Package index • niflowr

All functions

ni_afni_a_boverlap(): AFNI ABoverlap
ni_afni_afn_ito_nifti(): AFNI AFNItoNIFTI
ni_afni_align_epi_anat_py(): AFNI AlignEpiAnatPy
ni_afni_allineate(): AFNI Allineate
ni_afni_auto_tcorrelate(): AFNI AutoTcorrelate
ni_afni_auto_tlrc(): AFNI AutoTLRC
ni_afni_autobox(): AFNI Autobox
ni_afni_automask(): AFNI Automask
ni_afni_axialize(): AFNI Axialize
ni_afni_bandpass(): AFNI Bandpass
ni_afni_blur_in_mask(): AFNI BlurInMask
ni_afni_blur_to_fwhm(): AFNI BlurToFWHM
ni_afni_brick_stat(): AFNI BrickStat
ni_afni_bucket(): AFNI Bucket
ni_afni_calc(): AFNI Calc
ni_afni_cat(): AFNI Cat
ni_afni_cat_matvec(): AFNI CatMatvec
ni_afni_center_mass(): AFNI CenterMass
ni_afni_clip_level(): AFNI ClipLevel
ni_afni_convert_dset(): AFNI ConvertDset
ni_afni_copy(): AFNI Copy
ni_afni_deconvolve(): AFNI Deconvolve
ni_afni_degree_centrality(): AFNI DegreeCentrality
ni_afni_despike(): AFNI Despike
ni_afni_detrend(): AFNI Detrend
ni_afni_dot(): AFNI Dot
ni_afni_ecm(): AFNI ECM
ni_afni_edge3(): AFNI Edge3
ni_afni_eval(): AFNI Eval
ni_afni_fim(): AFNI Fim
ni_afni_fourier(): AFNI Fourier
ni_afni_fwh_mx(): AFNI FWHMx
ni_afni_gcor(): AFNI GCOR
ni_afni_hist(): AFNI Hist
ni_afni_lfcd(): AFNI LFCD
ni_afni_local_bistat(): AFNI LocalBistat
ni_afni_localstat(): AFNI Localstat
ni_afni_mask_tool(): AFNI MaskTool
ni_afni_maskave(): AFNI Maskave
ni_afni_means(): AFNI Means
ni_afni_merge(): AFNI Merge
ni_afni_net_corr(): AFNI NetCorr
ni_afni_notes(): AFNI Notes
ni_afni_nwarp_adjust(): AFNI NwarpAdjust
ni_afni_nwarp_apply(): AFNI NwarpApply
ni_afni_nwarp_cat(): AFNI NwarpCat
ni_afni_one_d_tool_py(): AFNI OneDToolPy
ni_afni_outlier_count(): AFNI OutlierCount
ni_afni_quality_index(): AFNI QualityIndex
ni_afni_qwarp(): AFNI Qwarp
ni_afni_qwarp_plus_minus(): AFNI QwarpPlusMinus
ni_afni_re_ho(): AFNI ReHo
ni_afni_refit(): AFNI Refit
ni_afni_remlfit(): AFNI Remlfit
ni_afni_resample(): AFNI Resample
ni_afni_retroicor(): AFNI Retroicor
ni_afni_roi_stats(): AFNI ROIStats
ni_afni_seg(): AFNI Seg
ni_afni_skull_strip(): AFNI SkullStrip
ni_afni_svm_test(): AFNI SVMTest
ni_afni_svm_train(): AFNI SVMTrain
ni_afni_synthesize(): AFNI Synthesize
ni_afni_t_cat(): AFNI TCat
ni_afni_t_cat_sub_brick(): AFNI TCatSubBrick
ni_afni_t_corr1_d(): AFNI TCorr1D
ni_afni_t_corr_map(): AFNI TCorrMap
ni_afni_t_correlate(): AFNI TCorrelate
ni_afni_t_norm(): AFNI TNorm
ni_afni_t_project(): AFNI TProject
ni_afni_t_shift(): AFNI TShift
ni_afni_t_smooth(): AFNI TSmooth
ni_afni_t_stat(): AFNI TStat
ni_afni_to3_d(): AFNI To3D
ni_afni_undump(): AFNI Undump
ni_afni_unifize(): AFNI Unifize
ni_afni_volreg(): AFNI Volreg
ni_afni_warp(): AFNI Warp
ni_afni_z_cut_up(): AFNI ZCutUp
ni_afni_zcat(): AFNI Zcat
ni_afni_zeropad(): AFNI Zeropad
ni_ants_affine_initializer(): ANTS AffineInitializer
ni_ants_ai(): ANTS AI
ni_ants_ants(): ANTS ANTS
ni_ants_ants_introduction(): ANTS antsIntroduction
ni_ants_apply_transforms(): ANTS ApplyTransforms
ni_ants_apply_transforms_to_points(): ANTS ApplyTransformsToPoints
ni_ants_atropos(): ANTS Atropos
ni_ants_average_affine_transform(): ANTS AverageAffineTransform
ni_ants_average_images(): ANTS AverageImages
ni_ants_brain_extraction(): ANTS BrainExtraction
ni_ants_buildtemplateparallel(): ANTS buildtemplateparallel
ni_ants_compose_multi_transform(): ANTS ComposeMultiTransform
ni_ants_composite_transform_util(): ANTS CompositeTransformUtil
ni_ants_convert_scalar_image_to_rgb(): ANTS ConvertScalarImageToRGB
ni_ants_cortical_thickness(): ANTS CorticalThickness
ni_ants_create_jacobian_determinant_image(): ANTS CreateJacobianDeterminantImage
ni_ants_create_tiled_mosaic(): ANTS CreateTiledMosaic
ni_ants_denoise_image(): ANTS DenoiseImage
ni_ants_gen_warp_fields(): ANTS GenWarpFields
ni_ants_image_math(): ANTS ImageMath
ni_ants_joint_fusion(): ANTS JointFusion
ni_ants_kelly_kapowski(): ANTS KellyKapowski
ni_ants_label_geometry(): ANTS LabelGeometry
ni_ants_laplacian_thickness(): ANTS LaplacianThickness
ni_ants_measure_image_similarity(): ANTS MeasureImageSimilarity
ni_ants_multiply_images(): ANTS MultiplyImages
ni_ants_n4_bias_field_correction(): ANTS N4BiasFieldCorrection
ni_ants_registration(): ANTS Registration
ni_ants_registration_syn_quick(): ANTS RegistrationSynQuick
ni_ants_resample_image_by_spacing(): ANTS ResampleImageBySpacing
ni_ants_threshold_image(): ANTS ThresholdImage
ni_ants_transform_build(): ANTs Composite Transform Build
ni_ants_warp_image_multi_transform(): ANTS WarpImageMultiTransform
ni_ants_warp_time_series_image_multi_transform(): ANTS WarpTimeSeriesImageMultiTransform
ni_bids_app(): Create a bidsappr-based BIDS App pre-configured with niflowr
ni_bids_inputs(): Query a BIDS project for inputs matching a spec
ni_call(): Construct an ni_call: bind parameter values to a spec
ni_cmd(): Get the command + args that would be executed
ni_config(): Get or update niflowr runtime configuration
ni_constraints(): List spec constraints as a table
ni_dcm2niix_convert(): dcm2niix Convert
ni_deriv_path(): Generate a BIDS-derivatives output path
ni_doctor(): Run runtime diagnostics
ni_dry_run(): Run a spec as a dry run
ni_fastsurfer_run(): FastSurfer Run
ni_fastsurfer_segment(): FastSurfer Segment
ni_fmriprep_confounds(): Read fMRIPrep confounds timeseries
ni_fmriprep_derivatives(): List fMRIPrep derivatives overview
ni_fmriprep_preproc(): Locate fMRIPrep preprocessed files
ni_freesurfer_add_x_form_to_header(): FREESURFER AddXFormToHeader
ni_freesurfer_aparc2_aseg(): FREESURFER Aparc2Aseg
ni_freesurfer_apas2_aseg(): FREESURFER Apas2Aseg
ni_freesurfer_apply_mask(): FREESURFER ApplyMask
ni_freesurfer_apply_vol_transform(): FREESURFER ApplyVolTransform
ni_freesurfer_bb_register(): FREESURFER BBRegister
ni_freesurfer_binarize(): FREESURFER Binarize
ni_freesurfer_ca_label(): FREESURFER CALabel
ni_freesurfer_ca_normalize(): FREESURFER CANormalize
ni_freesurfer_ca_register(): FREESURFER CARegister
ni_freesurfer_check_talairach_alignment(): FREESURFER CheckTalairachAlignment
ni_freesurfer_concatenate(): FREESURFER Concatenate
ni_freesurfer_concatenate_lta(): FREESURFER ConcatenateLTA
ni_freesurfer_contrast(): FREESURFER Contrast
ni_freesurfer_curvature(): FREESURFER Curvature
ni_freesurfer_curvature_stats(): FREESURFER CurvatureStats
ni_freesurfer_dicom_convert(): FREESURFER DICOMConvert
ni_freesurfer_edit_w_mwith_aseg(): FREESURFER EditWMwithAseg
ni_freesurfer_em_register(): FREESURFER EMRegister
ni_freesurfer_euler_number(): FREESURFER EulerNumber
ni_freesurfer_extract_main_component(): FREESURFER ExtractMainComponent
ni_freesurfer_fit_ms_params(): FREESURFER FitMSParams
ni_freesurfer_fix_topology(): FREESURFER FixTopology
ni_freesurfer_fuse_segmentations(): FREESURFER FuseSegmentations
ni_freesurfer_glm_fit(): FREESURFER GLMFit
ni_freesurfer_gtm_seg(): FREESURFER GTMSeg
ni_freesurfer_gtmpvc(): FREESURFER GTMPVC
ni_freesurfer_image_info(): FREESURFER ImageInfo
ni_freesurfer_jacobian(): FREESURFER Jacobian
ni_freesurfer_label2_annot(): FREESURFER Label2Annot
ni_freesurfer_label2_label(): FREESURFER Label2Label
ni_freesurfer_label2_vol(): FREESURFER Label2Vol
ni_freesurfer_logan(): FREESURFER Logan
ni_freesurfer_lta_convert(): FREESURFER LTAConvert
ni_freesurfer_make_average_subject(): FREESURFER MakeAverageSubject
ni_freesurfer_make_surfaces(): FREESURFER MakeSurfaces
ni_freesurfer_mni_bias_correction(): FREESURFER MNIBiasCorrection
ni_freesurfer_mp_rto_mni305(): FREESURFER MPRtoMNI305
ni_freesurfer_mr_is_ca_label(): FREESURFER MRIsCALabel
ni_freesurfer_mr_is_calc(): FREESURFER MRIsCalc
ni_freesurfer_mr_is_combine(): FREESURFER MRIsCombine
ni_freesurfer_mr_is_convert(): FREESURFER MRIsConvert
ni_freesurfer_mr_is_expand(): FREESURFER MRIsExpand
ni_freesurfer_mr_is_inflate(): FREESURFER MRIsInflate
ni_freesurfer_mri_convert(): FREESURFER MRIConvert
ni_freesurfer_mri_coreg(): FREESURFER MRICoreg
ni_freesurfer_mri_fill(): FREESURFER MRIFill
ni_freesurfer_mri_marching_cubes(): FREESURFER MRIMarchingCubes
ni_freesurfer_mri_pretess(): FREESURFER MRIPretess
ni_freesurfer_mri_tessellate(): FREESURFER MRITessellate
ni_freesurfer_mris_preproc(): FREESURFER MRISPreproc
ni_freesurfer_mris_preproc_recon_all(): FREESURFER MRISPreprocReconAll
ni_freesurfer_mrtm1(): FREESURFER MRTM1
ni_freesurfer_mrtm2(): FREESURFER MRTM2
ni_freesurfer_ms_lda(): FREESURFER MS_LDA
ni_freesurfer_normalize(): FREESURFER Normalize
ni_freesurfer_one_sample_t_test(): FREESURFER OneSampleTTest
ni_freesurfer_paint(): FREESURFER Paint
ni_freesurfer_parcellation_stats(): FREESURFER ParcellationStats
ni_freesurfer_parse_dicom_dir(): FREESURFER ParseDICOMDir
ni_freesurfer_recon_all(): FREESURFER ReconAll
ni_freesurfer_register(): FREESURFER Register
ni_freesurfer_register_av_ito_talairach(): FREESURFER RegisterAVItoTalairach
ni_freesurfer_relabel_hypointensities(): FREESURFER RelabelHypointensities
ni_freesurfer_remove_intersection(): FREESURFER RemoveIntersection
ni_freesurfer_remove_neck(): FREESURFER RemoveNeck
ni_freesurfer_resample(): FREESURFER Resample
ni_freesurfer_robust_register(): FREESURFER RobustRegister
ni_freesurfer_robust_template(): FREESURFER RobustTemplate
ni_freesurfer_sample_to_surface(): FREESURFER SampleToSurface
ni_freesurfer_seg_stats(): FREESURFER SegStats
ni_freesurfer_seg_stats_recon_all(): FREESURFER SegStatsReconAll
ni_freesurfer_segment_cc(): FREESURFER SegmentCC
ni_freesurfer_segment_wm(): FREESURFER SegmentWM
ni_freesurfer_smooth(): FREESURFER Smooth
ni_freesurfer_smooth_tessellation(): FREESURFER SmoothTessellation
ni_freesurfer_sphere(): FREESURFER Sphere
ni_freesurfer_spherical_average(): FREESURFER SphericalAverage
ni_freesurfer_surface2_vol_transform(): FREESURFER Surface2VolTransform
ni_freesurfer_surface_smooth(): FREESURFER SurfaceSmooth
ni_freesurfer_surface_snapshots(): FREESURFER SurfaceSnapshots
ni_freesurfer_surface_transform(): FREESURFER SurfaceTransform
ni_freesurfer_synthesize_flash(): FREESURFER SynthesizeFLASH
ni_freesurfer_synthmorph_apply(): FreeSurfer SynthMorph Apply
ni_freesurfer_synthmorph_register(): FreeSurfer SynthMorph Register
ni_freesurfer_synthstrip(): FreeSurfer SynthStrip
ni_freesurfer_talairach_avi(): FREESURFER TalairachAVI
ni_freesurfer_talairach_qc(): FREESURFER TalairachQC
ni_freesurfer_tkregister2(): FREESURFER Tkregister2
ni_freesurfer_unpack_sdicom_dir(): FREESURFER UnpackSDICOMDir
ni_freesurfer_volume_mask(): FREESURFER VolumeMask
ni_freesurfer_watershed_skull_strip(): FREESURFER WatershedSkullStrip
ni_from_openneuro(): Fetch and prepare OpenNeuro dataset
ni_fsl_apply_mask(): FSL ApplyMask
ni_fsl_apply_topup(): FSL ApplyTOPUP
ni_fsl_apply_warp(): FSL ApplyWarp
ni_fsl_apply_xfm(): FSL ApplyXFM
ni_fsl_ar1_image(): FSL AR1Image
ni_fsl_av_scale(): FSL AvScale
ni_fsl_b0_calc(): FSL B0Calc
ni_fsl_bedpostx5(): FSL BEDPOSTX5
ni_fsl_bet(): FSL BET
ni_fsl_binary_maths(): FSL BinaryMaths
ni_fsl_change_data_type(): FSL ChangeDataType
ni_fsl_cluster(): FSL Cluster
ni_fsl_complex(): FSL Complex
ni_fsl_contrast_mgr(): FSL ContrastMgr
ni_fsl_convert_warp(): FSL ConvertWarp
ni_fsl_convert_xfm(): FSL ConvertXFM
ni_fsl_copy_geom(): FSL CopyGeom
ni_fsl_dilate_image(): FSL DilateImage
ni_fsl_distance_map(): FSL DistanceMap
ni_fsl_dti_fit(): FSL DTIFit
ni_fsl_dual_regression(): FSL DualRegression
ni_fsl_eddy(): FSL Eddy
ni_fsl_eddy_correct(): FSL EddyCorrect
ni_fsl_eddy_quad(): FSL EddyQuad
ni_fsl_epi_de_warp(): FSL EPIDeWarp
ni_fsl_epi_reg(): FSL EpiReg
ni_fsl_erode_image(): FSL ErodeImage
ni_fsl_extract_roi(): FSL ExtractROI
ni_fsl_fast(): FSL FAST
ni_fsl_feat(): FSL FEAT
ni_fsl_feat_model(): FSL FEATModel
ni_fsl_filmgls(): FSL FILMGLS
ni_fsl_filter_regressor(): FSL FilterRegressor
ni_fsl_find_the_biggest(): FSL FindTheBiggest
ni_fsl_first(): FSL FIRST
ni_fsl_flameo(): FSL FLAMEO
ni_fsl_flirt(): FSL FLIRT
ni_fsl_fnirt(): FSL FNIRT
ni_fsl_fugue(): FSL FUGUE
ni_fsl_glm(): FSL GLM
ni_fsl_ica_aroma(): FSL ICA_AROMA
ni_fsl_image_maths(): FSL ImageMaths
ni_fsl_image_meants(): FSL ImageMeants
ni_fsl_image_stats(): FSL ImageStats
ni_fsl_inv_warp(): FSL InvWarp
ni_fsl_isotropic_smooth(): FSL IsotropicSmooth
ni_fsl_make_dyadic_vectors(): FSL MakeDyadicVectors
ni_fsl_maths_command(): FSL MathsCommand
ni_fsl_max_image(): FSL MaxImage
ni_fsl_maxn_image(): FSL MaxnImage
ni_fsl_mcflirt(): FSL MCFLIRT
ni_fsl_mean_image(): FSL MeanImage
ni_fsl_median_image(): FSL MedianImage
ni_fsl_melodic(): FSL MELODIC
ni_fsl_merge(): FSL Merge
ni_fsl_min_image(): FSL MinImage
ni_fsl_motion_outliers(): FSL MotionOutliers
ni_fsl_multi_image_maths(): FSL MultiImageMaths
ni_fsl_overlay(): FSL Overlay
ni_fsl_percentile_image(): FSL PercentileImage
ni_fsl_plot_motion_params(): FSL PlotMotionParams
ni_fsl_plot_time_series(): FSL PlotTimeSeries
ni_fsl_power_spectrum(): FSL PowerSpectrum
ni_fsl_prelude(): FSL PRELUDE
ni_fsl_prepare_fieldmap(): FSL PrepareFieldmap
ni_fsl_prob_track_x(): FSL ProbTrackX
ni_fsl_prob_track_x2(): FSL ProbTrackX2
ni_fsl_proj_thresh(): FSL ProjThresh
ni_fsl_randomise(): FSL Randomise
ni_fsl_reorient2_std(): FSL Reorient2Std
ni_fsl_robust_fov(): FSL RobustFOV
ni_fsl_sig_loss(): FSL SigLoss
ni_fsl_slice(): FSL Slice
ni_fsl_slice_timer(): FSL SliceTimer
ni_fsl_slicer(): FSL Slicer
ni_fsl_smm(): FSL SMM
ni_fsl_smooth(): FSL Smooth
ni_fsl_smooth_estimate(): FSL SmoothEstimate
ni_fsl_spatial_filter(): FSL SpatialFilter
ni_fsl_split(): FSL Split
ni_fsl_std_image(): FSL StdImage
ni_fsl_susan(): FSL SUSAN
ni_fsl_swap_dimensions(): FSL SwapDimensions
ni_fsl_temporal_filter(): FSL TemporalFilter
ni_fsl_text2_vest(): FSL Text2Vest
ni_fsl_threshold(): FSL Threshold
ni_fsl_topup(): FSL TOPUP
ni_fsl_tract_skeleton(): FSL TractSkeleton
ni_fsl_unary_maths(): FSL UnaryMaths
ni_fsl_vec_reg(): FSL VecReg
ni_fsl_vest2_text(): FSL Vest2Text
ni_fsl_warp_points(): FSL WarpPoints
ni_fsl_warp_points_from_std(): FSL WarpPointsFromStd
ni_fsl_warp_points_to_std(): FSL WarpPointsToStd
ni_fsl_warp_utils(): FSL WarpUtils
ni_fsl_x_fibres5(): FSL XFibres5
ni_golden_cmdline_generate(): Generate golden command fixtures for all specs
ni_inputs(): List spec inputs as a table
ni_lint_specs(): Lint niflowr specs with optional autofix
ni_lock_read(): Read lockfile
ni_lock_validate(): Validate current runtime config against lockfile
ni_outputs(): Get output file paths from a result
ni_pin(): Create/update a runtime lockfile
ni_provenance(): Get provenance metadata from a result
ni_provenance_read(): Read a provenance JSON sidecar
ni_provenance_write(): Write a provenance JSON sidecar
ni_read_output(): Read an output from an ni_result as a neuroim2 object
ni_read_transform(): Read a transform output using neurotransform
ni_result: S3 class for execution results
ni_run(): Execute an ni_call
ni_run_files(): Run an niflowr call and return output file paths
ni_spec_list(): List available bundled specs
ni_spec_read(): Read a niflowr interface spec
tar_ni_step(): Create a targets-compatible neuroimaging processing step