def run_report_source(*,
cfg: SimpleNamespace,
subject: str,
session: Optional[str] = None,
report: mne.Report) -> mne.Report:
import matplotlib.pyplot as plt
msg = 'Generating source-space analysis report …'
logger.info(
**gen_log_kwargs(message=msg, subject=subject, session=session))
if report is None:
report = _gen_empty_report(cfg=cfg, subject=subject, session=session)
bids_path = BIDSPath(subject=subject,
session=session,
task=cfg.task,
acquisition=cfg.acq,
run=None,
recording=cfg.rec,
space=cfg.space,
extension='.fif',
datatype=cfg.datatype,
root=cfg.deriv_root,
check=False)
# Use this as a source for the Info dictionary
fname_info = bids_path.copy().update(processing='clean', suffix='epo')
fname_trans = bids_path.copy().update(suffix='trans')
if not fname_trans.fpath.exists():
msg = 'No coregistration found, skipping source space report.'
logger.info(
**gen_log_kwargs(message=msg, subject=subject, session=session))
return report
###########################################################################
#
# Visualize the coregistration & inverse solutions.
#
if cfg.conditions is None:
conditions = []
elif isinstance(cfg.conditions, dict):
conditions = list(cfg.conditions.keys())
else:
conditions = cfg.conditions.copy()
conditions.extend(cfg.contrasts)
msg = 'Rendering MRI slices with BEM contours.'
logger.info(
**gen_log_kwargs(message=msg, subject=subject, session=session))
report.add_bem(subject=cfg.fs_subject,
subjects_dir=cfg.fs_subjects_dir,
title='BEM',
width=256,
decim=8)
msg = 'Rendering sensor alignment (coregistration).'
logger.info(
**gen_log_kwargs(message=msg, subject=subject, session=session))
report.add_trans(
trans=fname_trans,
info=fname_info,
title='Sensor alignment',
subject=cfg.fs_subject,
subjects_dir=cfg.fs_subjects_dir,
)
for condition in conditions:
msg = f'Rendering inverse solution for {condition}'
logger.info(
**gen_log_kwargs(message=msg, subject=subject, session=session))
if condition in cfg.conditions:
title = f'Source: {config.sanitize_cond_name(condition)}'
else: # It's a contrast of two conditions.
# XXX Will change once we process contrasts here too
continue
method = cfg.inverse_method
cond_str = config.sanitize_cond_name(condition)
inverse_str = method
hemi_str = 'hemi' # MNE will auto-append '-lh' and '-rh'.
fname_stc = bids_path.copy().update(
suffix=f'{cond_str}+{inverse_str}+{hemi_str}', extension=None)
tags = ('source-estimate', condition.lower().replace(' ', '-'))
if Path(f'{fname_stc.fpath}-lh.stc').exists():
report.add_stc(stc=fname_stc,
title=title,
subject=cfg.fs_subject,
subjects_dir=cfg.fs_subjects_dir,
tags=tags)
plt.close('all') # close all figures to save memory
return report
