antspymm API documentation

# antspymm

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      1try:
      2    from .version import __version__
      3except:
      4    pass
      5
      6from .mm import get_data
      7from .mm import ants_to_nibabel_affine
      8from .mm import get_dti
      9from .mm import efficient_tensor_fit
     10from .mm import efficient_dwi_fit
     11from .mm import triangular_to_tensor
     12from .mm import dti_numpy_to_image
     13from .mm import transform_and_reorient_dti
     14from .mm import get_models
     15from .mm import nrg_format_path
     16from .mm import highest_quality_repeat
     17from .mm import average_blind_qc_by_modality
     18from .mm import match_modalities
     19from .mm import outlierness_by_modality
     20from .mm import dewarp_imageset
     21from .mm import super_res_mcimage
     22from .mm import dipy_dti_recon
     23from .mm import segment_timeseries_by_meanvalue
     24from .mm import wmh
     25from .mm import neuromelanin
     26from .mm import joint_dti_recon
     27from .mm import resting_state_fmri_networks
     28from .mm import t1_based_dwi_brain_extraction
     29from .mm import dwi_deterministic_tracking
     30from .mm import dwi_closest_peak_tracking
     31from .mm import dwi_streamline_connectivity
     32from .mm import hierarchical_modality_summary
     33from .mm import dwi_streamline_pairwise_connectivity
     34from .mm import write_bvals_bvecs
     35from .mm import mm
     36from .mm import mm_nrg
     37from .mm import mm_csv
     38from .mm import write_mm
     39from .mm import mask_snr
     40from .mm import crop_mcimage
     41from .mm import alff_image
     42from .mm import alffmap
     43from .mm import spec_taper
     44from .mm import spec_ci
     45from .mm import spec_pgram
     46from .mm import plot_spec
     47from .mm import down2iso
     48from .mm import tra_initializer
     49from .mm import mm_read
     50from .mm import mm_read_to_3d
     51from .mm import image_write_with_thumbnail
     52from .mm import nrg_filelist_to_dataframe
     53from .mm import bind_wide_mm_csvs
     54from .mm import augment_image
     55from .mm import boot_wmh
     56from .mm import threaded_bind_wide_mm_csvs
     57from .mm import average_mm_df
     58from .mm import get_names_from_data_frame
     59from .mm import read_mm_csv
     60from .mm import assemble_modality_specific_dataframes
     61from .mm import aggregate_antspymm_results
     62from .mm import aggregate_antspymm_results_sdf
     63from .mm import mc_denoise
     64from .mm import mc_reg
     65from .mm import dti_reg
     66from .mm import timeseries_reg
     67from .mm import timeseries_transform
     68from .mm import copy_spatial_metadata_from_3d_to_4d
     69from .mm import concat_dewarp
     70from .mm import mc_resample_image_to_target
     71from .mm import trim_dti_mask
     72from .mm import impute_fa
     73from .mm import get_average_dwi_b0
     74from .mm import dti_template
     75from .mm import merge_dwi_data
     76from .mm import merge_timeseries_data
     77from .mm import bvec_reorientation
     78from .mm import tsnr
     79from .mm import dvars
     80from .mm import slice_snr
     81from .mm import quick_viz_mm_nrg
     82from .mm import blind_image_assessment
     83from .mm import get_average_rsf
     84from .mm import version
     85from .mm import best_mmm
     86from .mm import nrg_2_bids
     87from .mm import bids_2_nrg
     88from .mm import validate_nrg_file_format
     89from .mm import parse_nrg_filename
     90from .mm import novelty_detection_ee
     91from .mm import novelty_detection_svm
     92from .mm import novelty_detection_lof
     93from .mm import novelty_detection_loop
     94from .mm import novelty_detection_quantile
     95from .mm import generate_mm_dataframe
     96from .mm import generate_mm_dataframe_gpt
     97from .mm import collect_blind_qc_by_modality
     98from .mm import get_valid_modalities
     99from .mm import study_dataframe_from_matched_dataframe
    100from .mm import merge_wides_to_study_dataframe
    101from .mm import map_scalar_to_labels
    102from .mm import template_figure_with_overlay
    103from .mm import brainmap_figure
    104from .mm import bold_perfusion
    105from .mm import bold_perfusion_minimal
    106from .mm import filter_image_files
    107from .mm import docsamson
    108from .mm import enantiomorphic_filling_without_mask
    109from .mm import loop_timeseries_censoring
    110from .mm import score_fmri_censoring
    111from .mm import replace_elements_in_numpy_array
    112from .mm import remove_elements_from_numpy_array
    113from .mm import remove_volumes_from_timeseries
    114from .mm import impute_timeseries
    115from .mm import impute_dwi
    116from .mm import censor_dwi
    117from .mm import timeseries_n3
    118from .mm import calculate_CBF
    119from .mm import estimate_optimal_pca_components
    120from .mm import filter_df
    121from .mm import remove_elements_from_list
    122from .mm import despike_time_series
    123from .mm import despike_time_series_afni
    124from .mm import convert_np_in_dict
    125from .mm import read_ants_transforms_to_numpy
    126from .mm import clean_tmp_directory
    127from .mm import dict_to_dataframe
    128from .mm import PerAF
    129from .mm import get_antsimage_keys
    130from .mm import filter_columns_by_nan_percentage
    131from .mm import nrg_filename_to_subjectvisit
    132from .mm import add_repeat_column
    133from .mm import mm_match_by_qc_scoring
    134from .mm import mm_match_by_qc_scoring_all
    135from .mm import fix_LR_RL_stuff
    136from .mm import segment_timeseries_by_bvalue
    137from .mm import shorten_pymm_names
    138from .mm import pet3d_summary
    139from .mm import deformation_gradient_optimized
    140from .mm import efficient_dwi_fit_voxelwise
    141from .mm import generate_voxelwise_bvecs
    142from .mm import distortion_correct_bvecs
    143from .mm import apply_transforms_mixed_interpolation
    144from .mm import t1w_super_resolution_with_hemispheres
    145from .mm import map_idps_to_rois