YAML Configuration Reference¶
Auto-generated from the Pydantic config models in osipy.cli.config and runtime registries. This page is rebuilt on every documentation build, so it always reflects the current code.
Top-level fields¶
Every configuration file has these top-level keys:
PipelineConfig¶
Top-level pipeline configuration from YAML.
| Field | Type | Default | Valid values |
|---|---|---|---|
modality |
string | required | dce, dsc, asl, ivim |
pipeline |
mapping | {} |
|
data |
DataConfig | (see DataConfig) | |
output |
OutputConfig | (see OutputConfig) | |
backend |
BackendConfig | (see BackendConfig) | |
logging |
LoggingConfig | (see LoggingConfig) |
Shared sections¶
These sections are common to all modalities.
data: (DataConfig)¶
Data loading configuration.
| Field | Type | Default | Valid values |
|---|---|---|---|
format |
string | "auto" |
auto, nifti, dicom, bids |
mask |
string or null | null | |
t1_map |
string or null | null | |
aif_file |
string or null | null | |
m0_data |
string or null | null | |
b_values |
list of numbers or null | null | |
b_values_file |
string or null | null | |
subject |
string or null | null | |
session |
string or null | null |
output: (OutputConfig)¶
Output configuration.
| Field | Type | Default | Valid values |
|---|---|---|---|
format |
string | "nifti" |
nifti |
backend: (BackendConfig)¶
GPU/CPU backend configuration.
| Field | Type | Default | Valid values |
|---|---|---|---|
force_cpu |
boolean | false |
logging: (LoggingConfig)¶
Logging configuration.
| Field | Type | Default | Valid values |
|---|---|---|---|
level |
string | "INFO" |
DEBUG, INFO, WARNING |
DCE Pipeline¶
Set modality: dce and configure these under pipeline:.
pipeline: (DCEPipelineYAML)¶
DCE pipeline settings from YAML.
| Field | Type | Default | Valid values |
|---|---|---|---|
model |
string | "extended_tofts" |
2cum, 2cxm, extended_tofts, patlak, tofts |
t1_mapping_method |
string | "vfa" |
vfa, look_locker |
aif_source |
string | "population" |
population, detect, manual |
population_aif |
string | "parker" |
fritz_hansen, georgiou, mcgrath, parker, weinmann |
save_intermediate |
boolean | false | |
acquisition |
DCEAcquisitionYAML | (see DCEAcquisitionYAML) | |
roi |
ROIConfig | (see ROIConfig) | |
fitting |
DCEFittingConfig | (see DCEFittingConfig) |
pipeline.acquisition: (DCEAcquisitionYAML)¶
DCE acquisition parameters from YAML.
| Field | Type | Default | Valid values |
|---|---|---|---|
tr |
number or null | null | |
flip_angles |
list of numbers or null | null | |
baseline_frames |
integer | 5 |
|
relaxivity |
number | 4.5 |
|
t1_assumed |
number or null | null |
pipeline.roi: (ROIConfig)¶
Region-of-interest configuration for limiting processing.
| Field | Type | Default | Valid values |
|---|---|---|---|
enabled |
boolean | false | |
center |
list of integers or null | null | |
radius |
integer | 10 |
pipeline.fitting: (DCEFittingConfig)¶
DCE model fitting configuration from YAML.
| Field | Type | Default | Valid values |
|---|---|---|---|
fitter |
string | "lm" |
bayesian, lm |
max_iterations |
integer | 100 |
|
tolerance |
number | 1e-06 |
|
r2_threshold |
number | 0.5 |
|
bounds |
mapping or null | null | |
initial_guess |
mapping or null | null |
DSC Pipeline¶
Set modality: dsc and configure these under pipeline:.
pipeline: (DSCPipelineYAML)¶
DSC pipeline settings from YAML.
| Field | Type | Default | Valid values |
|---|---|---|---|
te |
number | 30.0 |
|
deconvolution_method |
string | "oSVD" |
cSVD, oSVD, sSVD |
apply_leakage_correction |
boolean | true | |
svd_threshold |
number | 0.2 |
|
baseline_frames |
integer | 10 |
|
hematocrit_ratio |
number | 0.73 |
ASL Pipeline¶
Set modality: asl and configure these under pipeline:.
pipeline: (ASLPipelineYAML)¶
ASL pipeline settings from YAML.
| Field | Type | Default | Valid values |
|---|---|---|---|
labeling_scheme |
string | "pcasl" |
pasl, casl, pcasl |
pld |
number | 1800.0 |
|
label_duration |
number | 1800.0 |
|
t1_blood |
number | 1650.0 |
|
labeling_efficiency |
number | 0.85 |
|
m0_method |
string | "single" |
single, voxelwise, reference_region |
t1_tissue |
number | 1330.0 |
|
partition_coefficient |
number | 0.9 |
|
difference_method |
string | "pairwise" |
|
label_control_order |
string | "label_first" |
label_first, control_first |
IVIM Pipeline¶
Set modality: ivim and configure these under pipeline:.
pipeline: (IVIMPipelineYAML)¶
IVIM pipeline settings from YAML.
| Field | Type | Default | Valid values |
|---|---|---|---|
fitting_method |
string | "segmented" |
segmented, full, bayesian |
b_threshold |
number | 200.0 |
|
normalize_signal |
boolean | true | |
fitting |
IVIMFittingConfig | (see IVIMFittingConfig) |
pipeline.fitting: (IVIMFittingConfig)¶
IVIM model fitting configuration from YAML.
| Field | Type | Default | Valid values |
|---|---|---|---|
max_iterations |
integer | 500 |
|
tolerance |
number | 1e-06 |
|
bounds |
mapping or null | null | |
initial_guess |
mapping or null | null | |
bayesian |
BayesianIVIMFittingConfig | (see BayesianIVIMFittingConfig) |
pipeline.fitting.bayesian: (BayesianIVIMFittingConfig)¶
Bayesian IVIM fitting configuration from YAML.
| Field | Type | Default | Valid values |
|---|---|---|---|
prior_scale |
number | 1.5 |
|
noise_std |
number or null | null | |
compute_uncertainty |
boolean | true |