MRG: Add initial arguments to vol viz (#6046)

* ENH: Add initial arguments to vol viz

* DOC: Links

* FIX: Fix for deprecation

* WIP

* FIX: Fix affine treatment and vertices order

* FIX: Adjust tests

* FIX: Flake

* FIX: Check

* BUG: Fix axis limits

* FIX: Clip and desc

doc/changes/latest.inc

@@ -53,6 +53,8 @@ Changelog
 
 - Add function to check the type of a FIF file using :func:`mne.what` and `mne what <gen_mne_what>` by `Eric Larson`_
 
+- Add support for specifying the initial time and/or position and providing a :class:`mne.SourceMorph` instead of :class:`mne.SourceSpaces` in :func:`mne.viz.plot_volume_source_estimates` by `Eric Larson`_
+
 - Speed up morph map generation in :func:`mne.read_morph_map` by ~5-10x by using :func:`numba.jit` by `Eric Larson`_
 
 - Speed up :func:`mne.setup_volume_source_space`, especially when ``volume_label is not None`` by `Eric Larson`_
@@ -90,6 +92,14 @@ Bug
 
 - Fix one-sample baseline issue in :class:`mne.BaseEpochs` when using `tmin=0` by `Milan Rybář`_
 
+- Fix bug in :func:`mne.viz.plot_volume_source_estimates` where ``'glass_brain'`` MRIs were not transformed to MNI space, by `Eric Larson`_
+
+- Fix bug in :func:`mne.viz.plot_volume_source_estimates` where MRIs with voxels not in RAS orientation could not be browsed properly, by `Eric Larson`_
+
+- Fix bug in :meth:`mne.SourceMorph.apply` where output STCs had ``stc.vertices`` defined improperly, by `Eric Larson`_
+
+- Fix bug in :meth:`mne.SourceMorph.apply` where the default was errantly ``mri_space=False`` instead of ``mri_space=None`` (as documented), by `Eric Larson`_
+
 - Fix :meth:`mne.io.Raw.set_annotations` for ``meas_date`` previous to 1970 by `Joan Massich`_
 
 - Fix horizontal spacing issues in :meth:`mne.io.Raw.plot_psd` by `Jeff Hanna`_

doc/conf.py

@@ -533,9 +533,11 @@ def reset_warnings(gallery_conf, fname):
     # nibabel
     'Nifti1Image': 'nibabel.nifti1.Nifti1Image',
     'Nifti2Image': 'nibabel.nifti2.Nifti2Image',
+    'SpatialImage': 'nibabel.spatialimages.SpatialImage',
     # MNE
     'Label': 'mne.Label', 'Forward': 'mne.Forward', 'Evoked': 'mne.Evoked',
     'Info': 'mne.Info', 'SourceSpaces': 'mne.SourceSpaces',
+    'SourceMorph': 'mne.SourceMorph',
     'Epochs': 'mne.Epochs', 'Layout': 'mne.channels.Layout',
     'EvokedArray': 'mne.EvokedArray', 'BiHemiLabel': 'mne.BiHemiLabel',
     'AverageTFR': 'mne.time_frequency.AverageTFR',

examples/inverse/plot_lcmv_beamformer_volume.py

@@ -3,14 +3,13 @@
 Compute LCMV inverse solution in volume source space
 ====================================================
 
-Compute LCMV beamformer on an auditory evoked dataset in a volume source space.
+Compute LCMV beamformer on an auditory evoked dataset in a volume source space,
+and show activation on ``fsaverage``.
 """
 # Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
 #
 # License: BSD (3-clause)
 
-# sphinx_gallery_thumbnail_number = 3
-
 import mne
 from mne.datasets import sample
 from mne.beamformer import make_lcmv, apply_lcmv
@@ -22,8 +21,7 @@
 
 data_path = sample.data_path()
 subjects_dir = data_path + '/subjects'
-raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif'
-event_fname = data_path + '/MEG/sample/sample_audvis_raw-eve.fif'
+raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
 fname_fwd = data_path + '/MEG/sample/sample_audvis-meg-vol-7-fwd.fif'
 
 # Get epochs
@@ -35,7 +33,7 @@
 # Setup for reading the raw data
 raw = mne.io.read_raw_fif(raw_fname, preload=True)
 raw.info['bads'] = ['MEG 2443', 'EEG 053']  # 2 bads channels
-events = mne.read_events(event_fname)
+events = mne.find_events(raw)
 
 # Pick the channels of interest
 raw.pick(['meg', 'eog'])
@@ -83,15 +81,34 @@
 
 # You can save result in stc files with:
 # stc.save('lcmv-vol')
-
-clim = dict(kind='value', pos_lims=[0.3, 0.6, 0.9])
-stc.plot(src=forward['src'], subject='sample', subjects_dir=subjects_dir,
-         clim=clim)
+lims = [0.3, 0.6, 0.9]
+stc.plot(
+    src=forward['src'], subject='sample', subjects_dir=subjects_dir,
+    clim=dict(kind='value', pos_lims=lims), mode='stat_map',
+    initial_time=0.1, verbose=True)
 
 ###############################################################################
-# We can also visualize the activity on a "glass brain" (shown here with
-# absolute values):
+# Now let's plot this on a glass brain, which will automatically transform the
+# data to MNI Talairach space:
+
+# sphinx_gallery_thumbnail_number = 4
 
-clim = dict(kind='value', lims=[0.3, 0.6, 0.9])
-abs(stc).plot(src=forward['src'], subject='sample', subjects_dir=subjects_dir,
-              mode='glass_brain', clim=clim)
+stc.plot(
+    src=forward['src'], subject='sample', subjects_dir=subjects_dir,
+    mode='glass_brain', clim=dict(kind='value', lims=lims),
+    initial_time=0.1, verbose=True)
+
+###############################################################################
+# Finally let's get another view, this time plotting again a ``'stat_map'``
+# style but using volumetric morphing to get data to fsaverage space,
+# which we can get by passing a :class:`mne.SourceMorph` as the ``src``
+# argument to `mne.VolSourceEstimate.plot`. To save a bit of speed when
+# applying the morph, we will crop the STC:
+
+morph = mne.compute_source_morph(
+    forward['src'], 'sample', 'fsaverage', subjects_dir=subjects_dir,
+    zooms=7, verbose=True)
+stc.copy().crop(0.05, 0.18).plot(
+    src=morph, subject='fsaverage', subjects_dir=subjects_dir,
+    mode='stat_map', clim=dict(kind='value', pos_lims=lims),
+    initial_time=0.1, verbose=True)

mne/conftest.py

@@ -73,6 +73,7 @@ def pytest_configure(config):
     ignore:numpy.ufunc size changed:RuntimeWarning
     ignore:.*mne-realtime.*:DeprecationWarning
     ignore:.*imp.*:DeprecationWarning
+    always:.*get_data.* is deprecated in favor of.*:DeprecationWarning
     """  # noqa: E501
     for warning_line in warning_lines.split('\n'):
         warning_line = warning_line.strip()

mne/fixes.py

@@ -420,6 +420,14 @@ def minimum_phase(h):
 ###############################################################################
 # Misc utilities
 
+# Deal with nibabel 2.5 img.get_data() deprecation
+def _get_img_fdata(img):
+    try:
+        return img.get_fdata()
+    except AttributeError:
+        return img.get_data().astype(float)
+
+
 def _read_volume_info(fobj):
     """An implementation of nibabel.freesurfer.io._read_volume_info, since old
     versions of nibabel (<=2.1.0) don't have it.