[pull] main from mne-tools:main

doc/changes/dev/13068.bugfix.rst

@@ -0,0 +1 @@
+Fixed ICA getting sources for concatenated raw instances, by :newcontrib:`Beige Jin`.

doc/changes/dev/13307.newfeature.rst

@@ -0,0 +1 @@
+Added ``on_inside="raise"`` parameter to :func:`mne.make_forward_solution` and :func:`mne.make_forward_dipole` to control behavior when MEG sensors are inside the outer skin surface. This is useful for forward solutions that are computed with sensors just inside the outer skin surface (e.g., with some OPM coregistrations), by `Eric Larson`_.

doc/changes/names.inc

@@ -33,6 +33,7 @@
 .. _Ashley Drew: https://github.com/ashdrew
 .. _Asish Panda: https://github.com/kaichogami
 .. _Austin Hurst: https://github.com/a-hurst
+.. _Beige Jin: https://github.com/BeiGeJin
 .. _Ben Beasley: https://github.com/musicinmybrain
 .. _Bradley Voytek: https://github.com/voytek
 .. _Britta Westner: https://britta-wstnr.github.io

mne/forward/_make_forward.py

@@ -37,7 +37,15 @@
     apply_trans,
     invert_transform,
 )
-from ..utils import _check_fname, _pl, _validate_type, logger, verbose, warn
+from ..utils import (
+    _check_fname,
+    _on_missing,
+    _pl,
+    _validate_type,
+    logger,
+    verbose,
+    warn,
+)
 from ._compute_forward import (
     _compute_forwards,
     _compute_forwards_meeg,
@@ -437,13 +445,15 @@ def _prepare_for_forward(
     bem,
     mindist,
     n_jobs,
+    *,
     bem_extra="",
     trans="",
     info_extra="",
     meg=True,
     eeg=True,
     ignore_ref=False,
     allow_bem_none=False,
+    on_inside="raise",
     verbose=None,
 ):
     """Prepare for forward computation.
@@ -567,11 +577,12 @@ def check_inside_head(x):
                 meg_loc = apply_trans(invert_transform(mri_head_t), meg_loc)
             n_inside = check_inside_head(meg_loc).sum()
             if n_inside:
-                raise RuntimeError(
+                msg = (
                     f"Found {n_inside} MEG sensor{_pl(n_inside)} inside the "
                     f"{check_surface}, perhaps coordinate frames and/or "
-                    "coregistration must be incorrect"
+                    "coregistration are incorrect"
                 )
+                _on_missing(on_inside, msg, name="on_inside", error_klass=RuntimeError)
 
     if len(src):
         rr = np.concatenate([s["rr"][s["vertno"]] for s in src])
@@ -610,6 +621,7 @@ def make_forward_solution(
     mindist=0.0,
     ignore_ref=False,
     n_jobs=None,
+    on_inside="raise",
     verbose=None,
 ):
     """Calculate a forward solution for a subject.
@@ -640,6 +652,13 @@ def make_forward_solution(
         option should be True for KIT files, since forward computation
         with reference channels is not currently supported.
     %(n_jobs)s
+    on_inside : 'raise' | 'warn' | 'ignore'
+        What to do if MEG sensors are inside the outer skin surface. If 'raise'
+        (default), an error is raised. If 'warn' or 'ignore', the forward
+        solution is computed anyway and a warning is or isn't emitted,
+        respectively.
+
+        .. versionadded:: 1.10
     %(verbose)s
 
     Returns
@@ -710,12 +729,13 @@ def make_forward_solution(
         bem,
         mindist,
         n_jobs,
-        bem_extra,
-        trans,
-        info_extra,
-        meg,
-        eeg,
-        ignore_ref,
+        bem_extra=bem_extra,
+        trans=trans,
+        info_extra=info_extra,
+        meg=meg,
+        eeg=eeg,
+        ignore_ref=ignore_ref,
+        on_inside=on_inside,
     )
     del (src, mri_head_t, trans, info_extra, bem_extra, mindist, meg, eeg, ignore_ref)
 
@@ -741,7 +761,9 @@ def make_forward_solution(
 
 
 @verbose
-def make_forward_dipole(dipole, bem, info, trans=None, n_jobs=None, *, verbose=None):
+def make_forward_dipole(
+    dipole, bem, info, trans=None, n_jobs=None, *, on_inside="raise", verbose=None
+):
     """Convert dipole object to source estimate and calculate forward operator.
 
     The instance of Dipole is converted to a discrete source space,
@@ -767,6 +789,13 @@ def make_forward_dipole(dipole, bem, info, trans=None, n_jobs=None, *, verbose=N
         The head<->MRI transform filename. Must be provided unless BEM
         is a sphere model.
     %(n_jobs)s
+    on_inside : 'raise' | 'warn' | 'ignore'
+        What to do if MEG sensors are inside the outer skin surface. If 'raise'
+        (default), an error is raised. If 'warn' or 'ignore', the forward
+        solution is computed anyway and a warning is or isn't emitted,
+        respectively.
+
+        .. versionadded:: 1.10
     %(verbose)s
 
     Returns
@@ -805,7 +834,9 @@ def make_forward_dipole(dipole, bem, info, trans=None, n_jobs=None, *, verbose=N
 
     # Forward operator created for channels in info (use pick_info to restrict)
     # Use defaults for most params, including min_dist
-    fwd = make_forward_solution(info, trans, src, bem, n_jobs=n_jobs, verbose=verbose)
+    fwd = make_forward_solution(
+        info, trans, src, bem, n_jobs=n_jobs, on_inside=on_inside, verbose=verbose
+    )
     # Convert from free orientations to fixed (in-place)
     convert_forward_solution(
         fwd, surf_ori=False, force_fixed=True, copy=False, use_cps=False, verbose=None

mne/forward/tests/test_make_forward.py

@@ -894,8 +894,11 @@ def test_sensors_inside_bem():
     trans["trans"][2, 3] = 0.03
     sphere_noshell = make_sphere_model((0.0, 0.0, 0.0), None)
     sphere = make_sphere_model((0.0, 0.0, 0.0), 1.01)
-    with pytest.raises(RuntimeError, match=".* 15 MEG.*inside the scalp.*"):
-        make_forward_solution(info, trans, fname_src, fname_bem)
+    with pytest.warns(RuntimeWarning, match=".* 15 MEG.*inside the scalp.*"):
+        fwd = make_forward_solution(info, trans, fname_src, fname_bem, on_inside="warn")
+    assert fwd["nsource"] == 516
+    assert fwd["nchan"] == 42
+    assert np.isfinite(fwd["sol"]["data"]).all()
     make_forward_solution(info, trans, fname_src, fname_bem_meg)  # okay
     make_forward_solution(info, trans, fname_src, sphere_noshell)  # okay
     with pytest.raises(RuntimeError, match=".* 42 MEG.*outermost sphere sh.*"):

mne/preprocessing/ica.py

@@ -1295,8 +1295,10 @@ def _sources_as_raw(self, raw, add_channels, start, stop):
             picks = pick_channels(raw.ch_names, add_channels)
             data_ = np.concatenate([data_, raw.get_data(picks, start=start, stop=stop)])
         out._data = data_
-        out._first_samps = [out.first_samp]
-        out._last_samps = [out.last_samp]
+        out_first_samp = out.first_samp
+        out_last_samp = out.last_samp
+        out._first_samps = [out_first_samp]
+        out._last_samps = [out_last_samp]
         out.filenames = [None]
         out.preload = True
         out._projector = None

mne/preprocessing/tests/test_ica.py

@@ -25,6 +25,7 @@
     EpochsArray,
     EvokedArray,
     Info,
+    concatenate_raws,
     create_info,
     make_ad_hoc_cov,
     pick_channels_regexp,
@@ -1727,3 +1728,21 @@ def test_ica_ch_types(ch_type):
     for inst in [raw, epochs, evoked]:
         ica.apply(inst)
         ica.get_sources(inst)
+
+
+@testing.requires_testing_data
+def test_ica_get_sources_concatenated():
+    """Test ICA get_sources method with concatenated raws."""
+    # load data
+    raw = read_raw_fif(raw_fname).crop(0, 3).load_data()  # raw has 3 seconds of data
+    # create concatenated raw instances
+    raw_concat = concatenate_raws(
+        [raw.copy(), raw.copy()]
+    )  # raw_concat has 6 seconds of data
+    # do ICA
+    ica = ICA(n_components=2, max_iter=2)
+    with _record_warnings(), pytest.warns(UserWarning, match="did not converge"):
+        ica.fit(raw_concat)
+    # get sources
+    raw_sources = ica.get_sources(raw_concat)  # but this only has 3 seconds of data
+    assert raw_concat.n_times == raw_sources.n_times  # this will fail

mne/simulation/raw.py

@@ -46,6 +46,7 @@
     _check_preload,
     _pl,
     _validate_type,
+    _verbose_safe_false,
     check_random_state,
     logger,
     verbose,
@@ -793,7 +794,14 @@ def _iter_forward_solutions(
         info.update(projs=[], bads=[])  # Ensure no 'projs' or 'bads'
     mri_head_t, trans = _get_trans(trans)
     sensors, rr, info, update_kwargs, bem = _prepare_for_forward(
-        src, mri_head_t, info, bem, mindist, n_jobs, allow_bem_none=True, verbose=False
+        src,
+        mri_head_t,
+        info,
+        bem,
+        mindist,
+        n_jobs,
+        allow_bem_none=True,
+        verbose=_verbose_safe_false(),
     )
     del (src, mindist)