osl_ephys.source_recon#

Submodules#

Attributes#

`logger`
`__doc__`

Functions#

`validate_outdir`(outdir)	Checks if an output directory exists and if not creates it.
`find_run_id`(infile[, preload])
`set_random_seed`([seed])	Set all random seeds.
`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.
`setup_fsl`(directory)	Setup FSL.
`check_fsl`()	Check FSL is installed.
`setup_freesurfer`(directory[, subjects_dir])	Setup FreeSurfer.
`check_freesurfer`()	Check FreeSurfer is installed.
`recon_all`(smri_file, subjects_dir, subject)
`make_watershed_bem`(outdir, subject, **kwargs)	Wrapper for `mne.bem.make_watershed_bem` making a watershed BEM with FreeSurfer.
`make_fsaverage_src`(subjects_dir[, spacing])
`find_template_subject`(outdir, subjects[, ...])	Function to find a good subject to align other subjects to in the sign flipping.

Package Contents#

osl_ephys.source_recon.validate_outdir(outdir)[source]#: Checks if an output directory exists and if not creates it.

osl_ephys.source_recon.find_run_id(infile, preload=True)[source]#

osl_ephys.source_recon.set_random_seed(seed=None)[source]#

Set all random seeds.

This includes Python’s random module and NumPy.

Parameters:: seed (int) – Random seed.

osl_ephys.source_recon.logger = None[source]#

osl_ephys.source_recon.load_config(config)[source]#

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.find_func(method, extra_funcs)[source]#

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.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]#

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.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')[source]#

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

osl_ephys.source_recon.setup_fsl(directory)[source]#

Setup FSL.

Parameters:: directory (str) – Path to FSL installation.

osl_ephys.source_recon.check_fsl()[source]#: Check FSL is installed.

osl_ephys.source_recon.setup_freesurfer(directory, subjects_dir=None)[source]#

Setup FreeSurfer.

Parameters:: directory (str) – Path to FreeSurfer installation.

osl_ephys.source_recon.check_freesurfer()[source]#: Check FreeSurfer is installed.

osl_ephys.source_recon.recon_all(smri_file, subjects_dir, subject)[source]#

osl_ephys.source_recon.make_watershed_bem(outdir, subject, **kwargs)[source]#: Wrapper for mne.bem.make_watershed_bem making a watershed BEM with FreeSurfer.

osl_ephys.source_recon.make_fsaverage_src(subjects_dir, spacing='oct6')[source]#

osl_ephys.source_recon.find_template_subject(outdir, subjects, n_embeddings=1, standardize=True, epoched=False, source_method='lcmv')[source]#

Function to find a good subject to align other subjects to in the sign flipping.

Note, this function expects parcellated data to exist in the following location: outdir//parc/parc-.fif, the * here represents subject directories or ‘raw’ vs ‘epo’.

Parameters:

outdir (str) – Path to where to output the source reconstruction files.
subjects (str) – Subjects to include.
n_embeddings (int, optional) – Number of time-delay embeddings that we will use (if we are doing any).
standardize (bool, optional) – Should we standardize (z-transform) the data before sign flipping?
epoched (bool, optional) – Are we performing sign flipping on parc-raw.fif (epoched=False) or parc-epo.fif files (epoched=True)?
source_method (str, optional) – Method to used for inverse modelling (e.g., LCMV, MNE, eLORETA).

Returns:

template – Template subject.

Return type:

str

osl_ephys.source_recon.__doc__[source]#