Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')
FSL Bias Correct
Quick Tabulation for logical images
Mid-Sagittal Plane Alignment
Construct MNI Filename
Read MNI Filename
Run FIRST All
Extract Image scl_inter attribute
Extract Image scl_slope attribute
Extract Image sform_code attribute
Extract Image sizeof_hdr attribute
Extract Image slice_code attribute
Extract Image slice_duration attribute
Extract Image slice_end attribute
Extract Image slice_start attribute
FSL SUSAN Help
Apply Warp from FNIRT
Get FSL's Standard Data Directory
Scale Affine Matrix using avscale
fslrem Help
FSL Sum
fslswapdim help
Image Volume
Run MELODIC ICA
FSL Anatomical Processing Script
FSL applywarp help
Find FSL Version
fslabs Help
fsldiv Help
fslrecip Help
Extract Image aux.file attribute
Extract Image bitpix attribute
Extract Image cal.max attribute
Extract Image cal.min attribute
Wrapper for getForms with filename
Determine of Q and S forms are consistent
Extract Image data_type attribute
Extract Image datatype attribute
Extract Image descrip attribute
Extract Image dim_ attribute
Download FSL
applytopup - calling FSL applytopup
DTI Fitting Procedure from FSL
Eddy Current Correction
Eddy Current Correction
Enforce Either Qform or Sform is set
Face Removal Mask
FAST help
Applies FLIRT then FNIRT transformations
FSL FAST
FLIRT help
Register using FLIRT
Apply Warp from FLIRT
FNIRT help
Register using FNIRT
Register using FNIRT, but doing Affine Registration as well
fsl_anat help
Form clusters, report information about clusters and/or perform cluste...
Get FSL's Data Directory
Tool to deface a structural T1w image.
Calculate Dice Coefficient of 2 Binary images
Resample an Image to Specific Voxel Size
Smoothness Estimation using smoothest
Get FSL's Standard Data Directory
FSL Timeseries Plot using fsl_tsplot (not tsplot)
Absolute Value Image using FSL
fslacos Help
Arc Cosine Transform Image using FSL
fsladd Help
Add Images using FSL
Logical AND with Images using FSL
fslasin Help
Arc Sine Transform Image using FSL
fslatan Help
Arc Tangent Transform Image using FSL
Help for FSL BET
Use FSL's Brain Extraction Tool (BET)
fslbin Help
Binarize Image using FSL
fslbinv Help
Binarized Inverse Image using FSL
fslchfiletype help
FSL Change file type
FSL Command Wrapper
Image Center of Gravity (FSL)
fslcos Help
Cosine Transform Image using FSL
fslcpgeom help
FSL Copy Geometry
Dilate image using FSL
Get FSL's Directory
Divide Images using FSL
fsledge Help
Edge Strength Image using FSL
Image Mean Entropy
Register EPI images to Structural image
fslerode Help
Erode image using FSL
fslexp Help
Exponentiate Image using FSL
fslfill Help
Fill image holes
Fill image holes with dilation then erosion
FSLhd help
Parse FSL Header
Get NIfTI header using FSL
Wrapper for getting fsl help
fslindex Help
Convert a Transformation
Index Image using FSL
fsllog Help
Log Transform Image using FSL
fslmask Help
Mask image using FSL
FSL Maths Help
FSL Maths
Image Mean
FSLMerge help
Extract Image magic attribute
MCFLIRT help
Merge images using FSL
Get min/max of an image
fslmul Help
Multiply Images using FSL
fslnan Help
Replace NaNs in Image using FSL
fslnanm Help
Mask NaNs in Image using FSL
Reciprocal Image using FSL
Perform OR/Union operation on Images using FSL
fslorient help
FSL Orient
FSL Orientation Wrappers
Wrapper for FSL Get Orientation
fslrand Help
Add Random Uniform Noise Image using FSL
fslrandn Help
Add Random Standard Gaussian Noise Image using FSL
Get range of an image
Modulus Remainder of 2 Images using FSL
fslreorient2std help
FSL Orient to MNI
FSL Robust Field of View Help
FSL Robust Field of View
FSL ROI
Image Standard Deviation
fslsin Help
Sine Transform Image using FSL
FSL Slice Timing Correction
fslsmooth Help
Gaussian smooth image using FSL
Smooth Image Within a Mask Only
FSL Split help
Split images using FSL
fslsqr Help
FSL Motion Correction
Square Image using FSL
fslsqrt Help
Square Root Image using FSL
FSL Stats Help
FSL Stats
fslsub Help
Subtract Images using FSL
fslsub2 Help
Subsample image by factor of 2
MELODIC help
FSL Swap Dimensions
fsltan Help
Tangent Transform Image using FSL
fslthresh Help
Threshold an image
fslval help
Get value from FSL header
FSLView help
Open image in FSLView
FSL Volume in mL (or cubic centimeters)
Perform XOR/Exclusive Or operation on Images using FSL
Create command declaring FSLDIR
Determine FSL output type
Determine extension of image based on FSLOUTPUTTYPE
Face Removal Mask using "Quickshear Defacing for Neuroimages" (Schimke...
Get Q and S Forms of orientation matrix
Logical check if FSL is accessible
Extract Image intent_code attribute
Extract Image intent_name attribute
Extract Image intent_p1 attribute
Extract Image intent_p2 attribute
Extract Image intent_p3 attribute
MRI Defacer
Extract NIfTI 3D Image Orientation
Parse output from avscale
Extract Image pixdim attribute
Probabilistic diffusion tractography with multiple fibre orientations
Extract Image qform_code attribute
Read FSL Transformation
Read NIfTI file reoriented to RPI
Reverse Reorientation an Image to RPI orientation
Reorient an Image to RPI orientation
Run FIRST All Help
FSL SUSAN noise reduction
Extract Image toffset attribute
topup - calling FSL topup
Extract Image vox_offset attribute
Bayesian Estimation of Diffusion Parameters Obtained using Sampling Te...
Wrapper functions that interface with 'FSL' <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>, a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'FSL' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'FSL' command and returns an R object of class 'nifti' if desired.