Index

_

__version__ (in module resomapper)

A

acq_categories_BIDS (in module resomapper.core.misc) add_SUR_info_to_json() (in module resomapper.format_conversion.MRS_conversion) any_studies_in_dict() (in module resomapper.processing.processing) ascm_denoising() (in module resomapper.processing.preprocessing) ask_user() (in module resomapper.core.utils) ask_user_options() (in module resomapper.core.utils)

ask_user_parameters() (in module resomapper.core.utils) auto_init_logger() (in module resomapper.core.misc) auto_innited_logger (in module resomapper.core.misc) auto_prepare() (in module resomapper.auto) auto_process() (in module resomapper.auto) auto_processing_options (in module resomapper.core.misc) auto_save_heatmap() (in module resomapper.processing.heatmap)

B

btable_to_bval_bvlec() (in module resomapper.format_conversion.MRS_conversion)

C

check_mask_shape() (in module resomapper.processing.masking) check_slices_MT_images() (in module resomapper.model_fitting.MTRfit) check_slopes_MT_images() (in module resomapper.model_fitting.MTRfit) check_valid_dir_bruker() (in module resomapper.format_conversion.bruker_conversion) choose_if_reprocess() (in module resomapper.processing.processing) cli_ask_dti_info() (in module resomapper.model_fitting.DTIfit) cli_ask_indexes_to_rm() (in module resomapper.processing.processing) cli_DTI_remove_directions() (in module resomapper.processing.processing) cli_prepare() (in module resomapper.cli) cli_process() (in module resomapper.cli) cli_select_input_format() (in module resomapper.cli) cli_select_masking_mode() (in module resomapper.cli) cli_select_mt_runs() (in module resomapper.cli) cli_show_and_save_heatmap() (in module resomapper.processing.heatmap) cli_Tmap_remove_times() (in module resomapper.processing.processing) click() (in module resomapper.processing.masking) close_window() (in module resomapper.core.utils)

compute_dti_map() (in module resomapper.model_fitting.DTIfit) compute_MTR_map() (in module resomapper.model_fitting.MTRfit) compute_R2() (in module resomapper.model_fitting.DTIfit) conditions_dict_bruker (in module resomapper.core.misc) conditions_dict_MRS (in module resomapper.core.misc) convert_and_save_nifti_bruker() (in module resomapper.format_conversion.bruker_conversion) convert_dicom_localizer() (in module resomapper.format_conversion.DICOM_conversion) convert_dicom_series() (in module resomapper.format_conversion.DICOM_conversion) convert_single_study_bruker() (in module resomapper.format_conversion.bruker_conversion) convert_single_study_MRS() (in module resomapper.format_conversion.MRS_conversion) convert_studies_from_bruker() (in module resomapper.format_conversion.bruker_conversion) convert_studies_from_MRS() (in module resomapper.format_conversion.MRS_conversion) count_basal_dirs_bvals() (in module resomapper.model_fitting.DTIfit) create_metadata_json_bruker() (in module resomapper.format_conversion.bruker_conversion) create_metadata_json_MRS() (in module resomapper.format_conversion.MRS_conversion) create_options_template_auto() (in module resomapper.auto) create_readme() (in module resomapper.core.utils)

D

defaulr_map_units (in module resomapper.processing.heatmap) default_map_scales (in module resomapper.processing.heatmap)

denoise() (in module resomapper.processing.preprocessing) dicom_to_json_serializable() (in module resomapper.format_conversion.MRS_conversion)

F

Fobj_SSE_Tmaps() (in module resomapper.model_fitting.Tmapfit)

G

get_acq() (in module resomapper.core.utils) get_common_info_study_bruker() (in module resomapper.format_conversion.bruker_conversion) get_echo_times_from_dicom() (in module resomapper.format_conversion.DICOM_conversion) get_modality_bruker() (in module resomapper.format_conversion.bruker_conversion) get_modality_MRS() (in module resomapper.format_conversion.MRS_conversion) get_modality_nii_acq() (in module resomapper.core.utils)

get_modality_nii_map() (in module resomapper.core.utils) get_nifti_filenames() (in module resomapper.core.utils) get_rep_times_from_dicom() (in module resomapper.format_conversion.DICOM_conversion) get_studies_to_convert_bruker() (in module resomapper.format_conversion.bruker_conversion) get_studies_to_convert_MRS() (in module resomapper.format_conversion.MRS_conversion) get_studies_to_process() (in module resomapper.processing.processing) gibbs_suppress() (in module resomapper.processing.preprocessing)

H

heatmap_printer() (in module resomapper.processing.heatmap)

hist_strip_mask() (in module resomapper.processing.masking)

I

info_and_ask_denoising_params() (in module resomapper.processing.preprocessing) is_folder_and_not_occult() (in module resomapper.core.utils) is_folder_or_zip_and_not_occult() (in module resomapper.core.utils)

is_modality_bruker() (in module resomapper.format_conversion.bruker_conversion) is_modality_MRS() (in module resomapper.format_conversion.MRS_conversion) is_nii() (in module resomapper.core.utils) itera() (in module resomapper.processing.masking)

L

local_pca_denoising() (in module resomapper.processing.preprocessing)

Logger (class in resomapper.core.misc)

M

manual_mask() (in module resomapper.processing.masking) metadata_ref_BIDS_bruker (in module resomapper.core.misc) metadata_ref_DICOM_MRS (in module resomapper.core.misc) min_max_normalization() (in module resomapper.processing.masking) module resomapper resomapper.auto resomapper.cli resomapper.core resomapper.core.misc resomapper.core.utils resomapper.format_conversion resomapper.format_conversion.bruker_conversion resomapper.format_conversion.DICOM_conversion resomapper.format_conversion.MRS_conversion resomapper.model_fitting resomapper.model_fitting.DTIfit resomapper.model_fitting.MTRfit resomapper.model_fitting.Tmapfit resomapper.processing resomapper.processing.heatmap resomapper.processing.masking resomapper.processing.preprocessing resomapper.processing.processing resomapper.standalonetools

mp_pca_denoising() (in module resomapper.processing.preprocessing) MRsolutionsKeys (in module resomapper.format_conversion.MRS_conversion)

N

n4_bias_field_correct() (in module resomapper.processing.preprocessing) no_mask() (in module resomapper.processing.masking) NoModalsSelectedError

non_local_means_2_denoising() (in module resomapper.processing.preprocessing) non_local_means_denoising() (in module resomapper.processing.preprocessing) NotStudiesToConvertError NotStudiesToProcessError

P

parse_PPR_keywords() (in module resomapper.format_conversion.MRS_conversion) patch2self_denoising() (in module resomapper.processing.preprocessing) prepare_vol() (in module resomapper.processing.masking) print_bvals_bvecs() (in module resomapper.model_fitting.DTIfit)

process_dti() (in module resomapper.model_fitting.DTIfit) process_DTI() (in module resomapper.processing.processing) process_MTRmap() (in module resomapper.processing.processing) process_Tmap() (in module resomapper.processing.processing)

R

rename_associated_files() (in module resomapper.core.utils) resomapper module resomapper.auto module resomapper.cli module resomapper.core module resomapper.core.misc module resomapper.core.utils module resomapper.format_conversion module resomapper.format_conversion.bruker_conversion module resomapper.format_conversion.DICOM_conversion module resomapper.format_conversion.MRS_conversion module resomapper.model_fitting module

resomapper.model_fitting.DTIfit module resomapper.model_fitting.MTRfit module resomapper.model_fitting.Tmapfit module resomapper.processing module resomapper.processing.heatmap module resomapper.processing.masking module resomapper.processing.preprocessing module resomapper.processing.processing module resomapper.standalonetools module rotate() (in module resomapper.processing.heatmap) run_auto() (in module resomapper.auto) run_cli() (in module resomapper.cli) run_tools() (in module resomapper.standalonetools)

S

save_bvals_bvecs() (in module resomapper.model_fitting.DTIfit) select_denoising_filter() (in module resomapper.processing.preprocessing) select_directory() (in module resomapper.core.utils) select_file() (in module resomapper.core.utils) select_modalities_to_process() (in module resomapper.core.utils)

show_bias_field_correction_ask() (in module resomapper.processing.preprocessing) show_denoised_output() (in module resomapper.processing.preprocessing) signal_equation_T1() (in module resomapper.model_fitting.Tmapfit) signal_equation_T2T2star() (in module resomapper.model_fitting.Tmapfit) study_files_present_MRS() (in module resomapper.format_conversion.MRS_conversion) subject_file_present_bruker() (in module resomapper.format_conversion.bruker_conversion)

T

Tmapfit_image() (in module resomapper.model_fitting.Tmapfit) Tmapfit_slice() (in module resomapper.model_fitting.Tmapfit) Tmapfit_voxel_2timesanalitical() (in module resomapper.model_fitting.Tmapfit)

Tmapfit_voxel_GridSearch() (in module resomapper.model_fitting.Tmapfit) Tmapfit_voxel_linear() (in module resomapper.model_fitting.Tmapfit) Tmapfit_voxel_nonlinear() (in module resomapper.model_fitting.Tmapfit) tools_menu() (in module resomapper.standalonetools)

V

validate_directory() (in module resomapper.auto)

validate_json() (in module resomapper.auto)