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


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Documentation for package ‘fslr’ version 1.5.0

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A B C D F G H I M N O P Q R S T V W X Z

-- A --

aux.file-method Extract Image aux.file attribute
aux.file-methods Extract Image aux.file attribute

-- B --

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
checkimg Force object to filename with .nii extension
checkimg-method Force object to filename with .nii extension
checkimg-methods Force object to filename with .nii extension
checknii Force object to filename with .nii extension
checknii-method Force object to filename with .nii extension
checknii-methods Force object to filename with .nii extension
checkout Determine of Q and S forms are consistent
check_file Wrapper for getForms with filename
check_nifti Check if nifti image or read in a nifti image
check_nifti-method Check if nifti image or read in a nifti image
check_nifti-methods Check if nifti image or read in a nifti image
check_outfile Check output filename
cog Image Center of Gravity
colorbar Add a colorbar to an ortho2 object
copyNIfTIHeader Copy NIfTI Header to an array

-- D --

datatype Change Data type for img
datatype-method Extract Image datatype attribute
datatype-methods Extract Image datatype attribute
datatyper Change Data type for img
data_type-method Extract Image data_type attribute
data_type-methods Extract Image data_type attribute
descrip-method Extract Image descrip attribute
descrip-methods Extract Image descrip attribute
dim_-method Extract Image dim_ attribute
dim_-methods Extract Image dim_ attribute
double_ortho Double Orthographic Display
dropEmptyImageDimensions Drop Empty Image Dimensions

-- F --

fast FSL FAST
fast.help FAST help
file_imgext Get Image file extension
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
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
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
fslerode Erode image using FSL
fslerode.help fslerode Help
fslexp Exponentiate Image using FSL
fslexp.help fslexp Help
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
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
fslmerge Merge images using FSL
fslmerge.help FSLMerge help
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
fslorient FSL Orient
fslorient.help fslorient help
fslrand Add Random Uniform Noise Image using FSL
fslrand.help fslrand Help
fslrandn Add Random Standard Guassian 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
fslsin Sine Transform Image using FSL
fslsin.help fslsin Help
fslsmooth Gaussian smooth image using FSL
fslsmooth.help fslsmooth 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
fslview Open image in FSLView
fslview.help FSLView help
fslvol FSL Volume in mL (or cubic centimeters)
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_biascorrect FSL Bias Correct

-- 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

-- H --

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

-- M --

magic-method Extract Image magic attribute
magic-methods Extract Image magic attribute
mask_img Mask nifti Image
melodic Run MELODIC ICA
melodic.help MELODIC help

-- N --

newnii Resets image parameters for a copied nifti object
niftiarr Make new nifti from array
nii.stub Grab nii file stubname

-- O --

ortho2 Orthographic Display, added options
ortho_diff Plot differences for Prediction and Gold Standard

-- P --

pixdim-method Extract Image pixdim attribute
pixdim-methods Extract Image pixdim attribute

-- 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

-- R --

readNIfTI2 readNIfTI with default non-reoirientation
readnii readNIfTI with default non-reoirientation
rescale_img Image Rescaler
robust_window Window image based on quantiles of Image

-- 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 --

tempimg Create temporary nii.gz file for FSL
toffset-method Extract Image toffset attribute
toffset-methods Extract Image toffset attribute

-- V --

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

-- W --

window_img nifti image windower
writeNIfTI2 writeNIfTI with default non-reoirientation
writenii writeNIfTI with default non-reoirientation

-- X --

xyz Image Center of Gravity Wrapper

-- Z --

zscore_img Get Z-score over a margin of an img