Index

A

ants_applywarp() (in module cmind.pipeline.ants_applywarp)

ants_register() (in module cmind.pipeline.ants_register)

B

binstr2dec() (in module cmind.pipeline.cmind_fMRI_outliers)

C

calc_tSNR_regress() (in module cmind.utils.utils) calcCBF_Wang2002() (in module cmind.pipeline.cmind_baselineCBF_quantitative) calcflash() (in module cmind.pipeline.cmind_baselineCBF_quantitative) check_exist() (in module cmind.finders) cmind.finders (module) cmind.globals (module) cmind.pipeline.ants_applywarp (module) cmind.pipeline.ants_register (module) cmind.pipeline.cmind_age_to_template (module) cmind.pipeline.cmind_alpha (module) cmind.pipeline.cmind_apply_normalization (module) cmind.pipeline.cmind_atlas_to_subject (module) cmind.pipeline.cmind_baselineCBF_coregisterT1 (module) cmind.pipeline.cmind_baselineCBF_preprocess (module) cmind.pipeline.cmind_baselineCBF_quantitative (module) cmind.pipeline.cmind_bias_correct (module) cmind.pipeline.cmind_brain_extract (module) cmind.pipeline.cmind_build_feat_dir (module) cmind.pipeline.cmind_calculate_slice_coverage (module) cmind.pipeline.cmind_crop_robust (module) cmind.pipeline.cmind_DTI_HARDI_QA (module) cmind.pipeline.cmind_DWI_TRK_to_3plane (module) cmind.pipeline.cmind_fieldmap_process (module) cmind.pipeline.cmind_fieldmap_regBBR (module) cmind.pipeline.cmind_fMRI_level1_stats (module) cmind.pipeline.cmind_fMRI_norm (module) cmind.pipeline.cmind_fMRI_outliers (module) cmind.pipeline.cmind_fMRI_preprocess (module) cmind.pipeline.cmind_fMRI_preprocess2 (module) cmind.pipeline.cmind_normalize (module) cmind.pipeline.cmind_rigid_coregister (module) cmind.pipeline.cmind_segment (module) cmind.pipeline.cmind_stage_second_level (module) cmind.pipeline.cmind_struct_preprocess (module) cmind.pipeline.cmind_T1_tissue_averages (module) cmind.pipeline.cmind_T1map_fit (module) cmind.pipeline.cmind_T1map_preprocess (module) cmind.utils.cmind_HTML_report_gen (module) cmind.utils.decorators (module) cmind.utils.file_utils (module) cmind.utils.fsf_utils (module) cmind.utils.fsl_mcflirt_opt (module) cmind.utils.fsl_mcflirt_opt_ASLBOLD (module) cmind.utils.image_utils (module) cmind.utils.logging_utils (module) cmind.utils.nifti_utils (module) cmind.utils.utils (module)

cmind_age_to_template() (in module cmind.pipeline.cmind_age_to_template) cmind_alpha() (in module cmind.pipeline.cmind_alpha) cmind_apply_normalization() (in module cmind.pipeline.cmind_apply_normalization) cmind_atlas_to_subject() (in module cmind.pipeline.cmind_atlas_to_subject) cmind_baselineCBF_coregisterT1() (in module cmind.pipeline.cmind_baselineCBF_coregisterT1) cmind_baselineCBF_preprocess() (in module cmind.pipeline.cmind_baselineCBF_preprocess) cmind_baselineCBF_quantify() (in module cmind.pipeline.cmind_baselineCBF_quantitative) cmind_baselineCBF_quantitative() (in module cmind.pipeline.cmind_baselineCBF_quantitative) cmind_bias_correct() (in module cmind.pipeline.cmind_bias_correct) cmind_brain_extract() (in module cmind.pipeline.cmind_brain_extract) cmind_build_feat_dir() (in module cmind.pipeline.cmind_build_feat_dir) cmind_calculate_slice_coverage() (in module cmind.pipeline.cmind_calculate_slice_coverage) cmind_combine_HTML_reports() (in module cmind.utils.cmind_HTML_report_gen) cmind_copy_all() (in module cmind.utils.file_utils) cmind_crop_robust() (in module cmind.pipeline.cmind_crop_robust) cmind_DTI_HARDI_QA() (in module cmind.pipeline.cmind_DTI_HARDI_QA) cmind_DWI_TRK_to_3plane() (in module cmind.pipeline.cmind_DWI_TRK_to_3plane) cmind_feat_prep() (in module cmind.pipeline.cmind_fMRI_preprocess2) cmind_feat_stats() (in module cmind.pipeline.cmind_fMRI_level1_stats) cmind_fieldmap_process() (in module cmind.pipeline.cmind_fieldmap_process) cmind_fieldmap_regBBR() (in module cmind.pipeline.cmind_fieldmap_regBBR) cmind_fMRI_level1_stats() (in module cmind.pipeline.cmind_fMRI_level1_stats) cmind_fMRI_norm() (in module cmind.pipeline.cmind_fMRI_norm) cmind_fMRI_outliers() (in module cmind.pipeline.cmind_fMRI_outliers) cmind_fMRI_preprocess() (in module cmind.pipeline.cmind_fMRI_preprocess) cmind_fMRI_preprocess2() (in module cmind.pipeline.cmind_fMRI_preprocess2) cmind_func_info() (in module cmind.utils.logging_utils) cmind_HTML_report_gen() (in module cmind.utils.cmind_HTML_report_gen) cmind_HTML_reports() (in module cmind.utils.cmind_HTML_report_gen) cmind_init_logging() (in module cmind.utils.logging_utils) cmind_logger() (in module cmind.utils.logging_utils) cmind_normalize() (in module cmind.pipeline.cmind_normalize) cmind_plot_DTI_coverage() (in module cmind.pipeline.cmind_DTI_HARDI_QA) cmind_rigid_coregister() (in module cmind.pipeline.cmind_rigid_coregister) cmind_save_nii_mod_header() (in module cmind.utils.nifti_utils) cmind_segment() (in module cmind.pipeline.cmind_segment) cmind_stage_second_level() (in module cmind.pipeline.cmind_stage_second_level) cmind_struct_preprocess() (in module cmind.pipeline.cmind_struct_preprocess) cmind_T1_tissue_averages() (in module cmind.pipeline.cmind_T1_tissue_averages) cmind_T1map_fit() (in module cmind.pipeline.cmind_T1map_fit) cmind_T1map_preprocess() (in module cmind.pipeline.cmind_T1map_preprocess) cmind_timer() (in module cmind.utils.decorators) confirm() (in module cmind.utils.utils) create_con() (in module cmind.utils.fsf_utils) create_ev() (in module cmind.utils.fsf_utils) create_fsf() (in module cmind.utils.fsf_utils) csv2dict() (in module cmind.utils.file_utils)

D

dict2csv() (in module cmind.utils.file_utils)

dprint() (in module cmind.utils.utils)

E

export_tarfile() (in module cmind.utils.file_utils)

F

file_update_bool() (in module cmind.utils.file_utils) filecheck_bool() (in module cmind.utils.file_utils) find_AFNI() (in module cmind.finders) find_ANTS() (in module cmind.finders) find_DTIPrep() (in module cmind.finders) find_FSL() (in module cmind.finders) find_GraphicsMagick() (in module cmind.finders) find_ImageMagick() (in module cmind.finders)

find_MNI_templates() (in module cmind.finders) find_shellscripts() (in module cmind.finders) find_Slicer3D() (in module cmind.finders) fsf_substitute() (in module cmind.utils.fsf_utils) fsl_highpass_temporal_filter1D() (in module cmind.utils.utils) fsl_mcflirt_opt() (in module cmind.utils.fsl_mcflirt_opt) fsl_mcflirt_opt_ASLBOLD() (in module cmind.utils.fsl_mcflirt_opt_ASLBOLD)

G

gauss_bias_corr() (in module cmind.pipeline.cmind_bias_correct) get_Slicer3D_version() (in module cmind.finders)

get_unicode_type() (in module cmind.utils.utils)

I

ImageMagick_append_label() (in module cmind.utils.image_utils) ImageMagick_build_colorbar() (in module cmind.utils.image_utils) ImageMagick_crop_border() (in module cmind.utils.image_utils) ImageMagick_get_size() (in module cmind.utils.image_utils)

imexist() (in module cmind.utils.file_utils) input2bool() (in module cmind.utils.utils) input2list() (in module cmind.utils.utils) is_string_like() (in module cmind.utils.utils)

L

log_cmd() (in module cmind.utils.logging_utils) logger_info() (in module cmind.utils.logging_utils)

lprint() (in module cmind.utils.utils)

M

montager() (in module cmind.utils)

multiglob_list() (in module cmind.utils.file_utils)

O

orthogonalize() (in module cmind.pipeline.cmind_fMRI_outliers)

P

parser_to_bash() (in module cmind.utils.utils)

print_environment_info() (in module cmind.globals)

R

random_color_str() (in module cmind.utils.image_utils) reindent() (in module cmind.utils.utils) remove_file() (in module cmind.utils.file_utils)

rm_broken_links() (in module cmind.utils.file_utils) round_affine_to_axial() (in module cmind.utils.nifti_utils)

S

slicer_3plane_fig() (in module cmind.utils.image_utils) slicer_mid_sag_fig() (in module cmind.utils.image_utils) slicer_tile_slices() (in module cmind.utils.image_utils) sphere() (in module cmind.utils.utils)

split_atlas_outputs() (in module cmind.pipeline.cmind_atlas_to_subject) split_multiple_ext() (in module cmind.utils.file_utils) str2list() (in module cmind.utils.utils) str2none() (in module cmind.utils.utils)

T

T1fit_err() (in module cmind.pipeline.cmind_T1map_fit)

T1recovery_func() (in module cmind.pipeline.cmind_T1map_fit)

W

which() (in module cmind.utils.file_utils)

write_fsf() (in module cmind.utils.fsf_utils)