| applytopup - calling FSL applytopup | applytopup apply_topup fsl_applytopup |
| Extract Image aux.file attribute | aux.file,character-method aux.file-methods |
| Extract Image bitpix attribute | bitpix,character-method bitpix-methods |
| Extract Image cal.max attribute | cal.max,character-method cal.max-methods |
| Extract Image cal.min attribute | cal.min,character-method cal.min-methods |
| Wrapper for getForms with filename | check_file |
| Determine of Q and S forms are consistent | checkout |
| Extract Image data_type attribute | data_type,character-method data_type-methods |
| Extract Image datatype attribute | datatype,character-method datatype-methods |
| Extract Image descrip attribute | descrip,character-method descrip-methods |
| Extract Image dim_ attribute | dim_,character-method dim_-methods |
| Download FSL | download_fsl |
| DTI Fitting Procedure from FSL | dtifit |
| Eddy Current Correction | eddy |
| Eddy Current Correction | eddy_correct |
| Enforce Either Qform or Sform is set | enforce_form |
| Face Removal Mask | deface_image face_removal_mask |
| FSL FAST | fast fast_all fast_nobias fast_nobias_all fslfast fslfast_nobias fsl_fast fsl_fast_nobias |
| FAST help | fast.help |
| Register using FLIRT | flirt |
| Apply Warp from FLIRT | flirt_apply |
| FLIRT help | flirt.help flirt_apply.help |
| Register using FNIRT | fnirt |
| Register using FNIRT, but doing Affine Registration as well | fnirt_with_affine |
| Applies FLIRT then FNIRT transformations | fnirt_with_affine_apply |
| FNIRT help | fnirt.help |
| Absolute Value Image using FSL | fslabs fsl_abs |
| Arc Cosine Transform Image using FSL | fslacos fsl_acos |
| Add Images using FSL | fsladd fsl_add |
| FSL Anatomical Processing Script | fsl_anat |
| fsl_anat help | fsl_anat.help |
| Apply Warp from FNIRT | fsl_applywarp |
| FSL applywarp help | fsl_applywarp.help |
| Arc Sine Transform Image using FSL | fslasin fsl_asin |
| Arc Tangent Transform Image using FSL | fslatan fsl_atan |
| Get FSL's Standard Data Directory | fsl_atlas_dir |
| Scale Affine Matrix using 'avscale' | avscale fsl_avscale |
| Use FSL's Brain Extraction Tool (BET) | fslbet fsl_bet |
| FSL Bias Correct | fsl_biascorrect |
| Binarize Image using FSL | fslbin fsl_bin |
| Quick Tabulation for logical images | fsl_bin_tab |
| Binarized Inverse Image using FSL | fslbinv fsl_binv |
| Form clusters, report information about clusters and/or perform cluster-based inference. Wrapper for 'cluster' | fslcluster fsl_cluster read_cluster_table |
| Cosine Transform Image using FSL | fslcos fsl_cos |
| Get FSL's Data Directory | fsl_data_dir |
| Tool to deface a structural T1w image. | fsl_deface |
| Calculate Dice Coefficient of 2 Binary images | fsl_dice |
| Dilate image using FSL | fsldilate fsl_dilate |
| Divide Images using FSL | fsldiv fsl_div |
| Edge Strength Image using FSL | fsledge fsl_edge |
| Erode image using FSL | fslerode fsl_erode |
| Exponentiate Image using FSL | fslexp fsl_exp |
| Fill image holes | fslfill fsl_fill |
| Index Image using FSL | fslindex fsl_index |
| Log Transform Image using FSL | fsllog fsl_log |
| Mask image using FSL | fslmask fsl_mask |
| FSL Maths | fslmaths fsl_maths |
| Merge images using FSL | fslmerge fsl_merge |
| Multiply Images using FSL | fslmul fsl_mul |
| Replace NaNs in Image using FSL | fslnan fsl_nan |
| Mask NaNs in Image using FSL | fslnanm fsl_nanm |
| Add Random Uniform Noise Image using FSL | fslrand fsl_rand |
| Add Random Standard Gaussian Noise Image using FSL | fslrandn fsl_randn |
| Reciprocal Image using FSL | fslrecip fsl_recip |
| Modulus Remainder of 2 Images using FSL | fslrem fsl_rem |
| Resample an Image to Specific Voxel Size | fsl_resample |
| Gaussian smooth image using FSL | fslsmooth fsl_smooth |
| Smoothness Estimation using 'smoothest' | fsl_smoothest |
| Square Image using FSL | fslsqr fsl_sqr |
| Square Root Image using FSL | fslsqrt fsl_sqrt |
| FSL Standard Space ROI | fsl_standard_space_roi |
| Get FSL's Standard Data Directory | fsl_std_dir fsl_std_file |
| Subtract Images using FSL | fslsub fsl_sub |
| Subsample image by factor of 2 | fslsub2 fsl_sub2 |
| FSL Swap Dimensions | fslswapdim fsl_swapdim |
| Tangent Transform Image using FSL | fsltan fsl_tan |
| Threshold an image | fslthresh fsl_thresh |
| FSL Timeseries Plot using `fsl_tsplot` (not `tsplot`) | fsl_tsplot fsl_tsplot.help |
| Find FSL Version | fslversion fsl_version fsl_version_gt5 |
| fslabs Help | fslabs.help |
| fslacos Help | fslacos.help |
| fsladd Help | fsladd.help |
| Logical AND with Images using FSL | fsland fsl_and |
| fslasin Help | fslasin.help |
| fslatan Help | fslatan.help |
| Help for FSL BET | fslbet.help |
| fslbin Help | fslbin.help |
| fslbinv Help | fslbinv.help |
| FSL Change file type | fslchfiletype |
| fslchfiletype help | fslchfiletype.help |
| FSL Command Wrapper | fslcmd |
| Image Center of Gravity (FSL) | fslcog |
| fslcos Help | fslcos.help |
| FSL Copy Geometry | fslcpgeom |
| fslcpgeom help | fslcpgeom.help |
| Get FSL's Directory | fsldir fsl_dir |
| fsldiv Help | fsldiv.help |
| fsledge Help | fsledge.help |
| Image Mean Entropy | fslentropy |
| Register EPI images to Structural image | epi_reg fslepi_reg fsl_epi_reg |
| fslerode Help | fslerode.help |
| fslexp Help | fslexp.help |
| fslfill Help | fslfill.help |
| Fill image holes with dilation then erosion | fslfill2 |
| FSL Orientation Wrappers | fslgetorient fslgetqform fslgetqformcode fslgetsform fslgetsformcode |
| Get NIfTI header using FSL | fslhd |
| FSLhd help | fslhd.help |
| Parse FSL Header | fslhd.parse |
| Wrapper for getting fsl help | fslhelp |
| fslindex Help | fslindex.help |
| fsllog Help | fsllog.help |
| fslmask Help | fslmask.help |
| FSL Maths Help | fslmaths.help |
| Get min/max of an image | fslmax fslmin |
| Image Mean | fslmean |
| FSLMerge help | fslmerge.help |
| fslmul Help | fslmul.help |
| fslnan Help | fslnan.help |
| fslnanm Help | fslnanm.help |
| Perform OR/Union operation on Images using FSL | fslor fsl_or |
| FSL Orient | fslorient |
| fslorient help | fslorient.help |
| Wrapper for FSL Get Orientation | fslorienter |
| fslrand Help | fslrand.help |
| fslrandn Help | fslrandn.help |
| Get range of an image | fslrange |
| fslrecip Help | fslrecip.help |
| fslrem Help | fslrem.help |
| FSL Orient to MNI | fslreorient2std fslreorient2std_mat |
| fslreorient2std help | fslreorient2std.help |
| FSL Robust Field of View | fslrobustfov fsl_robustfov |
| FSL Robust Field of View Help | fslrobustfov.help |
| FSL ROI | fslroi fslroi_time fsl_roi |
| Image Standard Deviation | fslsd |
| Sine Transform Image using FSL | fslsin |
| fslsin Help | fslsin.help |
| FSL Slice Timing Correction | fslslicetimer fsl_slicetimer |
| Smooth Image Within a Mask Only | fslsmooth_in_mask fsl_smooth_in_mask |
| fslsmooth Help | fslsmooth.help |
| Split images using FSL | fslsplit fsl_split |
| FSL Split help | fslsplit.help |
| fslsqr Help | fslsqr.help |
| fslsqrt Help | fslsqrt.help |
| FSL Stats | fslstats |
| FSL Stats Help | fslentropy.help fslmean.help fslrange.help fslsd.help fslstats.help |
| fslsub Help | fslsub.help |
| fslsub2 Help | fslsub2.help |
| FSL Sum | fslsum |
| fslswapdim help | fslswapdim.help |
| fsltan Help | fsltan.help |
| fslthresh Help | fslthresh.help |
| Get value from FSL header | fslval |
| fslval help | fslval.help |
| Open image in FSLView | fsleyes fslview |
| FSLView help | fslview.help |
| FSL Volume in mL (or cubic centimeters) | fslvol |
| Image Volume | fslvolume |
| Perform XOR/Exclusive Or operation on Images using FSL | fslxor fsl_xor |
| Face Removal Mask using "Quickshear Defacing for Neuroimages" (Schimke et al. 2011) | get_quickshear_mask quickshear_deface_image |
| Create command declaring FSLDIR | get.fsl get_fsl |
| Determine FSL output type | get.fsloutput |
| Determine extension of image based on FSLOUTPUTTYPE | get.imgext |
| Get Q and S Forms of orientation matrix | getForms |
| Logical check if FSL is accessible | have.fsl have_fsl |
| Extract Image intent_code attribute | intent_code,character-method intent_code-methods |
| Extract Image intent_name attribute | intent_name,character-method intent_name-methods |
| Extract Image intent_p1 attribute | intent_p1,character-method intent_p1-methods |
| Extract Image intent_p2 attribute | intent_p2,character-method intent_p2-methods |
| Extract Image intent_p3 attribute | intent_p3,character-method intent_p3-methods |
| Convert a Transformation | concat_xfm fixscaleskew_xfm invert_xfm |
| Extract Image magic attribute | magic,character-method magic-methods |
| FSL Motion Correction | mcflirt |
| MCFLIRT help | mcflirt.help |
| Run MELODIC ICA | melodic |
| MELODIC help | melodic.help |
| Mid-Sagittal Plane Alignment | apply_mid_sagittal_align mid_sagittal_align |
| Construct MNI Filename | mni_face_fname mni_fname |
| Read MNI Filename | mni_img |
| MRI Defacer | get_mridefacer_mask mridefacer |
| Parse output from 'avscale' | parse_avscale |
| Extract Image pixdim attribute | pixdim,character-method pixdim-methods |
| Probabilistic diffusion tractography with multiple fibre orientations | probtrackx |
| Extract Image qform_code attribute | qform_code,character-method qform_code-methods |
| Extract NIfTI 3D Image Orientation | qform,character qform,character-method sform,character sform,character-method |
| Read FSL Transformation | read_xfm |
| Read NIfTI file reoriented to RPI | readrpi |
| Reverse Reorientation an Image to RPI orientation | reverse_rpi_orient reverse_rpi_orient_file |
| Reorient an Image to RPI orientation | is.rpi is_rpi rpi_orient rpi_orient_file |
| Run FIRST All | run_first_all |
| Run FIRST All Help | run_first_all.help |
| Extract Image scl_inter attribute | scl_inter,character-method scl_inter-methods |
| Extract Image scl_slope attribute | scl_slope,character-method scl_slope-methods |
| Extract Image sform_code attribute | sform_code,character-method sform_code-methods |
| Extract Image sizeof_hdr attribute | sizeof_hdr,character-method sizeof_hdr-methods |
| Extract Image slice_code attribute | slice_code,character-method slice_code-methods |
| Extract Image slice_duration attribute | slice_duration,character-method slice_duration-methods |
| Extract Image slice_end attribute | slice_end,character-method slice_end-methods |
| Extract Image slice_start attribute | slice_start,character-method slice_start-methods |
| FSL SUSAN noise reduction | susan |
| FSL SUSAN Help | susan.help |
| Extract Image toffset attribute | toffset,character-method toffset-methods |
| topup - calling FSL topup | fsl_topup topup |
| Extract Image vox_offset attribute | vox_offset,character-method vox_offset-methods |
| Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques with Crossing Fibers | bedpostx xfibres |
