xcp_d
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Running XCP-D
Processing Pipeline Details
Outputs of
XCP-D
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XCP-D
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xcp_d
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Index
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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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J
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L
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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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S
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T
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U
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V
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W
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X
A
AboutSummary (class in xcp_d.interfaces.report)
AnatomicalPlot (class in xcp_d.interfaces.plotting)
ApplyAffine (class in xcp_d.interfaces.workbench)
ApplyTransforms (class in xcp_d.interfaces.ants)
ApplyWarpfield (class in xcp_d.interfaces.workbench)
atlases (xcp_d.config.execution attribute)
,
[1]
B
band_stop_max (xcp_d.config.workflow attribute)
,
[1]
band_stop_min (xcp_d.config.workflow attribute)
,
[1]
bandpass_filter (xcp_d.config.workflow attribute)
,
[1]
before_send() (in module xcp_d.utils.sentry)
bids_database_dir (xcp_d.config.execution attribute)
,
[1]
bids_description_hash (xcp_d.config.execution attribute)
,
[1]
bids_filters (xcp_d.config.execution attribute)
,
[1]
BIDSError
BIDSWarning
BinaryMath (class in xcp_d.interfaces.nilearn)
boilerplate_only (xcp_d.config.execution attribute)
,
[1]
bpf_order (xcp_d.config.workflow attribute)
,
[1]
build_boilerplate() (in module xcp_d.cli.workflow)
build_workflow() (in module xcp_d.cli.workflow)
butter_bandpass() (in module xcp_d.utils.utils)
C
C3d (class in xcp_d.interfaces.c3)
Censor (class in xcp_d.interfaces.censoring)
CensoringPlot (class in xcp_d.interfaces.plotting)
ChangeXfmType (class in xcp_d.interfaces.workbench)
check_deps() (in module xcp_d.cli.parser_utils)
(in module xcp_d.utils.utils)
check_latest() (in module xcp_d.cli.version)
check_pipeline_version() (in module xcp_d.utils.bids)
cifti (xcp_d.config.workflow attribute)
,
[1]
CiftiChangeMapping (class in xcp_d.interfaces.workbench)
CiftiConnect (class in xcp_d.interfaces.connectivity)
CiftiConvert (class in xcp_d.interfaces.workbench)
CiftiCreateDenseFromTemplate (class in xcp_d.interfaces.workbench)
CiftiCreateDenseScalar (class in xcp_d.interfaces.workbench)
CiftiParcellate (class in xcp_d.interfaces.connectivity)
CiftiParcellateWorkbench (class in xcp_d.interfaces.workbench)
CiftiSeparateMetric (class in xcp_d.interfaces.workbench)
CiftiSeparateVolumeAll (class in xcp_d.interfaces.workbench)
CiftiSurfaceResample (class in xcp_d.interfaces.workbench)
CleanNameSource (class in xcp_d.interfaces.concatenation)
cli (xcp_d.config.loggers attribute)
,
[1]
collect_anatomical_files() (in module xcp_d.ingression.utils)
collect_data() (in module xcp_d.utils.bids)
collect_hcp_confounds() (in module xcp_d.ingression.utils)
collect_inputs() (xcp_d.interfaces.execsummary.ExecutiveSummary method)
collect_mesh_data() (in module xcp_d.utils.bids)
collect_meshes() (in module xcp_d.ingression.utils)
collect_morphometry_data() (in module xcp_d.utils.bids)
collect_morphs() (in module xcp_d.ingression.utils)
collect_participants() (in module xcp_d.utils.bids)
collect_run_data() (in module xcp_d.utils.bids)
collect_ukbiobank_confounds() (in module xcp_d.ingression.utils)
CollectRegistrationFiles (class in xcp_d.interfaces.bids)
combineruns (xcp_d.config.workflow attribute)
,
[1]
CompositeInvTransformUtil (class in xcp_d.interfaces.ants)
compute_2d_reho() (in module xcp_d.utils.restingstate)
compute_alff() (in module xcp_d.utils.restingstate)
compute_dvars() (in module xcp_d.utils.qcmetrics)
compute_fd() (in module xcp_d.utils.modified_data)
compute_registration_qc() (in module xcp_d.utils.qcmetrics)
ComputeALFF (class in xcp_d.interfaces.restingstate)
concatenate_niimgs() (in module xcp_d.utils.concatenation)
concatenate_tsvs() (in module xcp_d.utils.concatenation)
ConcatenateInputs (class in xcp_d.interfaces.concatenation)
confounds (xcp_d.utils.plotting.FMRIPlot attribute)
ConnectPlot (class in xcp_d.interfaces.connectivity)
convert_dcan2bids() (in module xcp_d.ingression.abcdbids)
convert_dcan_to_bids_single_subject() (in module xcp_d.ingression.abcdbids)
convert_hcp2bids() (in module xcp_d.ingression.hcpya)
convert_hcp_to_bids_single_subject() (in module xcp_d.ingression.hcpya)
convert_ukb2bids() (in module xcp_d.ingression.ukbiobank)
convert_ukb_to_bids_single_subject() (in module xcp_d.ingression.ukbiobank)
ConvertAffine (class in xcp_d.interfaces.workbench)
ConvertTo32 (class in xcp_d.interfaces.utils)
ConvertTransformFile (class in xcp_d.interfaces.ants)
copy_file() (in module xcp_d.ingression.utils)
copy_files_in_dict() (in module xcp_d.ingression.utils)
CopyAtlas (class in xcp_d.interfaces.bids)
correlate_timeseries() (in module xcp_d.interfaces.connectivity)
cpu_count (xcp_d.config.environment attribute)
,
[1]
crashfile_format (xcp_d.config.nipype attribute)
,
[1]
custom_confounds (xcp_d.config.execution attribute)
,
[1]
D
dcan_qc (xcp_d.config.workflow attribute)
,
[1]
debug (xcp_d.config.execution attribute)
,
[1]
default (xcp_d.config.loggers attribute)
,
[1]
denoise_with_nilearn() (in module xcp_d.utils.utils)
DenoiseCifti (class in xcp_d.interfaces.nilearn)
DenoiseNifti (class in xcp_d.interfaces.nilearn)
DerivativesDataSink (class in xcp_d.interfaces.bids)
describe_atlases() (in module xcp_d.utils.boilerplate)
describe_censoring() (in module xcp_d.utils.boilerplate)
describe_motion_parameters() (in module xcp_d.utils.boilerplate)
describe_regression() (in module xcp_d.utils.boilerplate)
despike (xcp_d.config.workflow attribute)
,
[1]
DespikePatch (class in xcp_d.interfaces.restingstate)
dice() (in module xcp_d.utils.qcmetrics)
downcast_to_32() (in module xcp_d.utils.modified_data)
download_example_data() (in module xcp_d.utils.doc)
dummy_scans (xcp_d.config.workflow attribute)
,
[1]
dumps() (in module xcp_d.config)
E
ensure_list() (in module xcp_d.utils.filemanip)
environment (class in xcp_d.config)
,
[1]
estimate_brain_radius() (in module xcp_d.utils.utils)
exact_time (xcp_d.config.workflow attribute)
,
[1]
exec_docker_version (xcp_d.config.environment attribute)
,
[1]
exec_env (xcp_d.config.environment attribute)
,
[1]
execution (class in xcp_d.config)
,
[1]
ExecutiveSummary (class in xcp_d.interfaces.execsummary)
extract_mean_signal() (in module xcp_d.ingression.utils)
F
fd_thresh (xcp_d.config.workflow attribute)
,
[1]
fill_doc() (in module xcp_d.utils.doc)
FilterOutFailedRuns (class in xcp_d.interfaces.concatenation)
FilterUndefined (class in xcp_d.interfaces.utils)
FixCiftiIntent (class in xcp_d.interfaces.workbench)
flag_bad_run() (in module xcp_d.utils.modified_data)
fmri_dir (xcp_d.config.execution attribute)
,
[1]
FMRIPlot (class in xcp_d.utils.plotting)
fname_presuffix() (in module xcp_d.utils.filemanip)
FormatForBrainSwipes (class in xcp_d.interfaces.execsummary)
free_mem (xcp_d.config.environment attribute)
,
[1]
from_dict() (in module xcp_d.config)
fs_license_file (xcp_d.config.execution attribute)
,
[1]
func_file (xcp_d.utils.plotting.FMRIPlot attribute)
FunctionalSummary (class in xcp_d.interfaces.report)
fwhm2sigma() (in module xcp_d.utils.utils)
G
generate_report() (xcp_d.interfaces.execsummary.ExecutiveSummary method)
generate_reports() (in module xcp_d.interfaces.report_core)
GenerateConfounds (class in xcp_d.interfaces.censoring)
get() (in module xcp_d.config)
get_atlas_cifti() (in module xcp_d.utils.atlas)
get_atlas_nifti() (in module xcp_d.utils.atlas)
get_bold2std_and_t1w_xfms() (in module xcp_d.utils.utils)
get_cifti_intents() (in module xcp_d.utils.write_save)
get_custom_confounds() (in module xcp_d.utils.confounds)
get_entity() (in module xcp_d.utils.bids)
get_freesurfer_dir() (in module xcp_d.utils.bids)
get_linked_libs (xcp_d.config.nipype attribute)
,
[1]
get_n_frames() (in module xcp_d.utils.execsummary)
get_parser() (in module xcp_d.cli.combineqc)
get_plugin() (xcp_d.config.nipype class method)
,
[1]
get_png_image_names() (in module xcp_d.utils.execsummary)
get_preproc_pipeline_info() (in module xcp_d.utils.bids)
get_std2bold_xfms() (in module xcp_d.utils.utils)
group_across_runs() (in module xcp_d.utils.bids)
H
head_radius (xcp_d.config.workflow attribute)
,
[1]
high_pass (xcp_d.config.workflow attribute)
,
[1]
I
IndexImage (class in xcp_d.interfaces.nilearn)
init() (xcp_d.config.execution class method)
,
[1]
(xcp_d.config.loggers class method)
,
[1]
(xcp_d.config.nipype class method)
,
[1]
(xcp_d.config.seeds class method)
(xcp_d.config.workflow class method)
init_alff_wf() (in module xcp_d.workflows.restingstate)
init_ants_xfm_to_fsl_wf() (in module xcp_d.workflows.anatomical)
init_brainsprite_figures_wf() (in module xcp_d.workflows.execsummary)
init_concatenate_data_wf() (in module xcp_d.workflows.concatenation)
init_copy_inputs_to_outputs_wf() (in module xcp_d.workflows.outputs)
init_denoise_bold_wf() (in module xcp_d.workflows.postprocessing)
init_despike_wf() (in module xcp_d.workflows.postprocessing)
init_execsummary_anatomical_plots_wf() (in module xcp_d.workflows.execsummary)
init_execsummary_functional_plots_wf() (in module xcp_d.workflows.execsummary)
init_functional_connectivity_cifti_wf() (in module xcp_d.workflows.connectivity)
init_functional_connectivity_nifti_wf() (in module xcp_d.workflows.connectivity)
init_generate_hcp_surfaces_wf() (in module xcp_d.workflows.anatomical)
init_load_atlases_wf() (in module xcp_d.workflows.connectivity)
init_parcellate_surfaces_wf() (in module xcp_d.workflows.connectivity)
init_plot_custom_slices_wf() (in module xcp_d.workflows.execsummary)
init_plot_overlay_wf() (in module xcp_d.workflows.execsummary)
init_postproc_derivatives_wf() (in module xcp_d.workflows.outputs)
init_postprocess_anat_wf() (in module xcp_d.workflows.anatomical)
init_postprocess_cifti_wf() (in module xcp_d.workflows.cifti)
init_postprocess_nifti_wf() (in module xcp_d.workflows.bold)
init_postprocess_surfaces_wf() (in module xcp_d.workflows.anatomical)
init_prepare_confounds_wf() (in module xcp_d.workflows.postprocessing)
init_qc_report_wf() (in module xcp_d.workflows.plotting)
init_reho_cifti_wf() (in module xcp_d.workflows.restingstate)
init_reho_nifti_wf() (in module xcp_d.workflows.restingstate)
init_resd_smoothing_wf() (in module xcp_d.workflows.postprocessing)
init_single_subject_wf() (in module xcp_d.workflows.base)
init_warp_one_hemisphere_wf() (in module xcp_d.workflows.anatomical)
init_warp_surfaces_to_template_wf() (in module xcp_d.workflows.anatomical)
init_xcpd_wf() (in module xcp_d.workflows.base)
input_type (xcp_d.config.workflow attribute)
,
[1]
interface (xcp_d.config.loggers attribute)
,
[1]
is_flagged() (in module xcp_d.cli.version)
is_interactive() (in module xcp_d.utils.debug)
J
json_file() (in module xcp_d.cli.parser_utils)
L
layout (xcp_d.config.execution attribute)
,
[1]
list_to_str() (in module xcp_d.utils.utils)
load() (in module xcp_d.config)
load_confound_matrix() (in module xcp_d.utils.confounds)
load_motion() (in module xcp_d.utils.confounds)
log_dir (xcp_d.config.execution attribute)
,
[1]
log_level (xcp_d.config.execution attribute)
,
[1]
loggers (class in xcp_d.config)
,
[1]
low_mem (xcp_d.config.execution attribute)
,
[1]
low_pass (xcp_d.config.workflow attribute)
,
[1]
M
main() (in module xcp_d.cli.combineqc)
(in module xcp_d.cli.run)
make_dcan_df() (in module xcp_d.utils.qcmetrics)
make_dcan_qc_file() (in module xcp_d.utils.qcmetrics)
make_mosaic() (in module xcp_d.utils.execsummary)
mask_data (xcp_d.utils.plotting.FMRIPlot attribute)
master (xcp_d.config.seeds attribute)
md_only_boilerplate (xcp_d.config.execution attribute)
,
[1]
memory_gb (xcp_d.config.nipype attribute)
,
[1]
Merge (class in xcp_d.interfaces.nilearn)
mesh_adjacency() (in module xcp_d.utils.restingstate)
min_coverage (xcp_d.config.workflow attribute)
,
[1]
min_time (xcp_d.config.workflow attribute)
,
[1]
modify_brainsprite_scene_template() (in module xcp_d.utils.execsummary)
modify_pngs_scene_template() (in module xcp_d.utils.execsummary)
module
xcp_d
xcp_d.cli
xcp_d.cli.combineqc
xcp_d.cli.parser
xcp_d.cli.parser_utils
xcp_d.cli.run
xcp_d.cli.version
xcp_d.cli.workflow
xcp_d.config
xcp_d.ingression
xcp_d.ingression.abcdbids
xcp_d.ingression.hcpya
xcp_d.ingression.ukbiobank
xcp_d.ingression.utils
xcp_d.interfaces
xcp_d.interfaces.ants
xcp_d.interfaces.bids
xcp_d.interfaces.c3
xcp_d.interfaces.censoring
xcp_d.interfaces.concatenation
xcp_d.interfaces.connectivity
xcp_d.interfaces.execsummary
xcp_d.interfaces.nilearn
xcp_d.interfaces.plotting
xcp_d.interfaces.report
xcp_d.interfaces.report_core
xcp_d.interfaces.restingstate
xcp_d.interfaces.utils
xcp_d.interfaces.workbench
xcp_d.utils
xcp_d.utils.atlas
xcp_d.utils.bids
xcp_d.utils.boilerplate
xcp_d.utils.concatenation
xcp_d.utils.confounds
xcp_d.utils.debug
xcp_d.utils.doc
xcp_d.utils.execsummary
xcp_d.utils.filemanip
xcp_d.utils.modified_data
xcp_d.utils.plotting
xcp_d.utils.qcmetrics
xcp_d.utils.restingstate
xcp_d.utils.sentry
xcp_d.utils.utils
xcp_d.utils.write_save
xcp_d.workflows
xcp_d.workflows.anatomical
xcp_d.workflows.base
xcp_d.workflows.bold
xcp_d.workflows.cifti
xcp_d.workflows.concatenation
xcp_d.workflows.connectivity
xcp_d.workflows.execsummary
xcp_d.workflows.outputs
xcp_d.workflows.plotting
xcp_d.workflows.postprocessing
xcp_d.workflows.restingstate
motion_filter_order (xcp_d.config.workflow attribute)
,
[1]
motion_filter_type (xcp_d.config.workflow attribute)
,
[1]
motion_regression_filter() (in module xcp_d.utils.confounds)
N
NiftiParcellate (class in xcp_d.interfaces.connectivity)
nipype (class in xcp_d.config)
,
[1]
nipype_version (xcp_d.config.environment attribute)
,
[1]
notrack (xcp_d.config.execution attribute)
,
[1]
nprocs (xcp_d.config.nipype attribute)
,
[1]
O
omp_nthreads (xcp_d.config.nipype attribute)
,
[1]
out_path_base (xcp_d.interfaces.bids.DerivativesDataSink attribute)
output_dir (xcp_d.config.execution attribute)
,
[1]
overcommit_limit (xcp_d.config.environment attribute)
,
[1]
overcommit_policy (xcp_d.config.environment attribute)
,
[1]
overlap() (in module xcp_d.utils.qcmetrics)
P
params (xcp_d.config.workflow attribute)
,
[1]
parse_args() (in module xcp_d.cli.parser)
participant_label (xcp_d.config.execution attribute)
,
[1]
pearson() (in module xcp_d.utils.qcmetrics)
plot() (xcp_d.utils.plotting.FMRIPlot method)
plot_alff_reho_surface() (in module xcp_d.utils.plotting)
plot_alff_reho_volumetric() (in module xcp_d.utils.plotting)
plot_bbreg() (in module xcp_d.ingression.utils)
plot_carpet() (in module xcp_d.utils.plotting)
plot_confounds() (in module xcp_d.utils.plotting)
plot_design_matrix() (in module xcp_d.utils.plotting)
plot_dvars_es() (in module xcp_d.utils.plotting)
plot_fmri_es() (in module xcp_d.utils.plotting)
plot_framewise_displacement_es() (in module xcp_d.utils.plotting)
plot_global_signal_es() (in module xcp_d.utils.plotting)
plot_matrix() (xcp_d.interfaces.connectivity.ConnectPlot method)
plugin (xcp_d.config.nipype attribute)
,
[1]
plugin_args (xcp_d.config.nipype attribute)
,
[1]
PNGAppend (class in xcp_d.interfaces.plotting)
process_crashfile() (in module xcp_d.utils.sentry)
process_surfaces (xcp_d.config.workflow attribute)
,
[1]
Q
QCPlots (class in xcp_d.interfaces.plotting)
QCPlotsES (class in xcp_d.interfaces.plotting)
R
RandomCensor (class in xcp_d.interfaces.censoring)
read_gii() (in module xcp_d.utils.write_save)
read_ndata() (in module xcp_d.utils.write_save)
ReHoNamePatch (class in xcp_d.interfaces.restingstate)
RemoveDummyVolumes (class in xcp_d.interfaces.censoring)
Report (class in xcp_d.interfaces.report_core)
reports_only (xcp_d.config.execution attribute)
,
[1]
ResampleToImage (class in xcp_d.interfaces.nilearn)
resource_monitor (xcp_d.config.nipype attribute)
,
[1]
run_reports() (in module xcp_d.interfaces.report_core)
run_uuid (xcp_d.config.execution attribute)
,
[1]
S
seeds (class in xcp_d.config)
seg_data (xcp_d.utils.plotting.FMRIPlot attribute)
select_atlases() (in module xcp_d.utils.atlas)
sentry_setup() (in module xcp_d.utils.sentry)
setup_exceptionhook() (in module xcp_d.utils.debug)
ShowScene (class in xcp_d.interfaces.workbench)
SlicesDir (class in xcp_d.interfaces.plotting)
Smooth (class in xcp_d.interfaces.nilearn)
smoothing (xcp_d.config.workflow attribute)
,
[1]
spikes (xcp_d.utils.plotting.FMRIPlot attribute)
split_filename() (in module xcp_d.utils.filemanip)
stop_on_first_crash (xcp_d.config.nipype attribute)
,
[1]
SubjectSummary (class in xcp_d.interfaces.report)
SummaryInterface (class in xcp_d.interfaces.report)
surf_data_from_cifti() (in module xcp_d.utils.plotting)
SurfaceAverage (class in xcp_d.interfaces.workbench)
SurfaceGenerateInflated (class in xcp_d.interfaces.workbench)
SurfaceReHo (class in xcp_d.interfaces.restingstate)
SurfaceSphereProjectUnproject (class in xcp_d.interfaces.workbench)
T
task_id (xcp_d.config.execution attribute)
,
[1]
templateflow_home (xcp_d.config.execution attribute)
,
[1]
templateflow_version (xcp_d.config.environment attribute)
,
[1]
to_filename() (in module xcp_d.config)
TR (xcp_d.utils.plotting.FMRIPlot attribute)
TSVConnect (class in xcp_d.interfaces.connectivity)
U
utils (xcp_d.config.loggers attribute)
,
[1]
V
version (xcp_d.config.environment attribute)
,
[1]
W
work_dir (xcp_d.config.execution attribute)
,
[1]
workflow (class in xcp_d.config)
,
[1]
(xcp_d.config.loggers attribute)
,
[1]
write_atlas_dataset_description() (in module xcp_d.utils.bids)
write_dataset_description() (in module xcp_d.utils.bids)
write_gii() (in module xcp_d.utils.write_save)
write_graph (xcp_d.config.execution attribute)
,
[1]
write_html() (xcp_d.interfaces.execsummary.ExecutiveSummary method)
write_json() (in module xcp_d.ingression.utils)
write_ndata() (in module xcp_d.utils.write_save)
X
xcp_d
module
xcp_d.cli
module
xcp_d.cli.combineqc
module
xcp_d.cli.parser
module
xcp_d.cli.parser_utils
module
xcp_d.cli.run
module
xcp_d.cli.version
module
xcp_d.cli.workflow
module
xcp_d.config
module
xcp_d.ingression
module
xcp_d.ingression.abcdbids
module
xcp_d.ingression.hcpya
module
xcp_d.ingression.ukbiobank
module
xcp_d.ingression.utils
module
xcp_d.interfaces
module
xcp_d.interfaces.ants
module
xcp_d.interfaces.bids
module
xcp_d.interfaces.c3
module
xcp_d.interfaces.censoring
module
xcp_d.interfaces.concatenation
module
xcp_d.interfaces.connectivity
module
xcp_d.interfaces.execsummary
module
xcp_d.interfaces.nilearn
module
xcp_d.interfaces.plotting
module
xcp_d.interfaces.report
module
xcp_d.interfaces.report_core
module
xcp_d.interfaces.restingstate
module
xcp_d.interfaces.utils
module
xcp_d.interfaces.workbench
module
xcp_d.utils
module
xcp_d.utils.atlas
module
xcp_d.utils.bids
module
xcp_d.utils.boilerplate
module
xcp_d.utils.concatenation
module
xcp_d.utils.confounds
module
xcp_d.utils.debug
module
xcp_d.utils.doc
module
xcp_d.utils.execsummary
module
xcp_d.utils.filemanip
module
xcp_d.utils.modified_data
module
xcp_d.utils.plotting
module
xcp_d.utils.qcmetrics
module
xcp_d.utils.restingstate
module
xcp_d.utils.sentry
module
xcp_d.utils.utils
module
xcp_d.utils.write_save
module
xcp_d.workflows
module
xcp_d.workflows.anatomical
module
xcp_d.workflows.base
module
xcp_d.workflows.bold
module
xcp_d.workflows.cifti
module
xcp_d.workflows.concatenation
module
xcp_d.workflows.connectivity
module
xcp_d.workflows.execsummary
module
xcp_d.workflows.outputs
module
xcp_d.workflows.plotting
module
xcp_d.workflows.postprocessing
module
xcp_d.workflows.restingstate
module
xcp_d_dir (xcp_d.config.execution attribute)
,
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