config
tit.pre.qsi.config ¶
Configuration dataclasses and enums for QSI integration.
This module defines type-safe configuration objects for QSIPrep and QSIRecon Docker runs, including resource allocation and pipeline specifications.
ReconSpec ¶
Bases: StrEnum
Available QSIRecon reconstruction specifications.
Each spec defines a complete reconstruction pipeline with specific algorithms and output formats.
QSIAtlas ¶
Bases: StrEnum
Available atlases for QSIRecon connectivity analysis.
These atlases can be used for structural connectivity matrix generation. The 4S series combines Schaefer cortical parcels with 56 subcortical ROIs.
ResourceConfig
dataclass
¶
ResourceConfig(cpus: int | None = None, memory_gb: int | None = None, omp_threads: int = (lambda: QSI_DEFAULT_OMP_THREADS)())
Resource allocation configuration for QSI containers.
Attributes¶
cpus : int Number of CPUs to allocate to the container. memory_gb : int Memory limit in gigabytes. omp_threads : int Number of OpenMP threads (affects ANTS, MRtrix, etc.).
QSIPrepConfig
dataclass
¶
QSIPrepConfig(subject_id: str, output_resolution: float = QSI_DEFAULT_OUTPUT_RESOLUTION, resources: ResourceConfig = ResourceConfig(), image_tag: str = QSI_QSIPREP_IMAGE_TAG, skip_bids_validation: bool = True, denoise_method: str = 'dwidenoise', unringing_method: str = 'mrdegibbs', use_syn_sdc: bool = False, mni_normalization: bool = False, use_gpu: bool = False)
Configuration for a QSIPrep run.
Attributes¶
subject_id : str
Subject identifier (without 'sub-' prefix).
output_resolution : float
Target output resolution in mm (default: 2.0).
resources : ResourceConfig
Resource allocation settings.
image_tag : str
Docker image tag for QSIPrep.
skip_bids_validation : bool
Whether to skip BIDS validation (useful for non-BIDS datasets).
denoise_method : str
Denoising method: 'dwidenoise', 'patch2self', or 'none'.
unringing_method : str
Unringing method: 'mrdegibbs', 'rpg', or 'none' (already resolved; the
pipeline setting 'auto' is resolved by run_qsiprep).
use_syn_sdc : bool
Run fieldmap-less SyN distortion correction.
Set by run_qsiprep when the subject has no usable fieldmap.
mni_normalization : bool
Run QSIPrep's anatomical normalization to MNI. Off by default: only
QSIRecon atlases/template-space specs need it. Always on with SyN SDC,
which uses the MNI transform to place its fieldmap prior.
use_gpu : bool
Run eddy on the GPU (requires NVIDIA Docker runtime).
QSIReconConfig
dataclass
¶
QSIReconConfig(subject_id: str, recon_specs: list[str] = (lambda: [QSI_DEFAULT_RECON_SPEC])(), atlases: list[str] | None = None, use_gpu: bool = False, resources: ResourceConfig = ResourceConfig(), image_tag: str = QSI_QSIRECON_IMAGE_TAG, skip_odf_reports: bool = True)
Configuration for a QSIRecon run.
Attributes¶
subject_id : str Subject identifier (without 'sub-' prefix). recon_specs : list[str] List of reconstruction specs to run. Defaults to ['dsi_studio_gqi'] (scalar maps only; the SimNIBS DTI tensor does not need QSIRecon). atlases : list[str] | None List of atlases for connectivity analysis. None (default) = no connectivity. Set to e.g. ['4S156Parcels', 'AAL116'] if needed. use_gpu : bool Whether to enable GPU acceleration (requires NVIDIA Docker runtime). resources : ResourceConfig Resource allocation settings. image_tag : str Docker image tag for QSIRecon. skip_odf_reports : bool Whether to skip ODF report generation (saves time).