osl_ephys.source_recon.batch

Batch processing for source reconstruction.

Attributes

logger

Functions

load_config(config)	Load config.
find_func(method, extra_funcs)	Find a source reconstruction function.
run_src_chain(config, outdir, subject[, preproc_file, ...])	Source reconstruction.
run_src_batch(config, outdir, subjects[, ...])	Batch source reconstruction.

Module Contents

osl_ephys.source_recon.batch.logger = None

osl_ephys.source_recon.batch.load_config(config)

Load config.

Parameters:

config (str or dict) – Path to yaml file or str to convert to dict or a dict.

Returns:

config – Source reconstruction config.

Return type:

dict

osl_ephys.source_recon.batch.find_func(method, extra_funcs)

Find a source reconstruction function.

Parameters:

• method (str) – Function name.

• extra_funcs (list of functions) – Custom functions.

Returns:

func – Function to use.

Return type:

function

osl_ephys.source_recon.batch.run_src_chain(config, outdir, subject, preproc_file=None, smri_file=None, epoch_file=None, surface_extraction_method='fsl', logsdir=None, reportdir=None, gen_report=True, verbose='INFO', mneverbose='WARNING', extra_funcs=None, random_seed='auto')

Source reconstruction.

Parameters:

• config (str or dict) – Source reconstruction config.

• outdir (str) – Source reconstruction directory.

• subject (str) – Subject name.

• surface_extraction_method (str) – Can be ‘fsl’ or ‘freesurfer’.

• preproc_file (str) – Preprocessed fif file.

• smri_file (str) – Structural MRI file.

• epoch_file (str) – Epoched fif file.

• logsdir (str) – Directory to save log files to.

• reportdir (str) – Directory to save report files to.

• gen_report (bool) – Should we generate a report?

• verbose (str) – Level of verbose.

• mneverbose (str) – Level of MNE verbose.

• extra_funcs (list of functions) – Custom functions.

• random_seed ('auto' (default), int or None) – Random seed to set. If ‘auto’, a random seed will be generated. Random seeds are set for both Python and NumPy. If None, no random seed is set.

Returns:

flag – Flag indicating whether source reconstruction was successful.

Return type:

bool

osl_ephys.source_recon.batch.run_src_batch(config, outdir, subjects, preproc_files=None, smri_files=None, epoch_files=None, surface_extraction_method='fsl', logsdir=None, reportdir=None, gen_report=True, verbose='INFO', mneverbose='WARNING', extra_funcs=None, dask_client=False, random_seed='auto')

Batch source reconstruction.

Parameters:

• config (str or dict) – Source reconstruction config.

• outdir (str) – Source reconstruction directory.

• subjects (list of str) – Subject names.

• surface_extraction_method (str) – Can be ‘fsl’ or ‘freesurfer’.

• preproc_files (list of str) – Preprocessed fif files.

• smri_files (list of str or str) – Structural MRI files. Can be ‘standard’ to use MNI152_T1_2mm.nii for the structural.

• epoch_files (list of str) – Epoched fif file.

• logsdir (str) – Directory to save log files to.

• reportdir (str) – Directory to save report files to.

• gen_report (bool) – Should we generate a report?

• verbose (str) – Level of verbose.

• mneverbose (str) – Level of MNE verbose.

• extra_funcs (list of functions) – Custom functions.

• dask_client (bool) – Are we using a dask client?

• random_seed ('auto' (default), int or None) – Random seed to set. If ‘auto’, a random seed will be generated. Random seeds are set for both Python and NumPy. If None, no random seed is set.

Returns:

flags – Flags indicating whether coregistration was successful.

Return type:

list of bool