Add more docu to rest_epochs_duration

[skjerns]

Currently my pipeline fails with this error

│13:19:55│  sub-01 A critical error occurred. The error message was: unsupported operand type(s) for -: 'float' and 'NoneType'
Starting post-mortem debugger.
<traceback object at 0x7fb746892300>
> /home/anaconda3/lib/python3.11/site-packages/mne_bids_pipeline/_import_data.py(56)make_epochs()
-> stop = raw.times[-1] - rest_epochs_duration

However, from the documentation it is not clear to me what this parameter actually does. Maybe that could be added?

Additionally, it would be nice if the pipeline would detect the missing parameter already at the start and not at the moment it encounters the error.

---

My current pipeline's should simply preprocess all FIF files in our dataset without epoching, i.e. apply ICA, filtering and downsampling and output the files to derivatives, from where I will deal with them outside of the pipeline. The epoching is done in a separate script, therefore, I treat all data as "rest"

``pipeline_preproc.conf

config

###############################################################################
### Preprocessing pipeline settings for mne-bids-pipeline |
###############################################################################
from collections.abc import Callable, Sequence
from typing import Annotated, Any, Literal

from annotated_types import Ge, Interval, Len, MinLen
from mne import Covariance
from mne_bids import BIDSPath

from mne_bids_pipeline.typing import (
  # ArbitraryContrast,
  # DigMontageType,
  # FloatArrayLike,
  PathLike,
)

# %%05
# # General settings
# Configuration file for mne-bids-pipeline

from typing import Sequence, Literal, Optional
from mne import Covariance
from mne_bids import BIDSPath

# %%
# General Settings

bids_root: PathLike | None = '/data/fastreplay/Fast-Replay-MEG-bids/'
deriv_root: PathLike = f"{bids_root}/derivatives/"  # Save all processed data under /derivatives/
subjects_dir: Optional[PathLike] = f"{deriv_root}/freesurfer/subjects/"  # Path to FreeSurfer subject reconstructions
interactive: bool = False  # Disable interactive elements
# sessions: Literal["all"] = "all"  # Process all sessions
# task: str = ""  # Process all tasks by leaving empty
task_is_rest: bool = True  # Treat data as resting-state, disable epoching
# runs: Literal["all"] = "all"  # Process all runs
exclude_runs: Optional[dict[str, list[str]]] = None  # No excluded runs
subjects: Sequence[str] | Literal["all"] = "all"  # Analyze all subjects
exclude_subjects: Sequence[str] = ['23']  # No excluded subjects
process_empty_room: bool = True  # Preprocess empty-room data
process_rest: bool = True  # Preprocess resting-state data
ch_types: Sequence[Literal["meg"]] = ["meg"]  # Include MEG and EEG channels
data_type: Literal["meg", "eeg"] = "meg"  # Data type is MEG
eog_channels: Sequence[str] = ["BIO0002", "BIO0003"]  # Specify EOG channels
ecg_channel: str = "BIO0001"  # Specify ECG channel
spatial_filter: Literal["ica"] = "ica"  # Use ICA for artifact removal
ica_n_components: int = 50  # Number of ICA components
ica_algorithm: str = 'picard'

# %%
# Preprocessing

raw_resample_sfreq: float = 100.0  # Resample data to 100 Hz
l_freq: float = 0.1  # Apply high-pass filter at 0.1 Hz
h_freq: Optional[float] = None  # Disable low-pass filter
notch_freq: Sequence[float] = [50.0]  # Apply notch filter at 50 Hz
notch_trans_bandwidth: float = 1.0  # Set notch filter transition bandwidth to 1 Hz

# %%
# Artifact Removal via ICA

# The pipeline will automatically identify and remove ICA components related to EOG and ECG.

# %%
# Source-level Analysis

run_source_estimation: bool = True  # Enable source-level analysis
inverse_method: Literal["dSPM"] = "dSPM"  # Use dSPM as the inverse solution method
loose: float = 0.2  # Weigh parallel dipole components by 0.2
depth: float = 0.8  # Set depth weighting exponent to 0.8
noise_cov = "emptyroom"  # Use resting-state recording for noise covariance

# %%
# FreeSurfer recon-all Settings

recon_all: bool = True  # Enable FreeSurfer's recon-all
freesurfer_verbose: bool = True  # print the complete recon-all pipeline

# %%
# Parallelization

n_jobs: int = 4  # Use all available CPU cores
parallel_backend: Literal["loky"] = "loky"  # Use 'loky' backend for parallel processing

# %%
# Logging

log_level: Literal["info"] = "info"  # Set pipeline logging verbosity to 'info'
mne_log_level: Literal["error"] = "error"  # Set MNE-Python logging verbosity to 'error'

# %%
# Error Handling

on_error: Literal["abort"] = "abort"  # Abort processing on errors
config_validation: Literal["raise"] = "raise"  # Raise exceptions on config validation issues

[larsoner]

Before we use this variable we should raise an informative error telling people to set this value. Presumably no default is set (e.g., like 1.) because we want the end-user to make a conscious decision about what the duration should be.