Index

A | B | C | D | E | F | G | I | L | M | O | P | R | S | T | W

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)