Wrapper Functions for 'FSL' ('FMRIB' Software Library) from
Functional MRI of the Brain ('FMRIB')
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Documentation for package ‘fslr’ version 2.25.2
Help Pages
A B C D E F G H I M P Q R S T V X
-- A --
| applytopup | applytopup - calling FSL applytopup |
| apply_topup | applytopup - calling FSL applytopup |
| aux.file-method | Extract Image aux.file attribute |
| aux.file-methods | Extract Image aux.file attribute |
| avscale | Scale Affine Matrix using 'avscale' |
-- B --
| bedpostx | Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques with Crossing Fibers |
| 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 |
| checkout | Determine of Q and S forms are consistent |
| check_file | Wrapper for getForms with filename |
| concat_xfm | Convert a Transformation |
-- D --
| datatype-method | Extract Image datatype attribute |
| datatype-methods | Extract Image datatype attribute |
| data_type-method | Extract Image data_type attribute |
| data_type-methods | Extract Image data_type attribute |
| deface_image | Face Removal Mask |
| descrip-method | Extract Image descrip attribute |
| descrip-methods | Extract Image descrip attribute |
| dim_-method | Extract Image dim_ attribute |
| dim_-methods | Extract Image dim_ attribute |
| download_fsl | Download FSL |
| dtifit | DTI Fitting Procedure from FSL |
-- E --
| eddy | Eddy Current Correction |
| eddy_correct | Eddy Current Correction |
| enforce_form | Enforce Either Qform or Sform is set |
| epi_reg | Register EPI images to Structural image |
-- F --
| face_removal_mask | Face Removal Mask |
| fast | FSL FAST |
| fast.help | FAST help |
| fast_all | FSL FAST |
| fast_nobias | FSL FAST |
| fast_nobias_all | FSL FAST |
| fixscaleskew_xfm | Convert a Transformation |
| 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 |
| fsland | Logical AND with Images using FSL |
| 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 |
| fslcluster | Form clusters, report information about clusters and/or perform cluster-based inference. Wrapper for 'cluster' |
| 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 |
| fslentropy | Image Mean Entropy |
| fslentropy.help | FSL Stats Help |
| fslepi_reg | Register EPI images to Structural image |
| fslerode | Erode image using FSL |
| fslerode.help | fslerode Help |
| fslexp | Exponentiate Image using FSL |
| fslexp.help | fslexp Help |
| fsleyes | Open image in FSLView |
| fslfast | FSL FAST |
| fslfast_nobias | FSL FAST |
| fslfill | Fill image holes |
| fslfill.help | fslfill Help |
| fslfill2 | Fill image holes with dilation then erosion |
| fslgetorient | FSL Orientation Wrappers |
| fslgetqform | FSL Orientation Wrappers |
| fslgetqformcode | FSL Orientation Wrappers |
| fslgetsform | FSL Orientation Wrappers |
| fslgetsformcode | 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 | 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 |
| fslmax | Get min/max of an image |
| fslmean | Image Mean |
| fslmean.help | FSL Stats Help |
| fslmerge | Merge images using FSL |
| fslmerge.help | FSLMerge help |
| fslmin | Get min/max of an image |
| 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 |
| fslor | Perform OR/Union operation on Images using FSL |
| fslorient | FSL Orient |
| fslorient.help | fslorient help |
| fslorienter | Wrapper for FSL Get Orientation |
| fslrand | Add Random Uniform Noise Image using FSL |
| fslrand.help | fslrand Help |
| fslrandn | Add Random Standard Gaussian 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 |
| fslreorient2std_mat | FSL Orient to MNI |
| fslrobustfov | FSL Robust Field of View |
| fslrobustfov.help | FSL Robust Field of View Help |
| fslroi | FSL ROI |
| fslroi_time | FSL ROI |
| fslsd | Image Standard Deviation |
| fslsd.help | FSL Stats Help |
| fslsin | Sine Transform Image using FSL |
| fslsin.help | fslsin Help |
| fslslicetimer | FSL Slice Timing Correction |
| fslsmooth | Gaussian smooth image using FSL |
| fslsmooth.help | fslsmooth Help |
| fslsmooth_in_mask | Smooth Image Within a Mask Only |
| fslsplit | Split images using FSL |
| fslsplit.help | FSL Split 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 |
| fslversion | Find FSL Version |
| 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 |
| 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_and | Logical AND with Images using FSL |
| fsl_applytopup | applytopup - calling FSL applytopup |
| 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_binv | Binarized Inverse Image using FSL |
| fsl_bin_tab | Quick Tabulation for logical images |
| 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_dir | Get FSL's Directory |
| fsl_div | Divide Images using FSL |
| fsl_edge | Edge Strength Image using FSL |
| fsl_epi_reg | Register EPI images to Structural image |
| fsl_erode | Erode image using FSL |
| fsl_exp | Exponentiate Image using FSL |
| fsl_fast | FSL FAST |
| fsl_fast_nobias | FSL FAST |
| 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_or | Perform OR/Union operation on Images 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_robustfov | FSL Robust Field of View |
| fsl_roi | FSL ROI |
| fsl_slicetimer | FSL Slice Timing Correction |
| fsl_smooth | Gaussian smooth image using FSL |
| fsl_smoothest | Smoothness Estimation using 'smoothest' |
| fsl_smooth_in_mask | Smooth Image Within a Mask Only |
| fsl_split | Split images using FSL |
| fsl_sqr | Square Image using FSL |
| fsl_sqrt | Square Root Image using FSL |
| fsl_std_dir | Get FSL's Standard Data Directory |
| fsl_std_file | 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_topup | topup - calling FSL topup |
| fsl_tsplot | FSL Timeseries Plot using 'fsl_tsplot' (not 'tsplot') |
| fsl_tsplot.help | FSL Timeseries Plot using 'fsl_tsplot' (not 'tsplot') |
| fsl_version | Find FSL Version |
| fsl_version_gt5 | Find FSL Version |
| fsl_xor | Perform XOR/Exclusive Or operation on Images using FSL |
-- 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 |
| get_fsl | Create command declaring FSLDIR |
| get_mridefacer_mask | MRI Defacer |
| get_quickshear_mask | Face Removal Mask using "Quickshear Defacing for Neuroimages" (Schimke et al. 2011) |
-- H --
| have.fsl | Logical check if FSL is accessible |
| 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 |
| invert_xfm | Convert a Transformation |
| is.rpi | Reorient an Image to RPI orientation |
| is_rpi | Reorient an Image to RPI orientation |
-- M --
| magic-method | Extract Image magic attribute |
| 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_face_fname | Construct MNI Filename |
| mni_fname | Construct MNI Filename |
| mni_img | Read MNI Filename |
| mridefacer | MRI Defacer |
-- P --
| parse_avscale | Parse output from 'avscale' |
| pixdim-method | Extract Image pixdim attribute |
| pixdim-methods | Extract Image pixdim attribute |
| probtrackx | Probabilistic diffusion tractography with multiple fibre orientations |
-- 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 |
| quickshear_deface_image | Face Removal Mask using "Quickshear Defacing for Neuroimages" (Schimke et al. 2011) |
-- R --
| readrpi | Read NIfTI file reoriented to RPI |
| read_cluster_table | Form clusters, report information about clusters and/or perform cluster-based inference. Wrapper for 'cluster' |
| read_xfm | Read FSL Transformation |
| reverse_rpi_orient | Reverse Reorientation an Image to RPI orientation |
| reverse_rpi_orient_file | Reverse Reorientation an Image to RPI orientation |
| rpi_orient | Reorient an Image to RPI orientation |
| rpi_orient_file | Reorient an Image to RPI orientation |
| run_first_all | Run FIRST All |
| run_first_all.help | Run FIRST All Help |
-- 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 --
| toffset-method | Extract Image toffset attribute |
| toffset-methods | Extract Image toffset attribute |
| topup | topup - calling FSL topup |
-- V --
| vox_offset-method | Extract Image vox_offset attribute |
| vox_offset-methods | Extract Image vox_offset attribute |
-- X --
| xfibres | Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques with Crossing Fibers |