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PUMI
PUMI
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B
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C
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D
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E
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F
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G
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H
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I
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M
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N
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O
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P
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Q
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R
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T
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V
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)