Package: niflowr 0.1.0
niflowr: Spec-Driven Neuroimaging Command-Line Tool Wrappers
A lightweight, declarative framework for wrapping neuroimaging command-line tools (FSL, AFNI, ANTs, FreeSurfer) in R. Tool interfaces are defined as JSON specifications that describe inputs, outputs, CLI rendering rules, and validation constraints. The package builds safe argument vectors (never shell strings), executes via 'processx', captures provenance, and integrates with 'targets' for pipeline orchestration.
Authors:
niflowr_0.1.0.tar.gz
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niflowr_0.1.0.tgz(r-4.6-any)niflowr_0.1.0.tgz(r-4.5-any)
niflowr_0.1.0.tar.gz(r-4.7-any)niflowr_0.1.0.tar.gz(r-4.6-any)
niflowr_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
niflowr/json (API)
| # Install 'niflowr' in R: |
| install.packages('niflowr', repos = c('https://bbuchsbaum.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bbuchsbaum/niflowr/issues
Pkgdown/docs site:https://bbuchsbaum.github.io
Last updated from:f600660bc3. Checks:4 WARNING, 2 OK, 3 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | WARNING | 283 | ||
| source / vignettes | OK | 261 | ||
| linux-release-x86_64 | WARNING | 266 | ||
| macos-release-arm64 | WARNING | 107 | ||
| macos-oldrel-arm64 | WARNING | 129 | ||
| windows-devel | ERROR | 337 | ||
| windows-release | ERROR | 351 | ||
| windows-oldrel | ERROR | 303 | ||
| wasm-release | OK | 154 |
Exports:ni_afni_a_boverlapni_afni_afn_ito_niftini_afni_align_epi_anat_pyni_afni_allineateni_afni_auto_tcorrelateni_afni_auto_tlrcni_afni_autoboxni_afni_automaskni_afni_axializeni_afni_bandpassni_afni_blur_in_maskni_afni_blur_to_fwhmni_afni_brick_statni_afni_bucketni_afni_calcni_afni_catni_afni_cat_matvecni_afni_center_massni_afni_clip_levelni_afni_convert_dsetni_afni_copyni_afni_deconvolveni_afni_degree_centralityni_afni_despikeni_afni_detrendni_afni_dotni_afni_ecmni_afni_edge3ni_afni_evalni_afni_fimni_afni_fourierni_afni_fwh_mxni_afni_gcorni_afni_histni_afni_lfcdni_afni_local_bistatni_afni_localstatni_afni_mask_toolni_afni_maskaveni_afni_meansni_afni_mergeni_afni_net_corrni_afni_notesni_afni_nwarp_adjustni_afni_nwarp_applyni_afni_nwarp_catni_afni_one_d_tool_pyni_afni_outlier_countni_afni_quality_indexni_afni_qwarpni_afni_qwarp_plus_minusni_afni_re_honi_afni_refitni_afni_remlfitni_afni_resampleni_afni_retroicorni_afni_roi_statsni_afni_segni_afni_skull_stripni_afni_svm_testni_afni_svm_trainni_afni_synthesizeni_afni_t_catni_afni_t_cat_sub_brickni_afni_t_corr_mapni_afni_t_corr1_dni_afni_t_correlateni_afni_t_normni_afni_t_projectni_afni_t_shiftni_afni_t_smoothni_afni_t_statni_afni_to3_dni_afni_undumpni_afni_unifizeni_afni_volregni_afni_warpni_afni_z_cut_upni_afni_zcatni_afni_zeropadni_ants_affine_initializerni_ants_aini_ants_antsni_ants_ants_introductionni_ants_apply_transformsni_ants_apply_transforms_to_pointsni_ants_atroposni_ants_average_affine_transformni_ants_average_imagesni_ants_brain_extractionni_ants_buildtemplateparallelni_ants_compose_multi_transformni_ants_composite_transform_utilni_ants_convert_scalar_image_to_rgbni_ants_cortical_thicknessni_ants_create_jacobian_determinant_imageni_ants_create_tiled_mosaicni_ants_denoise_imageni_ants_gen_warp_fieldsni_ants_image_mathni_ants_joint_fusionni_ants_kelly_kapowskini_ants_label_geometryni_ants_laplacian_thicknessni_ants_measure_image_similarityni_ants_multiply_imagesni_ants_n4_bias_field_correctionni_ants_registrationni_ants_registration_syn_quickni_ants_resample_image_by_spacingni_ants_threshold_imageni_ants_transform_buildni_ants_warp_image_multi_transformni_ants_warp_time_series_image_multi_transformni_bids_appni_bids_inputsni_callni_cmdni_configni_constraintsni_dcm2niix_convertni_deriv_pathni_doctorni_dry_runni_fastsurfer_runni_fastsurfer_segmentni_fmriprep_confoundsni_fmriprep_derivativesni_fmriprep_preprocni_freesurfer_add_x_form_to_headerni_freesurfer_aparc2_asegni_freesurfer_apas2_asegni_freesurfer_apply_maskni_freesurfer_apply_vol_transformni_freesurfer_bb_registerni_freesurfer_binarizeni_freesurfer_ca_labelni_freesurfer_ca_normalizeni_freesurfer_ca_registerni_freesurfer_check_talairach_alignmentni_freesurfer_concatenateni_freesurfer_concatenate_ltani_freesurfer_contrastni_freesurfer_curvatureni_freesurfer_curvature_statsni_freesurfer_dicom_convertni_freesurfer_edit_w_mwith_asegni_freesurfer_em_registerni_freesurfer_euler_numberni_freesurfer_extract_main_componentni_freesurfer_fit_ms_paramsni_freesurfer_fix_topologyni_freesurfer_fuse_segmentationsni_freesurfer_glm_fitni_freesurfer_gtm_segni_freesurfer_gtmpvcni_freesurfer_image_infoni_freesurfer_jacobianni_freesurfer_label2_annotni_freesurfer_label2_labelni_freesurfer_label2_volni_freesurfer_loganni_freesurfer_lta_convertni_freesurfer_make_average_subjectni_freesurfer_make_surfacesni_freesurfer_mni_bias_correctionni_freesurfer_mp_rto_mni305ni_freesurfer_mr_is_ca_labelni_freesurfer_mr_is_calcni_freesurfer_mr_is_combineni_freesurfer_mr_is_convertni_freesurfer_mr_is_expandni_freesurfer_mr_is_inflateni_freesurfer_mri_convertni_freesurfer_mri_coregni_freesurfer_mri_fillni_freesurfer_mri_marching_cubesni_freesurfer_mri_pretessni_freesurfer_mri_tessellateni_freesurfer_mris_preprocni_freesurfer_mris_preproc_recon_allni_freesurfer_mrtm1ni_freesurfer_mrtm2ni_freesurfer_ms_ldani_freesurfer_normalizeni_freesurfer_one_sample_t_testni_freesurfer_paintni_freesurfer_parcellation_statsni_freesurfer_parse_dicom_dirni_freesurfer_recon_allni_freesurfer_registerni_freesurfer_register_av_ito_talairachni_freesurfer_relabel_hypointensitiesni_freesurfer_remove_intersectionni_freesurfer_remove_neckni_freesurfer_resampleni_freesurfer_robust_registerni_freesurfer_robust_templateni_freesurfer_sample_to_surfaceni_freesurfer_seg_statsni_freesurfer_seg_stats_recon_allni_freesurfer_segment_ccni_freesurfer_segment_wmni_freesurfer_smoothni_freesurfer_smooth_tessellationni_freesurfer_sphereni_freesurfer_spherical_averageni_freesurfer_surface_smoothni_freesurfer_surface_snapshotsni_freesurfer_surface_transformni_freesurfer_surface2_vol_transformni_freesurfer_synthesize_flashni_freesurfer_synthmorph_applyni_freesurfer_synthmorph_registerni_freesurfer_synthstripni_freesurfer_talairach_avini_freesurfer_talairach_qcni_freesurfer_tkregister2ni_freesurfer_unpack_sdicom_dirni_freesurfer_volume_maskni_freesurfer_watershed_skull_stripni_from_openneuroni_fsl_apply_maskni_fsl_apply_topupni_fsl_apply_warpni_fsl_apply_xfmni_fsl_ar1_imageni_fsl_av_scaleni_fsl_b0_calcni_fsl_bedpostx5ni_fsl_betni_fsl_binary_mathsni_fsl_change_data_typeni_fsl_clusterni_fsl_complexni_fsl_contrast_mgrni_fsl_convert_warpni_fsl_convert_xfmni_fsl_copy_geomni_fsl_dilate_imageni_fsl_distance_mapni_fsl_dti_fitni_fsl_dual_regressionni_fsl_eddyni_fsl_eddy_correctni_fsl_eddy_quadni_fsl_epi_de_warpni_fsl_epi_regni_fsl_erode_imageni_fsl_extract_roini_fsl_fastni_fsl_featni_fsl_feat_modelni_fsl_filmglsni_fsl_filter_regressorni_fsl_find_the_biggestni_fsl_firstni_fsl_flameoni_fsl_flirtni_fsl_fnirtni_fsl_fugueni_fsl_glmni_fsl_ica_aromani_fsl_image_mathsni_fsl_image_meantsni_fsl_image_statsni_fsl_inv_warpni_fsl_isotropic_smoothni_fsl_make_dyadic_vectorsni_fsl_maths_commandni_fsl_max_imageni_fsl_maxn_imageni_fsl_mcflirtni_fsl_mean_imageni_fsl_median_imageni_fsl_melodicni_fsl_mergeni_fsl_min_imageni_fsl_motion_outliersni_fsl_multi_image_mathsni_fsl_overlayni_fsl_percentile_imageni_fsl_plot_motion_paramsni_fsl_plot_time_seriesni_fsl_power_spectrumni_fsl_preludeni_fsl_prepare_fieldmapni_fsl_prob_track_xni_fsl_prob_track_x2ni_fsl_proj_threshni_fsl_randomiseni_fsl_reorient2_stdni_fsl_robust_fovni_fsl_sig_lossni_fsl_sliceni_fsl_slice_timerni_fsl_slicerni_fsl_smmni_fsl_smoothni_fsl_smooth_estimateni_fsl_spatial_filterni_fsl_splitni_fsl_std_imageni_fsl_susanni_fsl_swap_dimensionsni_fsl_temporal_filterni_fsl_text2_vestni_fsl_thresholdni_fsl_topupni_fsl_tract_skeletonni_fsl_unary_mathsni_fsl_vec_regni_fsl_vest2_textni_fsl_warp_pointsni_fsl_warp_points_from_stdni_fsl_warp_points_to_stdni_fsl_warp_utilsni_fsl_x_fibres5ni_golden_cmdline_generateni_inputsni_lint_specsni_lock_readni_lock_validateni_outputsni_pinni_provenanceni_provenance_readni_provenance_writeni_read_outputni_read_transformni_runni_run_filesni_spec_listni_spec_readtar_ni_step
Dependencies:clicurldigestfsgluejsonlitejsonvalidateprocessxpsR6RcppV8yaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| AFNI ABoverlap | ni_afni_a_boverlap |
| AFNI AFNItoNIFTI | ni_afni_afn_ito_nifti |
| AFNI AlignEpiAnatPy | ni_afni_align_epi_anat_py |
| AFNI Allineate | ni_afni_allineate |
| AFNI AutoTcorrelate | ni_afni_auto_tcorrelate |
| AFNI AutoTLRC | ni_afni_auto_tlrc |
| AFNI Autobox | ni_afni_autobox |
| AFNI Automask | ni_afni_automask |
| AFNI Axialize | ni_afni_axialize |
| AFNI Bandpass | ni_afni_bandpass |
| AFNI BlurInMask | ni_afni_blur_in_mask |
| AFNI BlurToFWHM | ni_afni_blur_to_fwhm |
| AFNI BrickStat | ni_afni_brick_stat |
| AFNI Bucket | ni_afni_bucket |
| AFNI Calc | ni_afni_calc |
| AFNI Cat | ni_afni_cat |
| AFNI CatMatvec | ni_afni_cat_matvec |
| AFNI CenterMass | ni_afni_center_mass |
| AFNI ClipLevel | ni_afni_clip_level |
| AFNI ConvertDset | ni_afni_convert_dset |
| AFNI Copy | ni_afni_copy |
| AFNI Deconvolve | ni_afni_deconvolve |
| AFNI DegreeCentrality | ni_afni_degree_centrality |
| AFNI Despike | ni_afni_despike |
| AFNI Detrend | ni_afni_detrend |
| AFNI Dot | ni_afni_dot |
| AFNI ECM | ni_afni_ecm |
| AFNI Edge3 | ni_afni_edge3 |
| AFNI Eval | ni_afni_eval |
| AFNI Fim | ni_afni_fim |
| AFNI Fourier | ni_afni_fourier |
| AFNI FWHMx | ni_afni_fwh_mx |
| AFNI GCOR | ni_afni_gcor |
| AFNI Hist | ni_afni_hist |
| AFNI LFCD | ni_afni_lfcd |
| AFNI LocalBistat | ni_afni_local_bistat |
| AFNI Localstat | ni_afni_localstat |
| AFNI MaskTool | ni_afni_mask_tool |
| AFNI Maskave | ni_afni_maskave |
| AFNI Means | ni_afni_means |
| AFNI Merge | ni_afni_merge |
| AFNI NetCorr | ni_afni_net_corr |
| AFNI Notes | ni_afni_notes |
| AFNI NwarpAdjust | ni_afni_nwarp_adjust |
| AFNI NwarpApply | ni_afni_nwarp_apply |
| AFNI NwarpCat | ni_afni_nwarp_cat |
| AFNI OneDToolPy | ni_afni_one_d_tool_py |
| AFNI OutlierCount | ni_afni_outlier_count |
| AFNI QualityIndex | ni_afni_quality_index |
| AFNI Qwarp | ni_afni_qwarp |
| AFNI QwarpPlusMinus | ni_afni_qwarp_plus_minus |
| AFNI ReHo | ni_afni_re_ho |
| AFNI Refit | ni_afni_refit |
| AFNI Remlfit | ni_afni_remlfit |
| AFNI Resample | ni_afni_resample |
| AFNI Retroicor | ni_afni_retroicor |
| AFNI ROIStats | ni_afni_roi_stats |
| AFNI Seg | ni_afni_seg |
| AFNI SkullStrip | ni_afni_skull_strip |
| AFNI SVMTest | ni_afni_svm_test |
| AFNI SVMTrain | ni_afni_svm_train |
| AFNI Synthesize | ni_afni_synthesize |
| AFNI TCat | ni_afni_t_cat |
| AFNI TCatSubBrick | ni_afni_t_cat_sub_brick |
| AFNI TCorrMap | ni_afni_t_corr_map |
| AFNI TCorr1D | ni_afni_t_corr1_d |
| AFNI TCorrelate | ni_afni_t_correlate |
| AFNI TNorm | ni_afni_t_norm |
| AFNI TProject | ni_afni_t_project |
| AFNI TShift | ni_afni_t_shift |
| AFNI TSmooth | ni_afni_t_smooth |
| AFNI TStat | ni_afni_t_stat |
| AFNI To3D | ni_afni_to3_d |
| AFNI Undump | ni_afni_undump |
| AFNI Unifize | ni_afni_unifize |
| AFNI Volreg | ni_afni_volreg |
| AFNI Warp | ni_afni_warp |
| AFNI ZCutUp | ni_afni_z_cut_up |
| AFNI Zcat | ni_afni_zcat |
| AFNI Zeropad | ni_afni_zeropad |
| ANTS AffineInitializer | ni_ants_affine_initializer |
| ANTS AI | ni_ants_ai |
| ANTS ANTS | ni_ants_ants |
| ANTS antsIntroduction | ni_ants_ants_introduction |
| ANTS ApplyTransforms | ni_ants_apply_transforms |
| ANTS ApplyTransformsToPoints | ni_ants_apply_transforms_to_points |
| ANTS Atropos | ni_ants_atropos |
| ANTS AverageAffineTransform | ni_ants_average_affine_transform |
| ANTS AverageImages | ni_ants_average_images |
| ANTS BrainExtraction | ni_ants_brain_extraction |
| ANTS buildtemplateparallel | ni_ants_buildtemplateparallel |
| ANTS ComposeMultiTransform | ni_ants_compose_multi_transform |
| ANTS CompositeTransformUtil | ni_ants_composite_transform_util |
| ANTS ConvertScalarImageToRGB | ni_ants_convert_scalar_image_to_rgb |
| ANTS CorticalThickness | ni_ants_cortical_thickness |
| ANTS CreateJacobianDeterminantImage | ni_ants_create_jacobian_determinant_image |
| ANTS CreateTiledMosaic | ni_ants_create_tiled_mosaic |
| ANTS DenoiseImage | ni_ants_denoise_image |
| ANTS GenWarpFields | ni_ants_gen_warp_fields |
| ANTS ImageMath | ni_ants_image_math |
| ANTS JointFusion | ni_ants_joint_fusion |
| ANTS KellyKapowski | ni_ants_kelly_kapowski |
| ANTS LabelGeometry | ni_ants_label_geometry |
| ANTS LaplacianThickness | ni_ants_laplacian_thickness |
| ANTS MeasureImageSimilarity | ni_ants_measure_image_similarity |
| ANTS MultiplyImages | ni_ants_multiply_images |
| ANTS N4BiasFieldCorrection | ni_ants_n4_bias_field_correction |
| ANTS Registration | ni_ants_registration |
| ANTS RegistrationSynQuick | ni_ants_registration_syn_quick |
| ANTS ResampleImageBySpacing | ni_ants_resample_image_by_spacing |
| ANTS ThresholdImage | ni_ants_threshold_image |
| ANTs Composite Transform Build | ni_ants_transform_build |
| ANTS WarpImageMultiTransform | ni_ants_warp_image_multi_transform |
| ANTS WarpTimeSeriesImageMultiTransform | ni_ants_warp_time_series_image_multi_transform |
| Create a bidsappr-based BIDS App pre-configured with niflowr | ni_bids_app |
| Query a BIDS project for inputs matching a spec | ni_bids_inputs |
| Construct an ni_call: bind parameter values to a spec | ni_call |
| Get the command + args that would be executed | ni_cmd |
| Get or update niflowr runtime configuration | ni_config |
| List spec constraints as a table | ni_constraints |
| dcm2niix Convert | ni_dcm2niix_convert |
| Generate a BIDS-derivatives output path | ni_deriv_path |
| Run runtime diagnostics | ni_doctor |
| Run a spec as a dry run | ni_dry_run |
| FastSurfer Run | ni_fastsurfer_run |
| FastSurfer Segment | ni_fastsurfer_segment |
| Read fMRIPrep confounds timeseries | ni_fmriprep_confounds |
| List fMRIPrep derivatives overview | ni_fmriprep_derivatives |
| Locate fMRIPrep preprocessed files | ni_fmriprep_preproc |
| FREESURFER AddXFormToHeader | ni_freesurfer_add_x_form_to_header |
| FREESURFER Aparc2Aseg | ni_freesurfer_aparc2_aseg |
| FREESURFER Apas2Aseg | ni_freesurfer_apas2_aseg |
| FREESURFER ApplyMask | ni_freesurfer_apply_mask |
| FREESURFER ApplyVolTransform | ni_freesurfer_apply_vol_transform |
| FREESURFER BBRegister | ni_freesurfer_bb_register |
| FREESURFER Binarize | ni_freesurfer_binarize |
| FREESURFER CALabel | ni_freesurfer_ca_label |
| FREESURFER CANormalize | ni_freesurfer_ca_normalize |
| FREESURFER CARegister | ni_freesurfer_ca_register |
| FREESURFER CheckTalairachAlignment | ni_freesurfer_check_talairach_alignment |
| FREESURFER Concatenate | ni_freesurfer_concatenate |
| FREESURFER ConcatenateLTA | ni_freesurfer_concatenate_lta |
| FREESURFER Contrast | ni_freesurfer_contrast |
| FREESURFER Curvature | ni_freesurfer_curvature |
| FREESURFER CurvatureStats | ni_freesurfer_curvature_stats |
| FREESURFER DICOMConvert | ni_freesurfer_dicom_convert |
| FREESURFER EditWMwithAseg | ni_freesurfer_edit_w_mwith_aseg |
| FREESURFER EMRegister | ni_freesurfer_em_register |
| FREESURFER EulerNumber | ni_freesurfer_euler_number |
| FREESURFER ExtractMainComponent | ni_freesurfer_extract_main_component |
| FREESURFER FitMSParams | ni_freesurfer_fit_ms_params |
| FREESURFER FixTopology | ni_freesurfer_fix_topology |
| FREESURFER FuseSegmentations | ni_freesurfer_fuse_segmentations |
| FREESURFER GLMFit | ni_freesurfer_glm_fit |
| FREESURFER GTMSeg | ni_freesurfer_gtm_seg |
| FREESURFER GTMPVC | ni_freesurfer_gtmpvc |
| FREESURFER ImageInfo | ni_freesurfer_image_info |
| FREESURFER Jacobian | ni_freesurfer_jacobian |
| FREESURFER Label2Annot | ni_freesurfer_label2_annot |
| FREESURFER Label2Label | ni_freesurfer_label2_label |
| FREESURFER Label2Vol | ni_freesurfer_label2_vol |
| FREESURFER Logan | ni_freesurfer_logan |
| FREESURFER LTAConvert | ni_freesurfer_lta_convert |
| FREESURFER MakeAverageSubject | ni_freesurfer_make_average_subject |
| FREESURFER MakeSurfaces | ni_freesurfer_make_surfaces |
| FREESURFER MNIBiasCorrection | ni_freesurfer_mni_bias_correction |
| FREESURFER MPRtoMNI305 | ni_freesurfer_mp_rto_mni305 |
| FREESURFER MRIsCALabel | ni_freesurfer_mr_is_ca_label |
| FREESURFER MRIsCalc | ni_freesurfer_mr_is_calc |
| FREESURFER MRIsCombine | ni_freesurfer_mr_is_combine |
| FREESURFER MRIsConvert | ni_freesurfer_mr_is_convert |
| FREESURFER MRIsExpand | ni_freesurfer_mr_is_expand |
| FREESURFER MRIsInflate | ni_freesurfer_mr_is_inflate |
| FREESURFER MRIConvert | ni_freesurfer_mri_convert |
| FREESURFER MRICoreg | ni_freesurfer_mri_coreg |
| FREESURFER MRIFill | ni_freesurfer_mri_fill |
| FREESURFER MRIMarchingCubes | ni_freesurfer_mri_marching_cubes |
| FREESURFER MRIPretess | ni_freesurfer_mri_pretess |
| FREESURFER MRITessellate | ni_freesurfer_mri_tessellate |
| FREESURFER MRISPreproc | ni_freesurfer_mris_preproc |
| FREESURFER MRISPreprocReconAll | ni_freesurfer_mris_preproc_recon_all |
| FREESURFER MRTM1 | ni_freesurfer_mrtm1 |
| FREESURFER MRTM2 | ni_freesurfer_mrtm2 |
| FREESURFER MS_LDA | ni_freesurfer_ms_lda |
| FREESURFER Normalize | ni_freesurfer_normalize |
| FREESURFER OneSampleTTest | ni_freesurfer_one_sample_t_test |
| FREESURFER Paint | ni_freesurfer_paint |
| FREESURFER ParcellationStats | ni_freesurfer_parcellation_stats |
| FREESURFER ParseDICOMDir | ni_freesurfer_parse_dicom_dir |
| FREESURFER ReconAll | ni_freesurfer_recon_all |
| FREESURFER Register | ni_freesurfer_register |
| FREESURFER RegisterAVItoTalairach | ni_freesurfer_register_av_ito_talairach |
| FREESURFER RelabelHypointensities | ni_freesurfer_relabel_hypointensities |
| FREESURFER RemoveIntersection | ni_freesurfer_remove_intersection |
| FREESURFER RemoveNeck | ni_freesurfer_remove_neck |
| FREESURFER Resample | ni_freesurfer_resample |
| FREESURFER RobustRegister | ni_freesurfer_robust_register |
| FREESURFER RobustTemplate | ni_freesurfer_robust_template |
| FREESURFER SampleToSurface | ni_freesurfer_sample_to_surface |
| FREESURFER SegStats | ni_freesurfer_seg_stats |
| FREESURFER SegStatsReconAll | ni_freesurfer_seg_stats_recon_all |
| FREESURFER SegmentCC | ni_freesurfer_segment_cc |
| FREESURFER SegmentWM | ni_freesurfer_segment_wm |
| FREESURFER Smooth | ni_freesurfer_smooth |
| FREESURFER SmoothTessellation | ni_freesurfer_smooth_tessellation |
| FREESURFER Sphere | ni_freesurfer_sphere |
| FREESURFER SphericalAverage | ni_freesurfer_spherical_average |
| FREESURFER SurfaceSmooth | ni_freesurfer_surface_smooth |
| FREESURFER SurfaceSnapshots | ni_freesurfer_surface_snapshots |
| FREESURFER SurfaceTransform | ni_freesurfer_surface_transform |
| FREESURFER Surface2VolTransform | ni_freesurfer_surface2_vol_transform |
| FREESURFER SynthesizeFLASH | ni_freesurfer_synthesize_flash |
| FreeSurfer SynthMorph Apply | ni_freesurfer_synthmorph_apply |
| FreeSurfer SynthMorph Register | ni_freesurfer_synthmorph_register |
| FreeSurfer SynthStrip | ni_freesurfer_synthstrip |
| FREESURFER TalairachAVI | ni_freesurfer_talairach_avi |
| FREESURFER TalairachQC | ni_freesurfer_talairach_qc |
| FREESURFER Tkregister2 | ni_freesurfer_tkregister2 |
| FREESURFER UnpackSDICOMDir | ni_freesurfer_unpack_sdicom_dir |
| FREESURFER VolumeMask | ni_freesurfer_volume_mask |
| FREESURFER WatershedSkullStrip | ni_freesurfer_watershed_skull_strip |
| Fetch and prepare OpenNeuro dataset | ni_from_openneuro |
| FSL ApplyMask | ni_fsl_apply_mask |
| FSL ApplyTOPUP | ni_fsl_apply_topup |
| FSL ApplyWarp | ni_fsl_apply_warp |
| FSL ApplyXFM | ni_fsl_apply_xfm |
| FSL AR1Image | ni_fsl_ar1_image |
| FSL AvScale | ni_fsl_av_scale |
| FSL B0Calc | ni_fsl_b0_calc |
| FSL BEDPOSTX5 | ni_fsl_bedpostx5 |
| FSL BET | ni_fsl_bet |
| FSL BinaryMaths | ni_fsl_binary_maths |
| FSL ChangeDataType | ni_fsl_change_data_type |
| FSL Cluster | ni_fsl_cluster |
| FSL Complex | ni_fsl_complex |
| FSL ContrastMgr | ni_fsl_contrast_mgr |
| FSL ConvertWarp | ni_fsl_convert_warp |
| FSL ConvertXFM | ni_fsl_convert_xfm |
| FSL CopyGeom | ni_fsl_copy_geom |
| FSL DilateImage | ni_fsl_dilate_image |
| FSL DistanceMap | ni_fsl_distance_map |
| FSL DTIFit | ni_fsl_dti_fit |
| FSL DualRegression | ni_fsl_dual_regression |
| FSL Eddy | ni_fsl_eddy |
| FSL EddyCorrect | ni_fsl_eddy_correct |
| FSL EddyQuad | ni_fsl_eddy_quad |
| FSL EPIDeWarp | ni_fsl_epi_de_warp |
| FSL EpiReg | ni_fsl_epi_reg |
| FSL ErodeImage | ni_fsl_erode_image |
| FSL ExtractROI | ni_fsl_extract_roi |
| FSL FAST | ni_fsl_fast |
| FSL FEAT | ni_fsl_feat |
| FSL FEATModel | ni_fsl_feat_model |
| FSL FILMGLS | ni_fsl_filmgls |
| FSL FilterRegressor | ni_fsl_filter_regressor |
| FSL FindTheBiggest | ni_fsl_find_the_biggest |
| FSL FIRST | ni_fsl_first |
| FSL FLAMEO | ni_fsl_flameo |
| FSL FLIRT | ni_fsl_flirt |
| FSL FNIRT | ni_fsl_fnirt |
| FSL FUGUE | ni_fsl_fugue |
| FSL GLM | ni_fsl_glm |
| FSL ICA_AROMA | ni_fsl_ica_aroma |
| FSL ImageMaths | ni_fsl_image_maths |
| FSL ImageMeants | ni_fsl_image_meants |
| FSL ImageStats | ni_fsl_image_stats |
| FSL InvWarp | ni_fsl_inv_warp |
| FSL IsotropicSmooth | ni_fsl_isotropic_smooth |
| FSL MakeDyadicVectors | ni_fsl_make_dyadic_vectors |
| FSL MathsCommand | ni_fsl_maths_command |
| FSL MaxImage | ni_fsl_max_image |
| FSL MaxnImage | ni_fsl_maxn_image |
| FSL MCFLIRT | ni_fsl_mcflirt |
| FSL MeanImage | ni_fsl_mean_image |
| FSL MedianImage | ni_fsl_median_image |
| FSL MELODIC | ni_fsl_melodic |
| FSL Merge | ni_fsl_merge |
| FSL MinImage | ni_fsl_min_image |
| FSL MotionOutliers | ni_fsl_motion_outliers |
| FSL MultiImageMaths | ni_fsl_multi_image_maths |
| FSL Overlay | ni_fsl_overlay |
| FSL PercentileImage | ni_fsl_percentile_image |
| FSL PlotMotionParams | ni_fsl_plot_motion_params |
| FSL PlotTimeSeries | ni_fsl_plot_time_series |
| FSL PowerSpectrum | ni_fsl_power_spectrum |
| FSL PRELUDE | ni_fsl_prelude |
| FSL PrepareFieldmap | ni_fsl_prepare_fieldmap |
| FSL ProbTrackX | ni_fsl_prob_track_x |
| FSL ProbTrackX2 | ni_fsl_prob_track_x2 |
| FSL ProjThresh | ni_fsl_proj_thresh |
| FSL Randomise | ni_fsl_randomise |
| FSL Reorient2Std | ni_fsl_reorient2_std |
| FSL RobustFOV | ni_fsl_robust_fov |
| FSL SigLoss | ni_fsl_sig_loss |
| FSL Slice | ni_fsl_slice |
| FSL SliceTimer | ni_fsl_slice_timer |
| FSL Slicer | ni_fsl_slicer |
| FSL SMM | ni_fsl_smm |
| FSL Smooth | ni_fsl_smooth |
| FSL SmoothEstimate | ni_fsl_smooth_estimate |
| FSL SpatialFilter | ni_fsl_spatial_filter |
| FSL Split | ni_fsl_split |
| FSL StdImage | ni_fsl_std_image |
| FSL SUSAN | ni_fsl_susan |
| FSL SwapDimensions | ni_fsl_swap_dimensions |
| FSL TemporalFilter | ni_fsl_temporal_filter |
| FSL Text2Vest | ni_fsl_text2_vest |
| FSL Threshold | ni_fsl_threshold |
| FSL TOPUP | ni_fsl_topup |
| FSL TractSkeleton | ni_fsl_tract_skeleton |
| FSL UnaryMaths | ni_fsl_unary_maths |
| FSL VecReg | ni_fsl_vec_reg |
| FSL Vest2Text | ni_fsl_vest2_text |
| FSL WarpPoints | ni_fsl_warp_points |
| FSL WarpPointsFromStd | ni_fsl_warp_points_from_std |
| FSL WarpPointsToStd | ni_fsl_warp_points_to_std |
| FSL WarpUtils | ni_fsl_warp_utils |
| FSL XFibres5 | ni_fsl_x_fibres5 |
| Generate golden command fixtures for all specs | ni_golden_cmdline_generate |
| List spec inputs as a table | ni_inputs |
| Lint niflowr specs with optional autofix | ni_lint_specs |
| Read lockfile | ni_lock_read |
| Validate current runtime config against lockfile | ni_lock_validate |
| Get output file paths from a result | ni_outputs |
| Create/update a runtime lockfile | ni_pin |
| Get provenance metadata from a result | ni_provenance |
| Read a provenance JSON sidecar | ni_provenance_read |
| Write a provenance JSON sidecar | ni_provenance_write |
| Read an output from an ni_result as a neuroim2 object | ni_read_output |
| Read a transform output using neurotransform | ni_read_transform |
| S3 class for execution results | ni_result |
| Execute an ni_call | ni_run |
| Run an niflowr call and return output file paths | ni_run_files |
| List available bundled specs | ni_spec_list |
| Read a niflowr interface spec | ni_spec_read |
| Create a targets-compatible neuroimaging processing step | tar_ni_step |
