Index

A

above_threshold() (in module PUMI.utils) anat2mni_ants() (in module PUMI.pipelines.anat.anat2mni) anat2mni_ants_hardcoded() (in module PUMI.pipelines.anat.anat2mni)

anat2mni_fsl() (in module PUMI.pipelines.anat.anat2mni) anat_noise_roi() (in module PUMI.pipelines.func.compcor) anat_proc() (in module PUMI.pipelines.anat.anat_proc) AnatPipeline (class in PUMI.engine)

B

bet_fsl() (in module PUMI.pipelines.anat.segmentation) bet_hd() (in module PUMI.pipelines.anat.segmentation)

BidsApp (class in PUMI.engine) BidsPipeline (class in PUMI.engine)

C

calc_friston_twenty_four() (in module PUMI.utils) calculate_FD_Jenkinson() (in module PUMI.utils) compcor() (in module PUMI.pipelines.func.compcor) compcor_qc() (in module PUMI.pipelines.func.compcor)

concat() (in module PUMI.pipelines.func.concat) concatenate() (in module PUMI.utils) connect() (PUMI.engine.NestedWorkflow method) create_coregistration_qc() (in module PUMI.utils) create_segmentation_qc() (in module PUMI.utils)

D

datacens_workflow_threshold() (in module PUMI.pipelines.func.data_censorer) defacing() (in module PUMI.pipelines.anat.segmentation)

despiking_afni() (in module PUMI.pipelines.func.deconfound) drop_first_line() (in module PUMI.utils)

E

examples.bet_bids_func_subworkflow module examples.bet_bids_subworkflow module examples.defacing_ex_bids module examples.despiking_bids_ex module examples.ex_bids_pipeline module examples.ex_compcor module

examples.ex_func_proc module examples.ex_func_to_anat_bids module examples.ex_motion_correction module examples.ex_tmpfilt module examples.get_rpn_model module examples.rpn_preproc module

F

func2anat() (in module PUMI.pipelines.anat.func_to_anat) func2anat_qc() (in module PUMI.pipelines.anat.func_to_anat)

func_proc_despike_afni() (in module PUMI.pipelines.func.func_proc) FuncPipeline (class in PUMI.engine)

G

get_config() (in module PUMI.utils) get_indx() (in module PUMI.utils) get_info() (in module PUMI.pipelines.multimodal.image_manipulation)

get_ref_from_templateflow() (in module PUMI.utils) get_ref_locally() (in module PUMI.utils) get_reference() (in module PUMI.utils) GroupPipeline (class in PUMI.engine)

H

HDBet (class in PUMI.interfaces.HDBet)

HDBetInputSpec (class in PUMI.interfaces.HDBet) HDBetOutputSpec (class in PUMI.interfaces.HDBet)

I

input_spec (PUMI.interfaces.HDBet.HDBet attribute)

M

max_from_txt() (in module PUMI.utils) mean_from_txt() (in module PUMI.utils) mist_labels() (in module PUMI.utils) mist_modules() (in module PUMI.utils) module examples.bet_bids_func_subworkflow examples.bet_bids_subworkflow examples.defacing_ex_bids examples.despiking_bids_ex examples.ex_bids_pipeline examples.ex_compcor examples.ex_func_proc examples.ex_func_to_anat_bids examples.ex_motion_correction examples.ex_tmpfilt examples.get_rpn_model examples.rpn_preproc PUMI.engine PUMI.interfaces.HDBet PUMI.pipelines.anat.anat2mni PUMI.pipelines.anat.anat_proc PUMI.pipelines.anat.func_to_anat PUMI.pipelines.anat.segmentation PUMI.pipelines.func.compcor PUMI.pipelines.func.concat PUMI.pipelines.func.data_censorer PUMI.pipelines.func.deconfound PUMI.pipelines.func.func_proc PUMI.pipelines.func.temporal_filtering PUMI.pipelines.multimodal.image_manipulation PUMI.plot.carpet_plot PUMI.utils tests.test_afni tests.test_ants

motion_correction_mcflirt() (in module PUMI.pipelines.func.deconfound)

N

NestedMapNode (class in PUMI.engine) NestedNode (class in PUMI.engine)

NestedWorkflow (class in PUMI.engine) nuisance_removal() (in module PUMI.pipelines.func.deconfound)

O

output_dir() (PUMI.engine.NestedMapNode method) (PUMI.engine.NestedNode method)

output_spec (PUMI.interfaces.HDBet.HDBet attribute)

P

pick_volume() (in module PUMI.pipelines.multimodal.image_manipulation) plot_carpet() (in module PUMI.plot.carpet_plot) plot_carpet_ts() (in module PUMI.utils) plot_roi() (in module PUMI.utils) PUMI.engine module PUMI.interfaces.HDBet module PUMI.pipelines.anat.anat2mni module PUMI.pipelines.anat.anat_proc module PUMI.pipelines.anat.func_to_anat module PUMI.pipelines.anat.segmentation module PUMI.pipelines.func.compcor module

PUMI.pipelines.func.concat module PUMI.pipelines.func.data_censorer module PUMI.pipelines.func.deconfound module PUMI.pipelines.func.func_proc module PUMI.pipelines.func.temporal_filtering module PUMI.pipelines.multimodal.image_manipulation module PUMI.plot.carpet_plot module PUMI.utils module PumiPipeline (class in PUMI.engine) pydeface_wrapper() (in module PUMI.pipelines.anat.segmentation)

Q

qc() (in module PUMI.pipelines.anat.anat2mni) (in module PUMI.pipelines.func.deconfound) qc_datacens() (in module PUMI.pipelines.func.data_censorer) qc_motion_correction_mcflirt() (in module PUMI.pipelines.func.deconfound)

qc_nuisance_removal() (in module PUMI.pipelines.func.deconfound) qc_segmentation() (in module PUMI.pipelines.anat.segmentation) qc_temporal_filtering() (in module PUMI.pipelines.func.temporal_filtering) qc_tissue_segmentation() (in module PUMI.pipelines.anat.segmentation) QcPipeline (class in PUMI.engine)

R

registration_ants_hardcoded() (in module PUMI.utils) relabel_atlas() (in module PUMI.utils)

rpn_model() (in module PUMI.utils) run() (PUMI.engine.BidsApp method)

S

scale_vol() (in module PUMI.utils)

scrub_image() (in module PUMI.utils)

T

temporal_filtering() (in module PUMI.pipelines.func.temporal_filtering) test_ants() (tests.test_ants.TestAnts method) test_despike() (tests.test_afni.TestDespike method) TestAnts (class in tests.test_ants) TestDespike (class in tests.test_afni) tests.test_afni module

tests.test_ants module timecourse2png() (in module PUMI.pipelines.multimodal.image_manipulation) tissue_segmentation_fsl() (in module PUMI.pipelines.anat.segmentation) TsExtractor() (in module PUMI.utils)

V

vol2png() (in module PUMI.pipelines.multimodal.image_manipulation)