Index

A

assemble_image() (in module Module.Visualization)

B

Basic module Basic.Brain_Template module Basic.Cluster_Computation module Basic.Computation_Environment module

Basic.Cropping module Basic.Matrix_Computation module bootstrap_scan() (in module Module.FN_Computation) Brain_Template (class in Basic.Brain_Template) brainmap_colorfunction() (in module Module.Visualization)

C

check_data_type_format() (in module Module.Data_Input) check_gFN() (in module Module.FN_Computation) check_template_type_format() (in module Module.Data_Input) color_theme() (in module Module.Visualization) colorize() (in module Module.Visualization) compress_image() (in module Module.Visualization) compute_brain_surface() (in module Module.Data_Input) compute_brain_template() (in module Module.Data_Input)

compute_gNb() (in module Module.FN_Computation) (in module Module.SR_NMF) compute_quality_control() (in module Module.Quality_Control) compute_quality_control_torch() (in module Module.Quality_Control_torch) compute_quality_control_torch_cluster() (in module Module.Quality_Control_torch) construct_Laplacian_gNb() (in module Module.FN_Computation) (in module Module.SR_NMF) construct_Laplacian_gNb_torch() (in module Module.SR_NMF)

D

data_fitting_error() (in module Module.FN_Computation)

data_fitting_error_torch() (in module Module.SR_NMF) default_computation_environment() (in module Basic.Computation_Environment)

F

fApply_Cropped_FOV() (in module Basic.Cropping) file_FS_surf (Basic.Brain_Template.Brain_Template attribute) file_HCP_surf (Basic.Brain_Template.Brain_Template attribute) file_HCP_surf_vol (Basic.Brain_Template.Brain_Template attribute) file_HCP_vol (Basic.Brain_Template.Brain_Template attribute)

file_MNI_vol (Basic.Brain_Template.Brain_Template attribute) fInverse_Crop_EPI_Image_3D_4D() (in module Basic.Cropping) fMass_Center() (in module Basic.Cropping) fTruncate_Image_3D_4D() (in module Basic.Cropping) fuse_FN_cluster() (in module Module.SR_NMF)

G

gFN_fusion_NCut() (in module Module.FN_Computation) gFN_fusion_NCut_torch() (in module Module.SR_NMF) gFN_NMF() (in module Module.FN_Computation) gFN_SR_NMF_boostrapping_cluster() (in module Module.SR_NMF) gFN_SR_NMF_torch() (in module Module.SR_NMF)

GIG_ICA_neg_entropy() (in module Module.GIG_ICA) guide_choice() (in module Workflow.Workflow_Func) guide_dir() (in module Workflow.Workflow_Func) guide_file() (in module Workflow.Workflow_Func) guide_number() (in module Workflow.Workflow_Func) guide_YN() (in module Workflow.Workflow_Func)

I

initialize_u() (in module Module.FN_Computation)

initialize_u_torch() (in module Module.SR_NMF)

L

large_3view_center() (in module Module.Visualization) load_brain_template() (in module Module.Data_Input) load_fmri_scan() (in module Module.Data_Input) load_json_setting() (in module Module.Data_Input)

load_matlab_array() (in module Module.Data_Input) load_matlab_single_array() (in module Module.Data_Input) load_matlab_single_variable() (in module Module.Data_Input) load_txt_list() (in module Module.Data_Input)

M

mat_corr() (in module Basic.Matrix_Computation) (in module Module.FN_Computation) mat_corr_() (in module Basic.Matrix_Computation) mat_corr_torch() (in module Basic.Matrix_Computation) merge_mask_LR() (in module Module.Visualization) merge_mesh_LR() (in module Module.Visualization) Module module module Basic Basic.Brain_Template Basic.Cluster_Computation Basic.Computation_Environment Basic.Cropping Basic.Matrix_Computation Module Module.Data_Input Module.FN_Computation Module.FN_Computation_torch Module.GIG_ICA Module.Quality_Control Module.Quality_Control_torch Module.SR_NMF Module.Visualization Report Report.Web_Report Workflow Workflow.Workflow_Func

Module.Data_Input module Module.FN_Computation module Module.FN_Computation_torch module Module.GIG_ICA module Module.Quality_Control module Module.Quality_Control_torch module Module.SR_NMF module Module.Visualization module

N

ndarray_list() (in module Module.Data_Input) normalize_data() (in module Module.Data_Input) (in module Module.FN_Computation)

normalize_data_torch() (in module Module.SR_NMF) normalize_u_v() (in module Module.FN_Computation) normalize_u_v_torch() (in module Module.SR_NMF)

O

output_FN() (in module Module.Data_Input)

P

pFN_GIG_ICA_cluster() (in module Module.GIG_ICA) pFN_GIG_ICA_torch() (in module Module.GIG_ICA) pFN_NMF() (in module Module.FN_Computation) pFN_SR_NMF_cluster() (in module Module.SR_NMF) pFN_SR_NMF_torch() (in module Module.SR_NMF) plot_brain_surface() (in module Module.Visualization) plot_FN_brain_surface_5view() (in module Module.Visualization)

plot_FN_brain_surface_volume_7view() (in module Module.Visualization) plot_FN_brain_volume_3view() (in module Module.Visualization) plot_voxel_map_3view() (in module Module.Visualization) prepare_BSPolyData() (in module Module.Visualization) prepare_color_map() (in module Module.Visualization) print_description_QC() (in module Module.Quality_Control) print_description_scan_info() (in module Module.Data_Input) print_log() (in module Module.Data_Input)

R

Report module Report.Web_Report module reshape_fmri_data() (in module Module.Data_Input) reshape_FN() (in module Module.Data_Input) robust_normalize_V() (in module Module.FN_Computation) (in module Module.SR_NMF) run_FN_Computation() (in module Module.FN_Computation) run_FN_Computation_torch() (in module Module.FN_Computation_torch)

run_FN_computation_torch_cluster() (in module Module.FN_Computation_torch) run_gFN_Visualization() (in module Module.Visualization) run_pFN_Visualization() (in module Module.Visualization) run_pFN_Visualization_cluster() (in module Module.Visualization) run_quality_control() (in module Module.Quality_Control) run_quality_control_torch() (in module Module.Quality_Control_torch) run_quality_control_torch_cluster() (in module Module.Quality_Control_torch) run_Visualization() (in module Module.Visualization) run_Visualization_cluster() (in module Module.Visualization) run_web_report() (in module Report.Web_Report)

S

save_brain_template() (in module Module.Data_Input) set_computation_environment() (in module Basic.Computation_Environment) set_data_precision() (in module Module.Data_Input) set_data_precision_torch() (in module Module.Data_Input) setup_brain_template() (in module Module.Data_Input) setup_cifti_volume() (in module Module.Data_Input) setup_cluster() (in module Basic.Cluster_Computation) setup_colorbar_style() (in module Module.Visualization) setup_FN_Computation (class in Module.FN_Computation_torch)

setup_GIG_ICA() (in module Module.GIG_ICA) (Module.FN_Computation_torch.setup_FN_Computation method) setup_pFN_folder() (in module Module.FN_Computation) setup_result_folder() (in module Module.Data_Input) setup_scan_info() (in module Module.Data_Input) setup_SR_NMF() (in module Module.SR_NMF) (Module.FN_Computation_torch.setup_FN_Computation method) setup_Visualization() (in module Module.Visualization) submit_bash_job() (in module Basic.Cluster_Computation)

U

update_model_parameter() (in module Module.GIG_ICA) (in module Module.SR_NMF)

V

visualize_quality_control() (in module Module.Quality_Control)

W

Workflow module workflow() (in module Workflow.Workflow_Func) Workflow.Workflow_Func module

workflow_cluster() (in module Workflow.Workflow_Func) workflow_guide() (in module Workflow.Workflow_Func) workflow_simple() (in module Workflow.Workflow_Func) write_json_setting() (in module Module.Data_Input)