xcp_d
0.3.0
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xcp_d Developer Guide
xcp_d
Index
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Index
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A
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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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W
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X
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Z
_
__init__() (xcp_d.interfaces.bids.BaseDerivativesDataSink method)
A
AboutSummary (class in xcp_d.interfaces.report)
add_image() (xcp_d.interfaces.layout_builder.ModalContainer method)
add_images() (xcp_d.interfaces.layout_builder.ModalContainer method)
ApplyAffine (class in xcp_d.interfaces.workbench)
ApplyTransformsx (class in xcp_d.interfaces.connectivity)
ApplyWarpfield (class in xcp_d.interfaces.workbench)
B
BaseDerivativesDataSink (class in xcp_d.interfaces.bids)
bbregplot() (in module xcp_d.utils.dcan2fmriprep)
before_send() (in module xcp_d.utils.sentry)
BIDSError
BIDSWarning
binarize_img() (in module xcp_d.utils.filemanip)
BinaryMath (class in xcp_d.interfaces.nilearn)
BrainPlot (class in xcp_d.interfaces.resting_state)
BrainPlotx (class in xcp_d.interfaces.surfplotting)
build_workflow() (in module xcp_d.cli.run)
butter_bandpass() (in module xcp_d.utils.utils)
C
C3d (class in xcp_d.interfaces.c3)
CensoringPlot (class in xcp_d.interfaces.qc_plot)
CensorScrub (class in xcp_d.interfaces.prepostcleaning)
ChangeXfmType (class in xcp_d.interfaces.workbench)
check_binary_mask() (in module xcp_d.utils.filemanip)
check_deps() (in module xcp_d.cli.run)
CiftiCorrelation (class in xcp_d.interfaces.workbench)
CiftiCreateDenseScalar (class in xcp_d.interfaces.workbench)
CiftiDespike (class in xcp_d.interfaces.regression)
CiftiParcellate (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)
collect_data() (in module xcp_d.utils.bids)
collect_participants() (in module xcp_d.utils.bids)
collect_run_data() (in module xcp_d.utils.bids)
CompositeInvTransformUtil (class in xcp_d.interfaces.ants)
compute_2d_reho() (in module xcp_d.utils.fcon)
compute_alff() (in module xcp_d.utils.fcon)
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.resting_state)
concatenate_derivatives() (in module xcp_d.utils.concatenation)
concatenate_tsv_files() (in module xcp_d.utils.concatenation)
confoundplot() (in module xcp_d.utils.plot)
confoundplotx() (in module xcp_d.utils.plot)
confounds (xcp_d.utils.plot.FMRIPlot attribute)
ConnectPlot (class in xcp_d.interfaces.connectivity)
consolidate_confounds() (in module xcp_d.utils.utils)
ConvertAffine (class in xcp_d.interfaces.workbench)
ConvertTransformFile (class in xcp_d.interfaces.ants)
copyfile() (in module xcp_d.utils.filemanip)
copyfileobj_example() (in module xcp_d.utils.dcan2fmriprep)
copyfiles() (in module xcp_d.utils.filemanip)
coverage() (in module xcp_d.utils.qcmetrics)
crosscorr() (in module xcp_d.utils.qcmetrics)
D
dc() (in module xcp_d.utils.qcmetrics)
dcan2fmriprep() (in module xcp_d.utils.dcan2fmriprep)
dcan2fmriprepx() (in module xcp_d.utils.dcan2fmriprep)
demean_detrend_data() (in module xcp_d.utils.utils)
DeprecatedStoreAction (class in xcp_d.cli.run)
derivative() (in module xcp_d.utils.confounds)
DerivativesDataSink (class in xcp_d.interfaces.bids)
despikedatacifti() (in module xcp_d.utils.write_save)
DespikePatch (class in xcp_d.interfaces.resting_state)
E
ensure_list() (in module xcp_d.utils.filemanip)
extract_timeseries_funct() (in module xcp_d.utils.fcon)
extractreg() (in module xcp_d.utils.dcan2fmriprep)
F
fill_doc() (in module xcp_d.utils.doc)
FilteringData (class in xcp_d.interfaces.filtering)
find_and_copy_files() (in module xcp_d.utils.filemanip)
find_one_file() (in module xcp_d.utils.filemanip)
FMRIPlot (class in xcp_d.utils.plot)
fname_presuffix() (in module xcp_d.utils.filemanip)
func_file (xcp_d.utils.plot.FMRIPlot attribute)
FunctionalSummary (class in xcp_d.interfaces.report)
fwhm2sigma() (in module xcp_d.utils.utils)
G
generate_brain_sprite() (in module xcp_d.utils.execsummary)
generate_mask() (in module xcp_d.utils.modified_data)
generate_reports() (in module xcp_d.interfaces.report_core)
get_atlas_cifti() (in module xcp_d.utils.atlas)
get_atlas_names() (in module xcp_d.utils.atlas)
get_atlas_nifti() (in module xcp_d.utils.atlas)
get_bold2std_and_t1w_xforms() (in module xcp_d.utils.utils)
get_button() (xcp_d.interfaces.layout_builder.ModalContainer method)
get_confounds_tsv() (in module xcp_d.utils.confounds)
get_container() (xcp_d.interfaces.layout_builder.ModalContainer method)
(xcp_d.interfaces.layout_builder.ModalSlider method)
get_customfile() (in module xcp_d.utils.utils)
get_image_class() (xcp_d.interfaces.layout_builder.ModalContainer method)
get_list_of_tasks() (xcp_d.interfaces.layout_builder.LayoutBuilder method)
get_modal_id() (xcp_d.interfaces.layout_builder.ModalContainer method)
get_parser() (in module xcp_d.cli.combineqc)
(in module xcp_d.cli.run)
get_preproc_pipeline_info() (in module xcp_d.utils.bids)
get_related_files() (in module xcp_d.utils.filemanip)
get_scripts() (xcp_d.interfaces.layout_builder.ModalContainer method)
(xcp_d.interfaces.layout_builder.ModalSlider method)
(xcp_d.interfaces.layout_builder.Section method)
get_section() (xcp_d.interfaces.layout_builder.Section method)
get_segfile() (in module xcp_d.utils.utils)
get_space() (in module xcp_d.interfaces.report)
get_std2bold_xforms() (in module xcp_d.utils.utils)
H
hash_infile() (in module xcp_d.utils.filemanip)
hash_timestamp() (in module xcp_d.utils.filemanip)
hcp2fmriprep() (in module xcp_d.utils.hcp2fmriprep)
hcpfmriprepx() (in module xcp_d.utils.hcp2fmriprep)
I
indirectory() (in module xcp_d.utils.filemanip)
init_anatomical_wf() (in module xcp_d.workflow.anatomical)
init_boldpostprocess_wf() (in module xcp_d.workflow.bold)
init_brainsprite_wf() (in module xcp_d.workflow.execsummary)
init_cifti_functional_connectivity_wf() (in module xcp_d.workflow.connectivity)
init_cifti_reho_wf() (in module xcp_d.workflow.restingstate)
init_ciftipostprocess_wf() (in module xcp_d.workflow.cifti)
init_compute_alff_wf() (in module xcp_d.workflow.restingstate)
init_execsummary_wf() (in module xcp_d.workflow.execsummary)
init_nifti_functional_connectivity_wf() (in module xcp_d.workflow.connectivity)
init_nifti_reho_wf() (in module xcp_d.workflow.restingstate)
init_resd_smoothing() (in module xcp_d.workflow.postprocessing)
init_subject_wf() (in module xcp_d.workflow.base)
init_t1w_wf() (in module xcp_d.workflow.anatomical)
init_writederivatives_wf() (in module xcp_d.workflow.outputs)
init_xcpd_wf() (in module xcp_d.workflow.base)
Interpolate (class in xcp_d.interfaces.prepostcleaning)
interpolate_masked_data() (in module xcp_d.utils.modified_data)
J
jc() (in module xcp_d.utils.qcmetrics)
L
LayoutBuilder (class in xcp_d.interfaces.layout_builder)
linear_regression() (in module xcp_d.utils.utils)
load_acompcor() (in module xcp_d.utils.confounds)
load_aroma() (in module xcp_d.utils.confounds)
load_confound() (in module xcp_d.utils.confounds)
load_confound_matrix() (in module xcp_d.utils.confounds)
load_cosine() (in module xcp_d.utils.confounds)
load_global_signal() (in module xcp_d.utils.confounds)
load_motion() (in module xcp_d.utils.confounds)
load_wm_csf() (in module xcp_d.utils.confounds)
M
main() (in module xcp_d.cli.combineqc)
(in module xcp_d.cli.run)
make_dcan_df() (in module xcp_d.utils.concatenation)
mask_data (xcp_d.utils.plot.FMRIPlot attribute)
Merge (class in xcp_d.interfaces.nilearn)
mesh_adjacency() (in module xcp_d.utils.fcon)
ModalContainer (class in xcp_d.interfaces.layout_builder)
ModalSlider (class in xcp_d.interfaces.layout_builder)
module
xcp_d
xcp_d.cli
xcp_d.cli.combineqc
xcp_d.cli.run
xcp_d.interfaces
xcp_d.interfaces.ants
xcp_d.interfaces.bids
xcp_d.interfaces.c3
xcp_d.interfaces.connectivity
xcp_d.interfaces.constants
xcp_d.interfaces.filtering
xcp_d.interfaces.layout_builder
xcp_d.interfaces.nilearn
xcp_d.interfaces.prepostcleaning
xcp_d.interfaces.qc_plot
xcp_d.interfaces.regression
xcp_d.interfaces.report
xcp_d.interfaces.report_core
xcp_d.interfaces.resting_state
xcp_d.interfaces.surfplotting
xcp_d.interfaces.workbench
xcp_d.utils
xcp_d.utils.atlas
xcp_d.utils.bids
xcp_d.utils.concatenation
xcp_d.utils.confounds
xcp_d.utils.dcan2fmriprep
xcp_d.utils.doc
xcp_d.utils.execsummary
xcp_d.utils.fcon
xcp_d.utils.filemanip
xcp_d.utils.hcp2fmriprep
xcp_d.utils.modified_data
xcp_d.utils.plot
xcp_d.utils.qcmetrics
xcp_d.utils.sentry
xcp_d.utils.utils
xcp_d.utils.write_save
xcp_d.workflow
xcp_d.workflow.anatomical
xcp_d.workflow.base
xcp_d.workflow.bold
xcp_d.workflow.cifti
xcp_d.workflow.connectivity
xcp_d.workflow.execsummary
xcp_d.workflow.outputs
xcp_d.workflow.postprocessing
xcp_d.workflow.restingstate
motion_regression_filter() (in module xcp_d.utils.confounds)
N
NiftiConnect (class in xcp_d.interfaces.connectivity)
O
on_cifs() (in module xcp_d.utils.filemanip)
out_path_base (xcp_d.interfaces.bids.BaseDerivativesDataSink attribute)
(xcp_d.interfaces.bids.DerivativesDataSink attribute)
P
plot() (xcp_d.utils.plot.FMRIPlot method)
plot_alff_reho_surface() (in module xcp_d.utils.plot)
plot_alff_reho_volumetric() (in module xcp_d.utils.plot)
plot_carpet() (in module xcp_d.utils.plot)
plot_design_matrix() (in module xcp_d.utils.plot)
plot_ribbon_svg() (in module xcp_d.utils.plot)
plot_svgx() (in module xcp_d.utils.plot)
PlotImage (class in xcp_d.interfaces.surfplotting)
plotimage() (in module xcp_d.utils.plot)
PlotSVGData (class in xcp_d.interfaces.surfplotting)
process_crashfile() (in module xcp_d.utils.sentry)
Q
QCPlot (class in xcp_d.interfaces.qc_plot)
R
read_gii() (in module xcp_d.utils.write_save)
read_ndata() (in module xcp_d.utils.write_save)
readjson() (in module xcp_d.utils.confounds)
Regress (class in xcp_d.interfaces.regression)
ReHoNamePatch (class in xcp_d.interfaces.resting_state)
relpath() (in module xcp_d.utils.filemanip)
RemoveTR (class in xcp_d.interfaces.prepostcleaning)
Report (class in xcp_d.interfaces.report_core)
ribbon_to_statmap() (in module xcp_d.utils.execsummary)
RibbontoStatmap (class in xcp_d.interfaces.surfplotting)
run() (xcp_d.interfaces.layout_builder.LayoutBuilder method)
(xcp_d.interfaces.layout_builder.TasksSection method)
(xcp_d.interfaces.layout_builder.TxSection method)
run_reports() (in module xcp_d.interfaces.report_core)
run_shell() (in module xcp_d.utils.write_save)
S
scalex() (in module xcp_d.utils.write_save)
Section (class in xcp_d.interfaces.layout_builder)
seg_data (xcp_d.utils.plot.FMRIPlot attribute)
sentry_setup() (in module xcp_d.utils.sentry)
setup() (xcp_d.interfaces.layout_builder.LayoutBuilder method)
Smooth (class in xcp_d.interfaces.nilearn)
spikes (xcp_d.utils.plot.FMRIPlot attribute)
split_filename() (in module xcp_d.utils.filemanip)
square_confound() (in module xcp_d.utils.confounds)
start_ping() (in module xcp_d.utils.sentry)
stringforparams() (in module xcp_d.utils.utils)
SubjectSummary (class in xcp_d.interfaces.report)
SummaryInterface (class in xcp_d.interfaces.report)
surf_data_from_cifti() (in module xcp_d.utils.plot)
SurfaceAverage (class in xcp_d.interfaces.workbench)
SurfaceGenerateInflated (class in xcp_d.interfaces.workbench)
SurfaceReHo (class in xcp_d.interfaces.resting_state)
SurfaceSphereProjectUnproject (class in xcp_d.interfaces.workbench)
T
t1_to_native() (in module xcp_d.workflow.execsummary)
TasksSection (class in xcp_d.interfaces.layout_builder)
teardown() (xcp_d.interfaces.layout_builder.LayoutBuilder method)
TR (xcp_d.utils.plot.FMRIPlot attribute)
TxSection (class in xcp_d.interfaces.layout_builder)
W
which() (in module xcp_d.utils.filemanip)
write_bold_gray_row() (xcp_d.interfaces.layout_builder.TasksSection method)
write_dataset_description() (in module xcp_d.utils.bids)
write_gii() (in module xcp_d.utils.write_save)
write_html() (xcp_d.interfaces.layout_builder.LayoutBuilder method)
write_ndata() (in module xcp_d.utils.write_save)
write_t1_reg_rows() (xcp_d.interfaces.layout_builder.TasksSection method)
writejson() (in module xcp_d.utils.dcan2fmriprep)
X
xcp_d
module
xcp_d.cli
module
xcp_d.cli.combineqc
module
xcp_d.cli.run
module
xcp_d.interfaces
module
xcp_d.interfaces.ants
module
xcp_d.interfaces.bids
module
xcp_d.interfaces.c3
module
xcp_d.interfaces.connectivity
module
xcp_d.interfaces.constants
module
xcp_d.interfaces.filtering
module
xcp_d.interfaces.layout_builder
module
xcp_d.interfaces.nilearn
module
xcp_d.interfaces.prepostcleaning
module
xcp_d.interfaces.qc_plot
module
xcp_d.interfaces.regression
module
xcp_d.interfaces.report
module
xcp_d.interfaces.report_core
module
xcp_d.interfaces.resting_state
module
xcp_d.interfaces.surfplotting
module
xcp_d.interfaces.workbench
module
xcp_d.utils
module
xcp_d.utils.atlas
module
xcp_d.utils.bids
module
xcp_d.utils.concatenation
module
xcp_d.utils.confounds
module
xcp_d.utils.dcan2fmriprep
module
xcp_d.utils.doc
module
xcp_d.utils.execsummary
module
xcp_d.utils.fcon
module
xcp_d.utils.filemanip
module
xcp_d.utils.hcp2fmriprep
module
xcp_d.utils.modified_data
module
xcp_d.utils.plot
module
xcp_d.utils.qcmetrics
module
xcp_d.utils.sentry
module
xcp_d.utils.utils
module
xcp_d.utils.write_save
module
xcp_d.workflow
module
xcp_d.workflow.anatomical
module
xcp_d.workflow.base
module
xcp_d.workflow.bold
module
xcp_d.workflow.cifti
module
xcp_d.workflow.connectivity
module
xcp_d.workflow.execsummary
module
xcp_d.workflow.outputs
module
xcp_d.workflow.postprocessing
module
xcp_d.workflow.restingstate
module
Z
zscore_nifti() (in module xcp_d.utils.utils)
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