Index

B

bruker_to_dicom() (in module qx_utilities.general.bruker)

C

change_dicom_files() (in module qx_utilities.general.dicomdeid) check_fidl() (in module qx_utilities.general.fidl) compute_bold_stats() (in module qx_utilities.processing.workflow) copy_study() (in module qx_utilities.general.utilities) create_batch() (in module qx_utilities.general.utilities) create_bold_brain_masks() (in module qx_utilities.processing.workflow)

create_conc() (in module qx_utilities.general.utilities) create_list() (in module qx_utilities.general.utilities) create_session_info() (in module qx_utilities.general.utilities) create_stats_report() (in module qx_utilities.processing.workflow) create_study() (in module qx_utilities.general.utilities) create_ws_palm_design() (in module qx_utilities.general.palm)

D

dwi_bedpostx_gpu() (in module qx_utilities.bash) dwi_dtifit() (in module qx_utilities.bash) dwi_eddy_qc() (in module qx_utilities.bash) dwi_f99() (in module qx_utilities.processing.dwi) dwi_legacy_gpu() (in module qx_utilities.bash)

dwi_noddi_gpu() (in module qx_utilities.processing.dwi) dwi_parcellate() (in module qx_utilities.bash) dwi_pre_tractography() (in module qx_utilities.bash) dwi_probtrackx_dense_gpu() (in module qx_utilities.bash) dwi_seed_tractography_dense() (in module qx_utilities.bash) dwi_xtract() (in module qx_utilities.processing.dwi)

E

extract_nuisance_signal() (in module qx_utilities.processing.workflow)

F

fc_compute_ab_corr() (in module qx_mri.fc) fc_compute_ab_corr_kca() (in module qx_mri.fc) fc_compute_gbc() (in module qx_mri.fc) fc_compute_gbcd() (in module qx_mri.fc) fc_compute_roifc() (in module qx_mri.fc) fc_compute_seedmaps() (in module qx_mri.fc)

fc_compute_wrapper() (in module qx_utilities.bash) fc_extract_roi_timeseries() (in module qx_mri.fc) fc_preprocess() (in module qx_mri.fc) fc_preprocess_conc() (in module qx_mri.fc) fc_segment_mri() (in module qx_mri.fc) fsl_feat() (in module qx_utilities.processing.fsl) fsl_melodic() (in module qx_utilities.processing.fsl)

G

general_compute_bold_list_stats() (in module qx_mri.general) general_compute_bold_stats() (in module qx_mri.general) general_compute_group_bold_stats() (in module qx_mri.general) general_create_roi() (in module qx_mri.general) general_extract_glm_volumes() (in module qx_mri.general) general_extract_roi_glm_values() (in module qx_mri.general) general_extract_roi_values() (in module qx_mri.general) general_find_peaks() (in module qx_mri.general)

general_glm_predict() (in module qx_mri.general) general_image_conjunction() (in module qx_mri.general) general_image_overlap() (in module qx_mri.general) general_parcellated2dense() (in module qx_mri.general) general_plot_bold_timeseries() (in module qx_mri.general) general_plot_bold_timeseries_list() (in module qx_mri.general) general_qa_concfile() (in module qx_mri.general) get_dicom_fields() (in module qx_utilities.general.dicomdeid)

H

hcp_apply_auto_reclean() (in module qx_utilities.hcp.process_hcp) hcp_asl() (in module qx_utilities.hcp.process_hcp) hcp_dedrift_and_resample() (in module qx_utilities.hcp.process_hcp) hcp_diffusion() (in module qx_utilities.hcp.process_hcp) hcp_fmri_surface() (in module qx_utilities.hcp.process_hcp) hcp_fmri_volume() (in module qx_utilities.hcp.process_hcp) hcp_freesurfer() (in module qx_utilities.hcp.process_hcp) hcp_icafix() (in module qx_utilities.hcp.process_hcp) hcp_long_freesurfer() (in module qx_utilities.hcp.process_hcp) hcp_long_msmall() (in module qx_utilities.hcp.process_hcp) hcp_long_post_freesurfer() (in module qx_utilities.hcp.process_hcp)

hcp_long_transmit_bias() (in module qx_utilities.hcp.process_hcp) hcp_make_average_dataset() (in module qx_utilities.hcp.process_hcp) hcp_msmall() (in module qx_utilities.hcp.process_hcp) hcp_post_fix() (in module qx_utilities.hcp.process_hcp) hcp_post_freesurfer() (in module qx_utilities.hcp.process_hcp) hcp_pre_freesurfer() (in module qx_utilities.hcp.process_hcp) hcp_prep_long() (in module qx_utilities.hcp.process_hcp) hcp_reapply_fix() (in module qx_utilities.hcp.process_hcp) hcp_task_fmri_analysis() (in module qx_utilities.hcp.process_hcp) hcp_temporal_ica() (in module qx_utilities.hcp.process_hcp) hcp_transmit_bias_individual() (in module qx_utilities.hcp.process_hcp)

I

import_bids() (in module qx_utilities.general.bids)

import_dicom() (in module qx_utilities.general.dicom) import_hcp() (in module qx_utilities.hcp.import_hcp)

J

join_fidl() (in module qx_utilities.general.fidl)

join_fidl_folder() (in module qx_utilities.general.fidl)

M

map_hcp_data() (in module qx_utilities.hcp.process_hcp)

map_mice_data() (in module qx_mice.process_mice) map_nii2bids() (in module qx_utilities.general.bids)

P

parcellate_anat() (in module qx_utilities.bash) parcellate_bold() (in module qx_utilities.bash)

preprocess_bold() (in module qx_utilities.processing.workflow) preprocess_conc() (in module qx_utilities.processing.workflow) preprocess_mice() (in module qx_mice.process_mice)

R

rapidtide() (in module qx_utilities.processing.rapidtide) run_palm() (in module qx_utilities.general.palm)

run_qa() (in module qx_utilities.qa.run_qa) run_qc() (in module qx_utilities.bash) run_recipe() (in module qx_utilities.general.utilities)

S

setup_hcp() (in module qx_utilities.hcp.setup_hcp) setup_mice() (in module qx_mice.setup_mice) split_fidl() (in module qx_utilities.general.fidl) stats_compute_behavioral_correlations() (in module qx_mri.stats)

stats_p2z() (in module qx_mri.stats) stats_ttest_dependent() (in module qx_mri.stats) stats_ttest_independent() (in module qx_mri.stats) stats_ttest_zero() (in module qx_mri.stats)