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"title": "AFNI Hist", "topics": [ "ni_afni_hist" ] }, { "page": "ni_afni_lfcd", "title": "AFNI LFCD", "topics": [ "ni_afni_lfcd" ] }, { "page": "ni_afni_local_bistat", "title": "AFNI LocalBistat", "topics": [ "ni_afni_local_bistat" ] }, { "page": "ni_afni_localstat", "title": "AFNI Localstat", "topics": [ "ni_afni_localstat" ] }, { "page": "ni_afni_mask_tool", "title": "AFNI MaskTool", "topics": [ "ni_afni_mask_tool" ] }, { "page": "ni_afni_maskave", "title": "AFNI Maskave", "topics": [ "ni_afni_maskave" ] }, { "page": "ni_afni_means", "title": "AFNI Means", "topics": [ "ni_afni_means" ] }, { "page": "ni_afni_merge", "title": "AFNI Merge", "topics": [ "ni_afni_merge" ] }, { "page": "ni_afni_net_corr", "title": "AFNI NetCorr", "topics": [ "ni_afni_net_corr" ] }, { "page": "ni_afni_notes", "title": "AFNI Notes", "topics": [ "ni_afni_notes" ] }, { "page": "ni_afni_nwarp_adjust", "title": "AFNI NwarpAdjust", "topics": [ "ni_afni_nwarp_adjust" ] }, { "page": "ni_afni_nwarp_apply", "title": "AFNI NwarpApply", "topics": [ "ni_afni_nwarp_apply" ] }, { "page": "ni_afni_nwarp_cat", "title": "AFNI NwarpCat", "topics": [ "ni_afni_nwarp_cat" ] }, { "page": "ni_afni_one_d_tool_py", "title": "AFNI OneDToolPy", "topics": [ "ni_afni_one_d_tool_py" ] }, { "page": "ni_afni_outlier_count", "title": "AFNI OutlierCount", "topics": [ "ni_afni_outlier_count" ] }, { "page": "ni_afni_quality_index", "title": "AFNI QualityIndex", "topics": [ "ni_afni_quality_index" ] }, { "page": "ni_afni_qwarp", "title": "AFNI Qwarp", "topics": [ "ni_afni_qwarp" ] }, { "page": "ni_afni_qwarp_plus_minus", "title": "AFNI QwarpPlusMinus", "topics": [ "ni_afni_qwarp_plus_minus" ] }, { "page": "ni_afni_re_ho", "title": "AFNI ReHo", "topics": [ "ni_afni_re_ho" ] }, { "page": "ni_afni_refit", "title": "AFNI Refit", "topics": [ "ni_afni_refit" ] }, { "page": "ni_afni_remlfit", "title": "AFNI Remlfit", "topics": [ "ni_afni_remlfit" ] }, { "page": "ni_afni_resample", "title": "AFNI Resample", "topics": [ "ni_afni_resample" ] }, { "page": "ni_afni_retroicor", "title": "AFNI Retroicor", "topics": [ "ni_afni_retroicor" ] }, { "page": "ni_afni_roi_stats", "title": "AFNI ROIStats", "topics": [ "ni_afni_roi_stats" ] }, { "page": "ni_afni_seg", "title": "AFNI Seg", "topics": [ "ni_afni_seg" ] }, { "page": "ni_afni_skull_strip", "title": "AFNI SkullStrip", "topics": [ "ni_afni_skull_strip" ] }, { "page": "ni_afni_svm_test", "title": "AFNI SVMTest", "topics": [ "ni_afni_svm_test" ] }, { "page": "ni_afni_svm_train", "title": "AFNI SVMTrain", "topics": [ "ni_afni_svm_train" ] }, { "page": "ni_afni_synthesize", "title": "AFNI Synthesize", "topics": [ "ni_afni_synthesize" ] }, { "page": "ni_afni_t_cat", "title": "AFNI TCat", "topics": [ "ni_afni_t_cat" ] }, { "page": "ni_afni_t_cat_sub_brick", "title": "AFNI TCatSubBrick", "topics": [ "ni_afni_t_cat_sub_brick" ] }, { "page": "ni_afni_t_corr_map", "title": "AFNI TCorrMap", "topics": [ "ni_afni_t_corr_map" ] }, { "page": "ni_afni_t_corr1_d", "title": "AFNI TCorr1D", "topics": [ "ni_afni_t_corr1_d" ] }, { "page": "ni_afni_t_correlate", "title": "AFNI TCorrelate", "topics": [ "ni_afni_t_correlate" ] }, { "page": "ni_afni_t_norm", "title": "AFNI TNorm", "topics": [ "ni_afni_t_norm" ] }, { "page": "ni_afni_t_project", "title": "AFNI TProject", "topics": [ "ni_afni_t_project" ] }, { "page": "ni_afni_t_shift", "title": "AFNI TShift", "topics": [ "ni_afni_t_shift" ] }, { "page": "ni_afni_t_smooth", "title": "AFNI TSmooth", "topics": [ "ni_afni_t_smooth" ] }, { "page": "ni_afni_t_stat", "title": "AFNI TStat", "topics": [ "ni_afni_t_stat" ] }, { "page": "ni_afni_to3_d", "title": "AFNI To3D", "topics": [ "ni_afni_to3_d" ] }, { "page": "ni_afni_undump", "title": "AFNI Undump", "topics": [ "ni_afni_undump" ] }, { "page": "ni_afni_unifize", "title": "AFNI Unifize", "topics": [ "ni_afni_unifize" ] }, { "page": "ni_afni_volreg", "title": "AFNI Volreg", "topics": [ "ni_afni_volreg" ] }, { "page": "ni_afni_warp", "title": "AFNI Warp", "topics": [ "ni_afni_warp" ] }, { "page": "ni_afni_z_cut_up", "title": "AFNI ZCutUp", "topics": [ "ni_afni_z_cut_up" ] }, { "page": "ni_afni_zcat", "title": "AFNI Zcat", "topics": [ "ni_afni_zcat" ] }, { "page": "ni_afni_zeropad", "title": "AFNI Zeropad", "topics": [ "ni_afni_zeropad" ] }, { "page": "ni_ants_affine_initializer", "title": "ANTS AffineInitializer", "topics": [ "ni_ants_affine_initializer" ] }, { "page": "ni_ants_ai", "title": "ANTS AI", "topics": [ "ni_ants_ai" ] }, { "page": "ni_ants_ants", "title": "ANTS ANTS", "topics": [ "ni_ants_ants" ] }, { "page": "ni_ants_ants_introduction", "title": "ANTS antsIntroduction", "topics": [ "ni_ants_ants_introduction" ] }, { "page": "ni_ants_apply_transforms", "title": "ANTS ApplyTransforms", "topics": [ "ni_ants_apply_transforms" ] }, { "page": "ni_ants_apply_transforms_to_points", "title": "ANTS ApplyTransformsToPoints", "topics": [ "ni_ants_apply_transforms_to_points" ] }, { "page": "ni_ants_atropos", "title": "ANTS Atropos", "topics": [ "ni_ants_atropos" ] }, { "page": "ni_ants_average_affine_transform", "title": "ANTS AverageAffineTransform", "topics": [ "ni_ants_average_affine_transform" ] }, { "page": "ni_ants_average_images", "title": "ANTS AverageImages", "topics": [ "ni_ants_average_images" ] }, { "page": "ni_ants_brain_extraction", "title": "ANTS BrainExtraction", "topics": [ "ni_ants_brain_extraction" ] }, { "page": "ni_ants_buildtemplateparallel", "title": "ANTS buildtemplateparallel", "topics": [ "ni_ants_buildtemplateparallel" ] }, { "page": "ni_ants_compose_multi_transform", "title": "ANTS ComposeMultiTransform", "topics": [ "ni_ants_compose_multi_transform" ] }, { "page": "ni_ants_composite_transform_util", "title": "ANTS CompositeTransformUtil", "topics": [ "ni_ants_composite_transform_util" ] }, { "page": "ni_ants_convert_scalar_image_to_rgb", "title": "ANTS ConvertScalarImageToRGB", "topics": [ "ni_ants_convert_scalar_image_to_rgb" ] }, { "page": "ni_ants_cortical_thickness", "title": "ANTS CorticalThickness", "topics": [ "ni_ants_cortical_thickness" ] }, { "page": "ni_ants_create_jacobian_determinant_image", "title": "ANTS CreateJacobianDeterminantImage", "topics": [ "ni_ants_create_jacobian_determinant_image" ] }, { "page": "ni_ants_create_tiled_mosaic", "title": "ANTS CreateTiledMosaic", "topics": [ "ni_ants_create_tiled_mosaic" ] }, { "page": "ni_ants_denoise_image", "title": "ANTS DenoiseImage", "topics": [ "ni_ants_denoise_image" ] }, { "page": "ni_ants_gen_warp_fields", "title": "ANTS GenWarpFields", "topics": [ "ni_ants_gen_warp_fields" ] }, { "page": "ni_ants_image_math", "title": "ANTS ImageMath", "topics": [ "ni_ants_image_math" ] }, { "page": "ni_ants_joint_fusion", "title": "ANTS JointFusion", "topics": [ "ni_ants_joint_fusion" ] }, { "page": "ni_ants_kelly_kapowski", "title": "ANTS KellyKapowski", "topics": [ "ni_ants_kelly_kapowski" ] }, { "page": "ni_ants_label_geometry", "title": "ANTS LabelGeometry", "topics": [ "ni_ants_label_geometry" ] }, { "page": "ni_ants_laplacian_thickness", "title": "ANTS LaplacianThickness", "topics": [ "ni_ants_laplacian_thickness" ] }, { "page": "ni_ants_measure_image_similarity", "title": "ANTS MeasureImageSimilarity", "topics": [ "ni_ants_measure_image_similarity" ] }, { "page": "ni_ants_multiply_images", "title": "ANTS MultiplyImages", "topics": [ "ni_ants_multiply_images" ] }, { "page": "ni_ants_n4_bias_field_correction", "title": "ANTS N4BiasFieldCorrection", "topics": [ "ni_ants_n4_bias_field_correction" ] }, { "page": "ni_ants_registration", "title": "ANTS Registration", "topics": [ "ni_ants_registration" ] }, { "page": "ni_ants_registration_syn_quick", "title": "ANTS RegistrationSynQuick", "topics": [ "ni_ants_registration_syn_quick" ] }, { "page": "ni_ants_resample_image_by_spacing", "title": "ANTS ResampleImageBySpacing", "topics": [ "ni_ants_resample_image_by_spacing" ] }, { "page": "ni_ants_threshold_image", "title": "ANTS ThresholdImage", "topics": [ "ni_ants_threshold_image" ] }, { "page": "ni_ants_warp_image_multi_transform", "title": "ANTS WarpImageMultiTransform", "topics": [ "ni_ants_warp_image_multi_transform" ] }, { "page": "ni_ants_warp_time_series_image_multi_transform", "title": "ANTS WarpTimeSeriesImageMultiTransform", "topics": [ "ni_ants_warp_time_series_image_multi_transform" ] }, { "page": "ni_bids_app", "title": "Create a bidsappr-based BIDS App pre-configured with niflowr", "topics": [ "ni_bids_app" ] }, { "page": "ni_bids_inputs", "title": "Query a BIDS project for inputs matching a spec", "topics": [ "ni_bids_inputs" ] }, { "page": "ni_call", "title": "Construct an ni_call: bind parameter values to a spec", "topics": [ "ni_call" ] }, { "page": "ni_cmd", "title": "Get the command + args that would be executed", "topics": [ "ni_cmd" ] }, { "page": "ni_config", "title": "Get or update niflowr runtime configuration", "topics": [ "ni_config" ] }, { "page": "ni_constraints", "title": "List spec constraints as a table", "topics": [ "ni_constraints" ] }, { "page": "ni_dcm2niix_convert", "title": "dcm2niix Convert", "topics": [ "ni_dcm2niix_convert" ] }, { "page": "ni_deriv_path", "title": "Generate a BIDS-derivatives output path", "topics": [ "ni_deriv_path" ] }, { "page": "ni_doctor", "title": "Run runtime diagnostics", "topics": [ "ni_doctor" ] }, { "page": "ni_dry_run", "title": "Run a spec as a dry run", "topics": [ "ni_dry_run" ] }, { "page": "ni_fastsurfer_run", "title": "FastSurfer Run", "topics": [ "ni_fastsurfer_run" ] }, { "page": "ni_fastsurfer_segment", "title": "FastSurfer Segment", "topics": [ "ni_fastsurfer_segment" ] }, { "page": "ni_fmriprep_confounds", "title": "Read fMRIPrep confounds timeseries", "topics": [ "ni_fmriprep_confounds" ] }, { "page": "ni_fmriprep_derivatives", "title": "List fMRIPrep derivatives overview", "topics": [ "ni_fmriprep_derivatives" ] }, { "page": "ni_fmriprep_preproc", "title": "Locate fMRIPrep preprocessed files", "topics": [ "ni_fmriprep_preproc" ] }, { "page": "ni_freesurfer_add_x_form_to_header", "title": "FREESURFER AddXFormToHeader", "topics": [ "ni_freesurfer_add_x_form_to_header" ] }, { "page": "ni_freesurfer_aparc2_aseg", "title": "FREESURFER Aparc2Aseg", "topics": [ "ni_freesurfer_aparc2_aseg" ] }, { "page": "ni_freesurfer_apas2_aseg", "title": "FREESURFER Apas2Aseg", "topics": [ "ni_freesurfer_apas2_aseg" ] }, { "page": "ni_freesurfer_apply_mask", "title": "FREESURFER ApplyMask", "topics": [ "ni_freesurfer_apply_mask" ] }, { "page": "ni_freesurfer_apply_vol_transform", "title": "FREESURFER ApplyVolTransform", "topics": [ "ni_freesurfer_apply_vol_transform" ] }, { "page": "ni_freesurfer_bb_register", "title": "FREESURFER BBRegister", "topics": [ "ni_freesurfer_bb_register" ] }, { "page": "ni_freesurfer_binarize", "title": "FREESURFER Binarize", "topics": [ "ni_freesurfer_binarize" ] }, { "page": "ni_freesurfer_ca_label", "title": "FREESURFER CALabel", "topics": [ "ni_freesurfer_ca_label" ] }, { "page": "ni_freesurfer_ca_normalize", "title": "FREESURFER CANormalize", "topics": [ "ni_freesurfer_ca_normalize" ] }, { "page": "ni_freesurfer_ca_register", "title": "FREESURFER CARegister", "topics": [ "ni_freesurfer_ca_register" ] }, { "page": "ni_freesurfer_check_talairach_alignment", "title": "FREESURFER CheckTalairachAlignment", "topics": [ "ni_freesurfer_check_talairach_alignment" ] }, { "page": "ni_freesurfer_concatenate", "title": "FREESURFER Concatenate", "topics": [ "ni_freesurfer_concatenate" ] }, { "page": "ni_freesurfer_concatenate_lta", "title": "FREESURFER ConcatenateLTA", "topics": [ "ni_freesurfer_concatenate_lta" ] }, { "page": "ni_freesurfer_contrast", "title": "FREESURFER Contrast", "topics": [ "ni_freesurfer_contrast" ] }, { "page": "ni_freesurfer_curvature", "title": "FREESURFER Curvature", "topics": [ "ni_freesurfer_curvature" ] }, { "page": "ni_freesurfer_curvature_stats", "title": "FREESURFER CurvatureStats", "topics": [ "ni_freesurfer_curvature_stats" ] }, { "page": "ni_freesurfer_dicom_convert", "title": "FREESURFER DICOMConvert", "topics": [ "ni_freesurfer_dicom_convert" ] }, { "page": "ni_freesurfer_edit_w_mwith_aseg", "title": "FREESURFER EditWMwithAseg", "topics": [ "ni_freesurfer_edit_w_mwith_aseg" ] }, { "page": "ni_freesurfer_em_register", "title": "FREESURFER EMRegister", "topics": [ "ni_freesurfer_em_register" ] }, { "page": "ni_freesurfer_euler_number", "title": "FREESURFER EulerNumber", "topics": [ "ni_freesurfer_euler_number" ] }, { "page": "ni_freesurfer_extract_main_component", "title": "FREESURFER ExtractMainComponent", "topics": [ "ni_freesurfer_extract_main_component" ] }, { "page": "ni_freesurfer_fit_ms_params", "title": "FREESURFER FitMSParams", "topics": [ "ni_freesurfer_fit_ms_params" ] }, { "page": "ni_freesurfer_fix_topology", "title": "FREESURFER FixTopology", "topics": [ "ni_freesurfer_fix_topology" ] }, { "page": "ni_freesurfer_fuse_segmentations", "title": "FREESURFER FuseSegmentations", "topics": [ "ni_freesurfer_fuse_segmentations" ] }, { "page": "ni_freesurfer_glm_fit", "title": "FREESURFER GLMFit", "topics": [ "ni_freesurfer_glm_fit" ] }, { "page": "ni_freesurfer_gtm_seg", "title": "FREESURFER GTMSeg", "topics": [ "ni_freesurfer_gtm_seg" ] }, { "page": "ni_freesurfer_gtmpvc", "title": "FREESURFER GTMPVC", "topics": [ "ni_freesurfer_gtmpvc" ] }, { "page": "ni_freesurfer_image_info", "title": "FREESURFER ImageInfo", "topics": [ "ni_freesurfer_image_info" ] }, { "page": "ni_freesurfer_jacobian", "title": "FREESURFER Jacobian", "topics": [ "ni_freesurfer_jacobian" ] }, { "page": "ni_freesurfer_label2_annot", "title": "FREESURFER Label2Annot", "topics": [ "ni_freesurfer_label2_annot" ] }, { "page": "ni_freesurfer_label2_label", "title": "FREESURFER Label2Label", "topics": [ "ni_freesurfer_label2_label" ] }, { "page": "ni_freesurfer_label2_vol", "title": "FREESURFER Label2Vol", "topics": [ "ni_freesurfer_label2_vol" ] }, { "page": "ni_freesurfer_logan", "title": "FREESURFER Logan", "topics": [ "ni_freesurfer_logan" ] }, { "page": "ni_freesurfer_lta_convert", "title": "FREESURFER LTAConvert", "topics": [ "ni_freesurfer_lta_convert" ] }, { "page": "ni_freesurfer_make_average_subject", "title": "FREESURFER MakeAverageSubject", "topics": [ "ni_freesurfer_make_average_subject" ] }, { "page": "ni_freesurfer_make_surfaces", "title": "FREESURFER MakeSurfaces", "topics": [ "ni_freesurfer_make_surfaces" ] }, { "page": "ni_freesurfer_mni_bias_correction", "title": "FREESURFER MNIBiasCorrection", "topics": [ "ni_freesurfer_mni_bias_correction" ] }, { "page": "ni_freesurfer_mp_rto_mni305", "title": "FREESURFER MPRtoMNI305", "topics": [ "ni_freesurfer_mp_rto_mni305" ] }, { "page": "ni_freesurfer_mr_is_ca_label", "title": "FREESURFER MRIsCALabel", "topics": [ "ni_freesurfer_mr_is_ca_label" ] }, { "page": "ni_freesurfer_mr_is_calc", "title": "FREESURFER MRIsCalc", "topics": [ "ni_freesurfer_mr_is_calc" ] }, { "page": "ni_freesurfer_mr_is_combine", "title": "FREESURFER MRIsCombine", "topics": [ "ni_freesurfer_mr_is_combine" ] }, { "page": "ni_freesurfer_mr_is_convert", "title": "FREESURFER MRIsConvert", "topics": [ "ni_freesurfer_mr_is_convert" ] }, { "page": "ni_freesurfer_mr_is_expand", "title": "FREESURFER MRIsExpand", "topics": [ "ni_freesurfer_mr_is_expand" ] }, { "page": "ni_freesurfer_mr_is_inflate", "title": "FREESURFER MRIsInflate", "topics": [ "ni_freesurfer_mr_is_inflate" ] }, { "page": "ni_freesurfer_mri_convert", "title": "FREESURFER MRIConvert", "topics": [ "ni_freesurfer_mri_convert" ] }, { "page": "ni_freesurfer_mri_coreg", "title": "FREESURFER MRICoreg", "topics": [ "ni_freesurfer_mri_coreg" ] }, { "page": "ni_freesurfer_mri_fill", "title": "FREESURFER MRIFill", "topics": [ "ni_freesurfer_mri_fill" ] }, { "page": "ni_freesurfer_mri_marching_cubes", "title": "FREESURFER MRIMarchingCubes", "topics": [ "ni_freesurfer_mri_marching_cubes" ] }, { "page": "ni_freesurfer_mri_pretess", "title": "FREESURFER MRIPretess", "topics": [ "ni_freesurfer_mri_pretess" ] }, { "page": "ni_freesurfer_mri_tessellate", "title": "FREESURFER MRITessellate", "topics": [ "ni_freesurfer_mri_tessellate" ] }, { "page": "ni_freesurfer_mris_preproc", "title": "FREESURFER MRISPreproc", "topics": [ "ni_freesurfer_mris_preproc" ] }, { "page": "ni_freesurfer_mris_preproc_recon_all", "title": "FREESURFER MRISPreprocReconAll", "topics": [ "ni_freesurfer_mris_preproc_recon_all" ] }, { "page": "ni_freesurfer_mrtm1", "title": "FREESURFER MRTM1", "topics": [ "ni_freesurfer_mrtm1" ] }, { "page": "ni_freesurfer_mrtm2", "title": "FREESURFER MRTM2", "topics": [ "ni_freesurfer_mrtm2" ] }, { "page": "ni_freesurfer_ms_lda", "title": "FREESURFER MS_LDA", "topics": [ "ni_freesurfer_ms_lda" ] }, { "page": "ni_freesurfer_normalize", "title": "FREESURFER Normalize", "topics": [ "ni_freesurfer_normalize" ] }, { "page": "ni_freesurfer_one_sample_t_test", "title": "FREESURFER OneSampleTTest", "topics": [ "ni_freesurfer_one_sample_t_test" ] }, { "page": "ni_freesurfer_paint", "title": "FREESURFER Paint", "topics": [ "ni_freesurfer_paint" ] }, { "page": "ni_freesurfer_parcellation_stats", "title": "FREESURFER ParcellationStats", "topics": [ "ni_freesurfer_parcellation_stats" ] }, { "page": "ni_freesurfer_parse_dicom_dir", "title": "FREESURFER ParseDICOMDir", "topics": [ "ni_freesurfer_parse_dicom_dir" ] }, { "page": "ni_freesurfer_recon_all", "title": "FREESURFER ReconAll", "topics": [ "ni_freesurfer_recon_all" ] }, { "page": "ni_freesurfer_register", "title": "FREESURFER Register", "topics": [ "ni_freesurfer_register" ] }, { "page": "ni_freesurfer_register_av_ito_talairach", "title": "FREESURFER RegisterAVItoTalairach", "topics": [ "ni_freesurfer_register_av_ito_talairach" ] }, { "page": "ni_freesurfer_relabel_hypointensities", "title": "FREESURFER RelabelHypointensities", "topics": [ "ni_freesurfer_relabel_hypointensities" ] }, { "page": "ni_freesurfer_remove_intersection", "title": "FREESURFER RemoveIntersection", "topics": [ "ni_freesurfer_remove_intersection" ] }, { "page": "ni_freesurfer_remove_neck", "title": "FREESURFER RemoveNeck", "topics": [ "ni_freesurfer_remove_neck" ] }, { "page": "ni_freesurfer_resample", "title": "FREESURFER Resample", "topics": [ "ni_freesurfer_resample" ] }, { "page": "ni_freesurfer_robust_register", "title": "FREESURFER RobustRegister", "topics": [ "ni_freesurfer_robust_register" ] }, { "page": "ni_freesurfer_robust_template", "title": "FREESURFER RobustTemplate", "topics": [ "ni_freesurfer_robust_template" ] }, { "page": "ni_freesurfer_sample_to_surface", "title": "FREESURFER SampleToSurface", "topics": [ "ni_freesurfer_sample_to_surface" ] }, { "page": "ni_freesurfer_seg_stats", "title": "FREESURFER SegStats", "topics": [ "ni_freesurfer_seg_stats" ] }, { "page": "ni_freesurfer_seg_stats_recon_all", "title": "FREESURFER SegStatsReconAll", "topics": [ "ni_freesurfer_seg_stats_recon_all" ] }, { "page": "ni_freesurfer_segment_cc", "title": "FREESURFER SegmentCC", "topics": [ "ni_freesurfer_segment_cc" ] }, { "page": 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