Example to extract time courses with labels from custom atlas

doc/changes/devel/12618.other.rst

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+Add an example to use :func:`mne.extract_label_time_course` with custom atlas, by `Fabrice Guibert`_.

doc/changes/names.inc

@@ -84,6 +84,7 @@
 .. _Evgeny Goldstein: https://github.com/evgenygoldstein
 .. _Ezequiel Mikulan: https://github.com/ezemikulan
 .. _Ezequiel Mikulan: https://github.com/ezemikulan
+.. _Fabrice Guibert: https/github.com/shrecki
 .. _Fahimeh Mamashli: https://github.com/fmamashli
 .. _Farzin Negahbani: https://github.com/Farzin-Negahbani
 .. _Federico Raimondo: https://github.com/fraimondo

examples/forward/source_space_custom_atlas.py

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+"""
+.. _ex-source-space-custom-atlas:
+
+=========================================
+Source reconstruction with a custom atlas
+=========================================
+
+This example shows how to use a custom atlas when performing source reconstruction.
+We showcase on the sample dataset how to apply the Yeo atlas during source
+ reconstruction.
+You should replace the atlas with your own atlas and your own subject.
+
+Any atlas can be used instead of Yeo, provided each region contains a single
+ label (ie: no probabilistic atlas).
+
+.. warning:: This tutorial uses FSL and FreeSurfer to perform MRI
+ coregistrations. If you use a different software, replace the
+ coregistration function appropriately.
+"""
+
+# Authors: Fabrice Guibert <[email protected]>
+#
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+# %%
+
+import subprocess
+from pathlib import Path as Path
+
+import nilearn.datasets
+
+import mne
+import mne.datasets
+from mne._freesurfer import read_freesurfer_lut
+from mne.minimum_norm import apply_inverse, make_inverse_operator
+
+# The atlas is in a template space. We download here as an example Yeo
+# 2011's atlas, which is in the MNI152 1mm template space.
+# Replace this part with your atlas and the template space you used.
+
+nilearn.datasets.fetch_atlas_yeo_2011()  # Download Yeo 2011
+yeo_path = Path(
+    nilearn.datasets.get_data_dirs()[0], "yeo_2011", "Yeo_JNeurophysiol11_MNI152"
+)
+atlas_path = Path(yeo_path, "Yeo2011_7Networks_MNI152_FreeSurferConformed1mm.nii.gz")
+atlas_template_T1_path = Path(yeo_path, "FSL_MNI152_FreeSurferConformed_1mm.nii.gz")
+
+# The participant's T1 data. Here, we consider the sample dataset
+# The brain should be skull stripped. After freesurfer preprocessing,
+# you can either use brain.mgz or antsdn.brain.mgz
+data_path = mne.datasets.sample.data_path()
+subjects_mri_dir = Path(data_path, "subjects")
+subject_mri_path = Path(subjects_mri_dir, "sample")
+mri_path = Path(subject_mri_path, "mri")
+T1_participant_path = Path(mri_path, "brain.mgz")
+
+assert atlas_path.is_file()
+assert atlas_template_T1_path.is_file()
+assert T1_participant_path.is_file()
+
+# %%
+# The first step is to put the atlas in subject space.
+# We show this step with FSL and freesurfer with linear coregistration.
+# If your atlas is already in participant space,
+# you can skip this step. Coregistration is done in two steps:
+# compute the atlas template to subject T1 transform and apply this transform
+# to the atlas file with nearest neighbour interpolation.
+
+# FSL does not know how to read .mgz, so we need to convert the T1 to nifti format
+# With FreeSurfer:
+T1_participant_nifti = Path(str(T1_participant_path).replace("mgz", "nii.gz"))
+subprocess.run(["mri_convert", T1_participant_path, T1_participant_nifti])
+
+# Compute template to subject anatomical transform using flirt
+template_to_anat_transform_path = Path(mri_path, "template_to_anat.mat")
+subprocess.run(
+    [
+        "flirt",
+        "-in",
+        atlas_template_T1_path,
+        "-ref",
+        T1_participant_nifti,
+        "-out",
+        Path(mri_path, "T1_atlas_coreg"),
+        "-omat",
+        template_to_anat_transform_path,
+    ]
+)
+
+# Apply the transform to the atlas
+atlas_participant = Path(mri_path, "yeo_atlas.nii.gz")
+
+subprocess.run(
+    [
+        "flirt",
+        "-in",
+        atlas_path,
+        "-ref",
+        T1_participant_nifti,
+        "-out",
+        atlas_participant,
+        "-applyxfm -init",
+        template_to_anat_transform_path,
+        "-interp nearestneighbour",
+    ]
+)
+
+# Convert resulting atlas from nifti to mgz
+# The filename must finish with aseg, to indicate to MNE that it is
+#  a proper atlas segmentation.
+atlas_converted = Path(str(atlas_participant).replace(".nii.gz", "aseg.mgz"))
+subprocess.run(["mri_convert", atlas_participant, atlas_converted])
+
+assert T1_participant_nifti.is_file()
+assert template_to_anat_transform_path.is_file()
+assert atlas_participant.is_file()
+assert atlas_converted.is_file()
+
+# %%
+# With the atlas in participant space, we're still missing one ingredient.
+# We need a dictionary mapping label to region ID / value in the fMRI.
+# In FreeSurfer and atlases, these typically take the form of lookup tables.
+# You can also build the dictionary by hand.
+
+atlas_labels = read_freesurfer_lut(Path(yeo_path, "Yeo2011_7Networks_ColorLUT.txt"))[0]
+print(atlas_labels)
+
+# Drop the key corresponding to outer region
+del atlas_labels["NONE"]
+
+# %%
+# For the purpose of source reconstruction, let's create a volumetric
+# source estimate and source reconstruction with e.g eLORETA.
+vol_src = mne.setup_volume_source_space(
+    "sample",
+    subjects_dir=subjects_mri_dir,
+    surface=Path(subject_mri_path, "bem", "inner_skull.surf"),
+)
+
+fif_path = Path(data_path, "MEG", "sample")
+fname_trans = Path(fif_path, "sample_audvis_raw-trans.fif")
+raw_fname = Path(fif_path, "sample_audvis_filt-0-40_raw.fif")
+
+model = mne.make_bem_model(
+    subject="sample", subjects_dir=subjects_mri_dir, ico=4, conductivity=(0.33,)
+)
+bem_sol = mne.make_bem_solution(model)
+
+info = mne.io.read_info(raw_fname)
+info = mne.pick_info(info, mne.pick_types(info, meg=True, eeg=False, exclude=[]))
+
+# Build the forward model with our custom source
+fwd = mne.make_forward_solution(info, trans=fname_trans, src=vol_src, bem=bem_sol)
+
+
+# Now perform typical source reconstruction steps
+raw = mne.io.read_raw_fif(raw_fname)  # already has an average reference
+events = mne.find_events(raw, stim_channel="STI 014")
+
+event_id = dict(aud_l=1)  # event trigger and conditions
+tmin = -0.2  # start of each epoch (200ms before the trigger)
+tmax = 0.5  # end of each epoch (500ms after the trigger)
+raw.info["bads"] = ["MEG 2443", "EEG 053"]
+baseline = (None, 0)  # means from the first instant to t = 0
+reject = dict(grad=4000e-13, mag=4e-12, eog=150e-6)
+
+epochs = mne.Epochs(
+    raw,
+    events,
+    event_id,
+    tmin,
+    tmax,
+    proj=True,
+    picks=("meg", "eog"),
+    baseline=baseline,
+    reject=reject,
+)
+
+# Compute noise covariances
+noise_cov = mne.compute_covariance(
+    epochs, tmax=0.0, method=["shrunk", "empirical"], rank=None, verbose=True
+)
+
+# Compute evoked response
+evoked = epochs.average().pick("meg")
+
+# Make inverse operator
+inverse_operator = make_inverse_operator(
+    evoked.info, fwd, noise_cov, loose=1, depth=0.8
+)
+
+# Compute source time courses
+method = "eLORETA"
+snr = 3.0
+lambda2 = 1.0 / snr**2
+stc, residual = apply_inverse(
+    evoked,
+    inverse_operator,
+    lambda2,
+    method=method,
+    pick_ori=None,
+    return_residual=True,
+    verbose=True,
+)
+
+# %%
+# Then, we can finally use our atlas!
+label_tcs = stc.extract_label_time_course(
+    labels=(atlas_converted, atlas_labels), src=vol_src
+)
+label_tcs.shape