diff --git a/docs/source/v1.9.md.inc b/docs/source/v1.9.md.inc index 308a36bb6..892e84078 100644 --- a/docs/source/v1.9.md.inc +++ b/docs/source/v1.9.md.inc @@ -10,20 +10,18 @@ - Changed default for `source_info_path_update` to `None`. In `_04_make_forward.py` and `_05_make_inverse.py`, we retrieve the info from the file from which the `noise_cov` is computed (#919 by @SophieHerbst) - -[//]: # (- Whatever (#000 by @whoever)) +- The [`depth`][mne_bids_pipeline._config.depth] parameter doesn't accept `None` + anymore. Please use `0` instead. (#915 by @hoechenberger) ### :package: Requirements - We dropped support for Python 3.9. You now need Python 3.10 or newer. (#908 by @hoechenberger) -[//]: # (- Whatever (#000 by @whoever)) - ### :book: Documentation - We removed the `Execution` section from configuration options documentation and replaced it with new, more explicit sections (namely, Caching, Parallelization, - Logging, and Error handling). (#914 by @hoechenberger) + Logging, and Error handling), and enhanced documentation. (#914 by @hoechenberger, #916 by @SophieHerbst) ### :bug: Bug fixes diff --git a/mne_bids_pipeline/_config.py b/mne_bids_pipeline/_config.py index 987a0617d..1d14b03bf 100644 --- a/mne_bids_pipeline/_config.py +++ b/mne_bids_pipeline/_config.py @@ -1979,24 +1979,33 @@ def mri_landmarks_kind(bids_path): # ## Inverse solution -loose: float | Literal["auto"] = 0.2 +loose: Annotated[float, Interval(ge=0, le=1)] | Literal["auto"] = 0.2 """ -Value that weights the source variances of the dipole components -that are parallel (tangential) to the cortical surface. If `0`, then the -inverse solution is computed with **fixed orientation.** -If `1`, it corresponds to **free orientation.** -The default value, `'auto'`, is set to `0.2` for surface-oriented source -spaces, and to `1.0` for volumetric, discrete, or mixed source spaces, -unless `fixed is True` in which case the value 0. is used. +A value between 0 and 1 that weights the source variances of the dipole components +that are parallel (tangential) to the cortical surface. + +If `0`, then the inverse solution is computed with **fixed orientation**, i.e., +only dipole components perpendicular to the cortical surface are considered. + +If `1`, it corresponds to **free orientation**, i.e., dipole components with any +orientation are considered. + +The default value, `0.2`, is suitable for surface-oriented source spaces. + +For volume or mixed source spaces, choose `1.0`. + +!!! info + Support for modeling volume and mixed source spaces will be added in a future + version of MNE-BIDS-Pipeline. """ -depth: float | dict | None = 0.8 +depth: Annotated[float, Interval(ge=0, le=1)] | dict = 0.8 """ -If float (default 0.8), it acts as the depth weighting exponent (`exp`) -to use (must be between 0 and 1). None is equivalent to 0, meaning no -depth weighting is performed. Can also be a `dict` containing additional -keyword arguments to pass to :func:`mne.forward.compute_depth_prior` -(see docstring for details and defaults). +If a number, it acts as the depth weighting exponent to use +(must be between `0` and`1`), with`0` meaning no depth weighting is performed. + +Can also be a dictionary containing additional keyword arguments to pass to +`mne.forward.compute_depth_prior` (see docstring for details and defaults). """ inverse_method: Literal["MNE", "dSPM", "sLORETA", "eLORETA"] = "dSPM" @@ -2187,8 +2196,12 @@ def noise_cov(bids_path): # %% # # Caching # -# These settings control if and how pipeline output is being cached to avoid unnecessary -# computations on a re-run. +# Per default, the pipeline output is cached (temporarily stored), +# to avoid unnecessary reruns of previously computed steps. +# Yet, for consistency, changes in configuration parameters trigger +# automatic reruns of previous steps. +# !!! info +# To force rerunning a given step, run the pipeline with the option: `--no-cache`. memory_location: PathLike | bool | None = True """