fslexpExponentiate Image using FSL
fslexp.helpfslexp Help
fslfillFill image holes
fslfill2Fill image holes with dilation then erosion
fslfill.helpfslfill Help
fslhdGet NIfTI header using FSL
fslhd.helpFSLhd help
fslhd.parseParse FSL Header
fslhelpWrapper for getting fsl help
fslindexIndex Image using FSL
fslindex.helpfslindex Help
fsllogLog Transform Image using FSL
fsllog.helpfsllog Help
fslmaskMask image using FSL
fslmask.helpfslmask Help
fslmathsFSL Maths
fslmaths.helpFSL Maths Help
fslmeanImage Mean
fslmergeMerge images using FSL
fslmerge.helpFSLMerge help
fslmin_maxGet min/max of an image
fslmulMultiply Images using FSL
fslmul.helpfslmul Help
fslnanReplace NaNs in Image using FSL
fslnan.helpfslnan Help
fslnanmMask NaNs in Image using FSL
fslnanm.helpfslnanm Help
fslorientFSL Orient
fslorienterWrapper for FSL Get Orientation
fslorient.helpfslorient help
fslorient_wrapFSL Orientation Wrappers
fslrandAdd Random Uniform Noise Image using FSL
fslrand.helpfslrand Help
fslrandnAdd Random Standard Guassian Noise Image using FSL
fslrandn.helpfslrandn Help
fslrangeGet range of an image
fslrecipReciprocal Image using FSL
fslrecip.helpfslrecip Help
fslremModulus Remainder of 2 Images using FSL
fslrem.helpfslrem Help
fslreorient2stdFSL Orient to MNI
fslreorient2std.helpfslreorient2std help
fslrobustfovFSL Robust Field of View
fslrobustfov.helpFSL Robust Field of View Help
fslroiFSL ROI
fslsdImage Standard Deviation
fslsinSine Transform Image using FSL
fslsin.helpfslsin Help
fslslicetimerFSL Slice Timing Correction
fslsmoothGaussian smooth image using FSL
fslsmooth.helpfslsmooth Help
fslsmooth_in_maskSmooth Image Within a Mask Only
fslsplitSplit images using FSL
fslsplit.helpFSL Split help
fslsqrSquare Image using FSL
fslsqr.helpfslsqr Help
fslsqrtSquare Root Image using FSL
fslsqrt.helpfslsqrt Help
fslstatsFSL Stats
fslstats.helpFSL Stats Help
fsl_std_dirGet FSL's Standard Data Directory
fslsubSubtract Images using FSL
fslsub2Subsample image by factor of 2
fslsub2.helpfslsub2 Help
fslsub.helpfslsub Help
fslsumFSL Sum
fslswapdimFSL Swap Dimensions
fslswapdim.helpfslswapdim help
fsltanTangent Transform Image using FSL
fsltan.helpfsltan Help
fslthreshThreshold an image
fslthresh.helpfslthresh Help
fslvalGet value from FSL header
fslval.helpfslval help
fsl_versionFind FSL Version
fslviewOpen image in FSLView
fslview.helpFSLView help
fslvolFSL Volume in mL (or cubic centimeters)
fslvolumeImage Volume
getFormsGet Q and S Forms of orientation matrix
get.fslCreate command declaring FSLDIR
get.fsloutputDetermine FSL output type
get.imgextDetermine extension of image based on FSLOUTPUTTYPE
have.fslLogical check if FSL is accessible
intent_code-methodsExtract Image intent_code attribute
intent_name-methodsExtract Image intent_name attribute
intent_p1-methodsExtract Image intent_p1 attribute
intent_p2-methodsExtract Image intent_p2 attribute
intent_p3-methodsExtract Image intent_p3 attribute
magic-methodsExtract Image magic attribute
mcflirtFSL Motion Correction
mcflirt.helpMCFLIRT help
melodicRun MELODIC ICA
melodic.helpMELODIC help
mid_sagittal_alignMid-Sagittal Plane Alignment
mni_fnameConstruct MNI Filename
mni_imgRead MNI Filename
orientation-methodsExtract NIfTI 3D Image Orientation
parse_avscaleParse output from 'avscale'
pixdim-methodsExtract Image pixdim attribute
probtrackxProbabilistic diffusion tractography with multiple fibre...
qform_code-methodsExtract Image qform_code attribute
readrpiRead NIfTI file reoriented to RPI
reverse_rpi_orientReverse Reorientation an Image to RPI orientation
rpi_orientReorient an Image to RPI orientation
run_first_allRun FIRST All
run_first_all.helpRun FIRST All Help
scl_inter-methodsExtract Image scl_inter attribute
scl_slope-methodsExtract Image scl_slope attribute
sform_code-methodsExtract Image sform_code attribute
sizeof_hdr-methodsExtract Image sizeof_hdr attribute
slice_code-methodsExtract Image slice_code attribute
slice_duration-methodsExtract Image slice_duration attribute
slice_end-methodsExtract Image slice_end attribute
slice_start-methodsExtract Image slice_start attribute
susanFSL SUSAN noise reduction
susan.helpFSL SUSAN Help
toffset-methodsExtract Image toffset attribute
topuptopup - calling FSL topup
vox_offset-methodsExtract Image vox_offset attribute
xfibresBayesian Estimation of Diffusion Parameters Obtained using...
fslr documentation built on May 29, 2017, 11:07 a.m.