niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/__init__.py

@@ -0,0 +1,726 @@
+"""
+FreeSurfer
+
+FreeSurfer is a software package for the analysis and visualization of
+neuroimaging data from cross-sectional and longitudinal studies. It is developed
+by the Laboratory for Computational Neuroimaging at the Martinos Center for
+Biomedical Imaging.
+
+FreeSurfer provides full processing streams for structural and functional MRI
+and includes tools for linear and nonlinear registration, cortical and
+subcortical segmentation, cortical surface reconstruction, statistical analysis
+of group morphometry, diffusion MRI, PET analysis, and much more. It is also the
+structural MRI analysis software of choice for the Human Connectome Project.
+
+URL: https://github.com/freesurfer/freesurfer
+"""
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+from .analyzeto4dfp import *
+from .anatomi_cuts_utils import *
+from .annot2std import *
+from .ants_denoise_image_fs import *
+from .ants_n4_bias_field_correction_fs import *
+from .aparc2feat import *
+from .aparc_stats_aseg import *
+from .aparcstats2table import *
+from .aparcstatsdiff import *
+from .apas2aseg import *
+from .apply_morph import *
+from .aseg2feat import *
+from .asegstats2table import *
+from .asegstatsdiff import *
+from .avi2talxfm import *
+from .bblabel import *
+from .bbmask import *
+from .bbregister import *
+from .bedpostx_mgh import *
+from .bet_fsl import *
+from .beta2sxa import *
+from .biasfield import *
+from .bmedits2surf import *
+from .brec import *
+from .browse_minc_header_tcl import *
+from .bugr import *
+from .build_desikan_killiany_gcs_csh import *
+from .cblumwmgyri import *
+from .check_mcr_sh import *
+from .check_recons_sh import *
+from .check_subject import *
+from .compute_interrater_variability_csh import *
+from .compute_label_volumes_csh import *
+from .compute_vox2vox import *
+from .conf2hires import *
+from .connected_components import *
+from .cor_to_minc import *
+from .cp_dicom import *
+from .create_morph import *
+from .csvprint import *
+from .dcmdir_info_mgh import *
+from .dcmdjpeg_fs import *
+from .dcmdrle_fs import *
+from .dcmsplit import *
+from .dcmunpack import *
+from .deface_subject import *
+from .defect2seg import *
+from .defect_seg import *
+from .dicom_rename import *
+from .diffusion_utils import *
+from .dmri_ac_sh import *
+from .dmri_anatomi_cuts import *
+from .dmri_bset import *
+from .dmri_colored_fa import *
+from .dmri_extract_surface_measurements import *
+from .dmri_forrest import *
+from .dmri_group import *
+from .dmri_group_by_endpoints import *
+from .dmri_match import *
+from .dmri_mergepaths import *
+from .dmri_motion import *
+from .dmri_neighboring_regions import *
+from .dmri_paths import *
+from .dmri_pathstats import *
+from .dmri_project_end_points import *
+from .dmri_save_histograms import *
+from .dmri_spline import *
+from .dmri_stats_ac import *
+from .dmri_train import *
+from .dmri_trk2trk import *
+from .dmri_violin_plots import *
+from .dmri_vox2vox import *
+from .dt_recon import *
+from .epidewarp_fsl import *
+from .export_gcam import *
+from .extract_seg_waveform import *
+from .exvivo_hemi_proc import *
+from .feat2segstats import *
+from .feat2surf import *
+from .fiducials_calibration import *
+from .fiducials_correction import *
+from .fix_subject import *
+from .fix_subject_corrected import *
+from .fix_subject_corrected_rh import *
+from .fix_subject_rh import *
+from .fixup_mni_paths import *
+from .flip_4dfp import *
+from .flirt_fsl import *
+from .flirt_newdefault_20080811_sch import *
+from .fname2ext import *
+from .fname2stem import *
+from .freeview import *
+from .fs_check_version import *
+from .fs_install_mcr import *
+from .fs_lib_check import *
+from .fs_print_help import *
+from .fs_run_from_mcr import *
+from .fs_spmreg_glnxa64 import *
+from .fs_temp_dir import *
+from .fs_temp_file import *
+from .fs_time import *
+from .fs_tutorial_data import *
+from .fs_update import *
+from .fscalc import *
+from .fscalc_fsl import *
+from .fsdcmdecompress import *
+from .fsfirst_fsl import *
+from .fsl_5_0_2_xyztrans_sch import *
+from .fsl_label2voxel import *
+from .fsl_rigid_register import *
+from .fsl_sub_mgh import *
+from .fslmaths_fsl import *
+from .fslorient_fsl import *
+from .fslregister import *
+from .fslswapdim_fsl import *
+from .fspalm import *
+from .fspython import *
+from .fsr_coreg import *
+from .fsr_getxopts import *
+from .fsr_import import *
+from .fsrealpath import *
+from .fsvglrun import *
+from .fvcompare import *
+from .gauss_4dfp import *
+from .gca_apply import *
+from .gcainit import *
+from .gcaprepone import *
+from .gcatrain import *
+from .gcatrainskull import *
+from .gdcmconv_fs import *
+from .gems_compute_atlas_probs import *
+from .get_label_thickness import *
+from .getfullpath import *
+from .grad_unwarp import *
+from .groupstats import *
+from .groupstatsdiff import *
+from .gtmseg import *
+from .hiam_make_surfaces import *
+from .hiam_make_template import *
+from .hiam_register import *
+from .histo_compute_joint_density import *
+from .histo_register_block import *
+from .histo_synthesize import *
+from .ico_supersample import *
+from .ifh2hdr import *
+from .imgreg_4dfp import *
+from .inflate_subject import *
+from .inflate_subject3 import *
+from .inflate_subject_lh import *
+from .inflate_subject_new import *
+from .inflate_subject_new_lh import *
+from .inflate_subject_new_rh import *
+from .inflate_subject_rh import *
+from .inflate_subject_sc import *
+from .irepifitvol import *
+from .irepifitvol_glnx64 import *
+from .is_lta import *
+from .is_surface import *
+from .isanalyze import *
+from .isnifti import *
+from .isolate_labels_csh import *
+from .isolate_labels_keeporigval_csh import *
+from .jkgcatrain import *
+from .label2flat import *
+from .label2patch import *
+from .label_elderly_subject import *
+from .label_subject import *
+from .label_subject_flash import *
+from .label_subject_mixed import *
+from .labels_disjoint import *
+from .labels_intersect import *
+from .labels_union import *
+from .list_otl_labels import *
+from .listsubj import *
+from .long_create_base_sigma import *
+from .long_create_orig import *
+from .long_mris_slopes import *
+from .long_qdec_table import *
+from .long_stats_combine import *
+from .long_stats_slopes import *
+from .long_stats_tps import *
+from .long_submit_jobs import *
+from .long_submit_postproc import *
+from .longmc import *
+from .lpcregister import *
+from .lta_convert import *
+from .lta_diff import *
+from .make_average_subcort import *
+from .make_average_subject import *
+from .make_average_surface import *
+from .make_average_volume import *
+from .make_cortex_label import *
+from .make_exvivo_filled import *
+from .make_folding_atlas import *
+from .make_hemi_mask import *
+from .make_segvol_table import *
+from .make_symmetric import *
+from .make_upright import *
+from .makevol import *
+from .map_all_labels import *
+from .map_all_labels_lh import *
+from .map_central_sulcus import *
+from .map_to_base import *
+from .meanval import *
+from .merge_stats_tables import *
+from .mergeseg import *
+from .mideface import *
+from .minc2seqinfo import *
+from .mkheadsurf import *
+from .mkima_index_tcl import *
+from .mkmnc_index_tcl import *
+from .mksubjdirs import *
+from .mksurfatlas import *
+from .mkxsubjreg import *
+from .mmppsp import *
+from .mni152reg import *
+from .morph_only_subject import *
+from .morph_only_subject_lh import *
+from .morph_only_subject_rh import *
+from .morph_rgb_lh import *
+from .morph_rgb_rh import *
+from .morph_subject import *
+from .morph_subject_lh import *
+from .morph_subject_rh import *
+from .morph_tables_lh import *
+from .morph_tables_rh import *
+from .mpr2mni305 import *
+from .mri_3d_photo_recon import *
+from .mri_add_new_tp import *
+from .mri_add_xform_to_header import *
+from .mri_align_long_csh import *
+from .mri_and import *
+from .mri_annotation2label import *
+from .mri_aparc2aseg import *
+from .mri_aparc2wmseg import *
+from .mri_apply_bias import *
+from .mri_average import *
+from .mri_binarize import *
+from .mri_brain_volume import *
+from .mri_brainvol_stats import *
+from .mri_ca_label import *
+from .mri_ca_normalize import *
+from .mri_ca_register import *
+from .mri_ca_tissue_parms import *
+from .mri_ca_train import *
+from .mri_cal_renormalize_gca import *
+from .mri_cc import *
+from .mri_cnr import *
+from .mri_compile_edits import *
+from .mri_compute_bias import *
+from .mri_compute_change_map import *
+from .mri_compute_distances import *
+from .mri_compute_layer_fractions import *
+from .mri_compute_overlap import *
+from .mri_compute_seg_overlap import *
+from .mri_compute_volume_fractions import *
+from .mri_compute_volume_intensities import *
+from .mri_concat import *
+from .mri_concatenate_gcam import *
+from .mri_concatenate_lta import *
+from .mri_convert import *
+from .mri_copy_params import *
+from .mri_copy_values import *
+from .mri_cor2label import *
+from .mri_coreg import *
+from .mri_correct_segmentations import *
+from .mri_create_t2combined import *
+from .mri_create_tests import *
+from .mri_cvs_check import *
+from .mri_cvs_data_copy import *
+from .mri_cvs_register import *
+from .mri_dct_align import *
+from .mri_dct_align_binary import *
+from .mri_deface import *
+from .mri_defacer import *
+from .mri_diff import *
+from .mri_dist_surf_label import *
+from .mri_distance_transform import *
+from .mri_easyreg import *
+from .mri_easywarp import *
+from .mri_edit_segmentation import *
+from .mri_edit_segmentation_with_surfaces import *
+from .mri_edit_wm_with_aseg import *
+from .mri_em_register import *
+from .mri_entowm_seg import *
+from .mri_evaluate_morph import *
+from .mri_extract import *
+from .mri_extract_fcd_features import *
+from .mri_extract_label import *
+from .mri_extract_largest_cc import *
+from .mri_exvivo_norm import *
+from .mri_exvivo_strip import *
+from .mri_fdr import *
+from .mri_fieldsign import *
+from .mri_fill import *
+from .mri_fit_bias import *
+from .mri_fslmat_to_lta import *
+from .mri_func2sph import *
+from .mri_funcvits import *
+from .mri_fuse_intensity_images import *
+from .mri_fuse_segmentations import *
+from .mri_fwhm import *
+from .mri_gca_ambiguous import *
+from .mri_gcab_train import *
+from .mri_gcut import *
+from .mri_gdfglm import *
+from .mri_glmfit import *
+from .mri_glmfit_sim import *
+from .mri_gradient_info import *
+from .mri_gradunwarp import *
+from .mri_gtmpvc import *
+from .mri_gtmseg import *
+from .mri_hausdorff_dist import *
+from .mri_head import *
+from .mri_hires_register import *
+from .mri_histo_eq import *
+from .mri_info import *
+from .mri_jacobian import *
+from .mri_joint_density import *
+from .mri_label2label import *
+from .mri_label2vol import *
+from .mri_label_histo import *
+from .mri_label_vals import *
+from .mri_label_volume import *
+from .mri_linear_align import *
+from .mri_linear_align_binary import *
+from .mri_linear_register import *
+from .mri_log_likelihood import *
+from .mri_long_normalize import *
+from .mri_make_bem_surfaces import *
+from .mri_make_uchar import *
+from .mri_map_cpdat import *
+from .mri_maps2csd import *
+from .mri_mark_temporal_lobe import *
+from .mri_mask import *
+from .mri_matrix_multiply import *
+from .mri_mc import *
+from .mri_mcsim import *
+from .mri_mergelabels import *
+from .mri_mi import *
+from .mri_modify import *
+from .mri_morphology import *
+from .mri_motion_correct import *
+from .mri_motion_correct2 import *
+from .mri_motion_correct_fsl import *
+from .mri_ms_fitparms import *
+from .mri_nl_align import *
+from .mri_nl_align_binary import *
+from .mri_nlfilter import *
+from .mri_normalize import *
+from .mri_normalize_tp2 import *
+from .mri_nu_correct_mni import *
+from .mri_or import *
+from .mri_paint import *
+from .mri_parse_sdcmdir import *
+from .mri_path2label import *
+from .mri_polv import *
+from .mri_pretess import *
+from .mri_probe_ima import *
+from .mri_probedicom import *
+from .mri_reduce import *
+from .mri_refine_seg import *
+from .mri_relabel_hypointensities import *
+from .mri_relabel_nonwm_hypos import *
+from .mri_remove_neck import *
+from .mri_reorient_lr_csh import *
+from .mri_rf_label import *
+from .mri_rf_long_label import *
+from .mri_rf_long_train import *
+from .mri_rf_train import *
+from .mri_ribbon import *
+from .mri_rigid_register import *
+from .mri_robust_register import *
+from .mri_robust_template import *
+from .mri_sbbr import *
+from .mri_sclimbic_seg import *
+from .mri_seg_diff import *
+from .mri_seg_overlap import *
+from .mri_segcentroids import *
+from .mri_seghead import *
+from .mri_segment import *
+from .mri_segment_hypothalamic_subunits import *
+from .mri_segment_thalamic_nuclei_dti_cnn import *
+from .mri_segreg import *
+from .mri_segstats import *
+from .mri_sph2surf import *
+from .mri_stats2seg import *
+from .mri_stopmask import *
+from .mri_strip_nonwhite import *
+from .mri_strip_subject_info import *
+from .mri_surf2surf import *
+from .mri_surf2vol import *
+from .mri_surf2volseg import *
+from .mri_surfacemask import *
+from .mri_surfcluster import *
+from .mri_synthesize import *
+from .mri_synthmorph import *
+from .mri_synthseg import *
+from .mri_synthsr import *
+from .mri_synthsr_hyperfine import *
+from .mri_synthstrip import *
+from .mri_tessellate import *
+from .mri_threshold import *
+from .mri_topologycorrection import *
+from .mri_train import *
+from .mri_transform import *
+from .mri_twoclass import *
+from .mri_validate_skull_stripped import *
+from .mri_vessel_segment import *
+from .mri_vol2label import *
+from .mri_vol2surf import *
+from .mri_vol2vol import *
+from .mri_volcluster import *
+from .mri_voldiff import *
+from .mri_volsynth import *
+from .mri_warp_convert import *
+from .mri_watershed import *
+from .mri_wbc import *
+from .mri_xvolavg import *
+from .mri_z2p import *
+from .mris2rgb import *
+from .mris_aa_shrinkwrap import *
+from .mris_add_template import *
+from .mris_anatomical_stats import *
+from .mris_annot_diff import *
+from .mris_annot_to_segmentation import *
+from .mris_apply_reg import *
+from .mris_autodet_gwstats import *
+from .mris_average_curvature import *
+from .mris_ba_segment import *
+from .mris_ca_deform import *
+from .mris_ca_label import *
+from .mris_ca_train import *
+from .mris_calc import *
+from .mris_compute_acorr import *
+from .mris_compute_layer_intensities import *
+from .mris_compute_lgi import *
+from .mris_compute_overlap import *
+from .mris_compute_parc_overlap import *
+from .mris_compute_volume_fractions import *
+from .mris_congeal import *
+from .mris_convert import *
+from .mris_copy_header import *
+from .mris_curvature import *
+from .mris_curvature2image import *
+from .mris_curvature_stats import *
+from .mris_defects_pointset import *
+from .mris_deform import *
+from .mris_diff import *
+from .mris_distance_map import *
+from .mris_distance_to_label import *
+from .mris_distance_transform import *
+from .mris_divide_parcellation import *
+from .mris_entropy import *
+from .mris_errors import *
+from .mris_estimate_wm import *
+from .mris_euler_number import *
+from .mris_expand import *
+from .mris_extract_main_component import *
+from .mris_extract_patches import *
+from .mris_extract_values import *
+from .mris_exvivo_surfaces import *
+from .mris_fill import *
+from .mris_find_flat_regions import *
+from .mris_fix_topology import *
+from .mris_flatten import *
+from .mris_fwhm import *
+from .mris_gradient import *
+from .mris_hausdorff_dist import *
+from .mris_image2vtk import *
+from .mris_inflate import *
+from .mris_info import *
+from .mris_init_global_tractography import *
+from .mris_intensity_profile import *
+from .mris_interpolate_warp import *
+from .mris_jacobian import *
+from .mris_label2annot import *
+from .mris_label_area import *
+from .mris_label_calc import *
+from .mris_label_mode import *
+from .mris_left_right_register import *
+from .mris_make_average_surface import *
+from .mris_make_face_parcellation import *
+from .mris_make_surfaces import *
+from .mris_make_template import *
+from .mris_map_cuts import *
+from .mris_mef_surfaces import *
+from .mris_merge_parcellations import *
+from .mris_mesh_subdivide import *
+from .mris_morph_stats import *
+from .mris_ms_refine import *
+from .mris_multimodal import *
+from .mris_multimodal_surface_placement import *
+from .mris_multiscale_stats import *
+from .mris_niters2fwhm import *
+from .mris_nudge import *
+from .mris_parcellate_connectivity import *
+from .mris_place_surface import *
+from .mris_pmake import *
+from .mris_preproc import *
+from .mris_profile_clustering import *
+from .mris_refine_surfaces import *
+from .mris_register import *
+from .mris_register_label_map import *
+from .mris_register_to_label import *
+from .mris_register_to_volume import *
+from .mris_remesh import *
+from .mris_remove_intersection import *
+from .mris_remove_negative_vertices import *
+from .mris_remove_variance import *
+from .mris_reposition_surface import *
+from .mris_resample import *
+from .mris_rescale import *
+from .mris_reverse import *
+from .mris_rf_label import *
+from .mris_rf_train import *
+from .mris_rotate import *
+from .mris_sample_label import *
+from .mris_sample_parc import *
+from .mris_seg2annot import *
+from .mris_segment import *
+from .mris_segment_vals import *
+from .mris_segmentation_stats import *
+from .mris_shrinkwrap import *
+from .mris_simulate_atrophy import *
+from .mris_skeletonize import *
+from .mris_smooth import *
+from .mris_smooth_intracortical import *
+from .mris_sphere import *
+from .mris_spherical_average import *
+from .mris_surf2vtk import *
+from .mris_surface_stats import *
+from .mris_surface_to_vol_distances import *
+from .mris_talairach import *
+from .mris_target_pos import *
+from .mris_thickness import *
+from .mris_thickness_comparison import *
+from .mris_thickness_diff import *
+from .mris_topo_fixer import *
+from .mris_transform import *
+from .mris_translate_annotation import *
+from .mris_transmantle_dysplasia_paths import *
+from .mris_volmask import *
+from .mris_volmask_novtk import *
+from .mris_volmask_vtk import *
+from .mris_volsmooth import *
+from .mris_volume import *
+from .mris_warp import *
+from .mris_watershed import *
+from .mris_wm_volume import *
+from .mrisp_paint import *
+from .mrisp_write import *
+from .ms_refine_subject import *
+from .nmovie_qt import *
+from .oct_register_mosaic import *
+from .optseq2 import *
+from .orient_las import *
+from .parc_atlas_jackknife_test import *
+from .pctsurfcon import *
+from .plot_structure_stats_tcl import *
+from .pointset2label import *
+from .polyorder import *
+from .post_recon_all import *
+from .predict_v1_sh import *
+from .print_unique_labels_csh import *
+from .qatools_py import *
+from .quantify_brainstem_structures_sh import *
+from .quantify_hasubregions_sh import *
+from .quantify_thalamic_nuclei_sh import *
+from .rbbr import *
+from .rca_base_init import *
+from .rca_config import *
+from .rca_config2csh import *
+from .rca_fix_ento import *
+from .rca_long_tp_init import *
+from .rcbf_prep import *
+from .recon_all import *
+from .recon_all_clinical_sh import *
+from .recon_all_exvivo import *
+from .reconbatchjobs import *
+from .reg2subject import *
+from .reg_feat2anat import *
+from .reg_mni305_2mm import *
+from .regdat2xfm import *
+from .register_child import *
+from .register_csh import *
+from .register_elderly_subject import *
+from .register_subject import *
+from .register_subject_flash import *
+from .reinflate_subject import *
+from .reinflate_subject_lh import *
+from .reinflate_subject_rh import *
+from .remove_talairach import *
+from .renormalize_subject_keep_editting import *
+from .renormalize_t1_subject import *
+from .reregister_subject_mixed import *
+from .rtview import *
+from .run_mris_preproc import *
+from .run_qdec_glm import *
+from .run_samseg import *
+from .run_samseg_long import *
+from .run_segment_subfields_t1_longitudinal_sh import *
+from .run_segment_subject_sh import *
+from .run_segment_subject_t1_auto_estimate_alveus_ml_sh import *
+from .run_segment_subject_t1_t2_auto_estimate_alveus_ml_sh import *
+from .run_segment_subject_t2_auto_estimate_alveus_ml_sh import *
+from .run_segment_thalamic_nuclei_sh import *
+from .samseg import *
+from .samseg2recon import *
+from .samseg_long import *
+from .samsegmesh2surf import *
+from .sbtiv import *
+from .seg2filled import *
+from .seg2recon import *
+from .segment_bs_sh import *
+from .segment_ha_t1_long_sh import *
+from .segment_ha_t1_sh import *
+from .segment_ha_t2_sh import *
+from .segment_monkey import *
+from .segment_subfields_t1_longitudinal import *
+from .segment_subject import *
+from .segment_subject_notal import *
+from .segment_subject_notal2 import *
+from .segment_subject_old_skull_strip import *
+from .segment_subject_sc import *
+from .segment_subject_t1_auto_estimate_alveus_ml import *
+from .segment_subject_t1_t2_auto_estimate_alveus_ml import *
+from .segment_subject_t2_auto_estimate_alveus_ml import *
+from .segment_subregions import *
+from .segment_thalamic_nuclei import *
+from .segment_thalamic_nuclei_sh import *
+from .segpons import *
+from .setlabelstat import *
+from .sfa2fieldsign import *
+from .slicedelay import *
+from .slicetimer_fsl import *
+from .sphere_subject import *
+from .sphere_subject_lh import *
+from .sphere_subject_rh import *
+from .spline3_test import *
+from .spm_t_to_b import *
+from .spmregister import *
+from .sratio import *
+from .stat_normalize import *
+from .stattablediff import *
+from .stem2fname import *
+from .surf2vol import *
+from .surfreg import *
+from .swi_preprocess import *
+from .swi_process import *
+from .t4img_4dfp import *
+from .t4imgs_4dfp import *
+from .table2map import *
+from .tal_compare import *
+from .tal_qc_azs import *
+from .talairach import *
+from .talairach2 import *
+from .talairach_afd import *
+from .talairach_avi import *
+from .talairach_mgh import *
+from .talsegprob import *
+from .test_orientation_planes_from_parcellation import *
+from .test_recon_all_csh import *
+from .test_tutorials_sh import *
+from .thickdiffmap import *
+from .tkmedit import *
+from .tkmeditfv import *
+from .tkregister2 import *
+from .tkregister2_cmdl import *
+from .tkregisterfv import *
+from .tksurfer import *
+from .tksurferfv import *
+from .trac_all import *
+from .trac_paths import *
+from .trac_preproc import *
+from .tractstats2table import *
+from .train_gcs_atlas import *
+from .tridec import *
+from .trk_tools import *
+from .unpack_ima1_tcl import *
+from .unpack_ima_tcl import *
+from .unpack_mnc_tcl import *
+from .unpackimadir import *
+from .unpackimadir2 import *
+from .unpackmincdir import *
+from .unpacksdcmdir import *
+from .update_needed import *
+from .v_3dvolreg_afni import *
+from .v_4dfptoanalyze import *
+from .ventfix import *
+from .vertexvol import *
+from .vno_match_check import *
+from .vol2segavg import *
+from .vol2subfield import *
+from .vol2symsurf import *
+from .vsm_smooth import *
+from .wfilemask import *
+from .wm_anat_snr import *
+from .wmedits2surf import *
+from .wmsaseg import *
+from .xcerebralseg import *
+from .xcorr import *
+from .xfmrot import *
+from .xhemi_tal import *
+from .xhemireg import *
+from .xsanatreg import *
+from .zero_lt_4dfp import *