ICA Artefact Rejection

doc/tutorials/0-1_meg_preprocessing.py

@@ -4,7 +4,7 @@
 
 This tutorial walks through the full MEG processing pipeline step by step:
 
-1. Preprocessing — Downsample, filter, detect bad segments/channels.
+1. Preprocessing — Downsample, filter, detect bad segments/channels, ICA artefact rejection.
 2. Surface Extraction — Extract skull/scalp surfaces from a structural MRI.
 3. Coregistration — Align MEG sensor space to MRI space.
 4. Forward Model — Compute the lead field matrix.
@@ -161,11 +161,36 @@
 #     raw = preproc.detect_bad_channels(raw, picks="grad")
 
 #%%
-# Save preprocessing QC plots (PSD, sum-of-squares time series, channel standard deviations). Check that bad segments and channels are being correctly identified.
+# ICA artefact rejection
+# **********************
+#
+# Automatic ICA artefact rejection to remove ECG and EOG artefacts.
+# Two approaches are available:
+#
+# **Option A: ECG/EOG correlation** — Uses MNE-Python's built-in
+# correlation-based detection.
+#
+# .. code-block:: python
+#
+#     raw, ica, ic_labels = preproc.ica_ecg_eog_correlation(raw, picks="meg")
+#
+# **Option B: MEGNet automatic labelling** — Uses ``mne-icalabel`` (included
+# in the osl-dynamics conda environments) to classify components with a
+# pre-trained deep learning model. Note, MEGNet was trained on ``'mag'``
+# sensor topographies.
+#
+# .. code-block:: python
+#
+#     raw, ica, ic_labels = preproc.ica_label(raw, picks="mag", method="megnet")
+
+#%%
+# Save preprocessing QC plots (PSD, sum-of-squares time series, channel
+# standard deviations, ICA component topographies). Check that bad segments,
+# channels, and ICA components are being correctly identified.
 #
 # .. code-block:: python
 #
-#     preproc.save_qc_plots(raw, plots_dir / id, show=True)
+#     preproc.save_qc_plots(raw, plots_dir / id, show=True, ica=ica, ic_labels=ic_labels)
 
 #%%
 # Save preprocessed data

envs/bmrc.yml

@@ -8,15 +8,14 @@ dependencies:
   - aiohttp=3.13.3=py312h5d8c7f2_0
   - aiosignal=1.4.0=pyhd8ed1ab_0
   - alsa-lib=1.2.15.3=hb03c661_0
-  - anyio=4.12.1=pyhcf101f3_0
+  - anyio=4.13.0=pyhcf101f3_0
   - aom=3.9.1=hac33072_0
   - argon2-cffi=25.1.0=pyhd8ed1ab_0
   - argon2-cffi-bindings=25.1.0=py312h4c3975b_2
   - arrow=1.4.0=pyhcf101f3_0
   - asttokens=3.0.1=pyhd8ed1ab_0
-  - async-lru=2.2.0=pyhcf101f3_0
-  - attr=2.5.2=h39aace5_0
-  - attrs=25.4.0=pyhcf101f3_1
+  - async-lru=2.3.0=pyhcf101f3_0
+  - attrs=26.1.0=pyhcf101f3_0
   - babel=2.18.0=pyhcf101f3_1
   - backports.zstd=1.3.0=py312h90b7ffd_0
   - beautifulsoup4=4.14.3=pyha770c72_0
@@ -38,12 +37,12 @@ dependencies:
   - certifi=2026.2.25=pyhd8ed1ab_0
   - cffi=2.0.0=py312h460c074_1
   - charls=2.4.3=hecca717_0
-  - charset-normalizer=3.4.5=pyhd8ed1ab_0
+  - charset-normalizer=3.4.6=pyhd8ed1ab_0
   - comm=0.2.3=pyhe01879c_0
   - contourpy=1.3.3=py312h0a2e395_4
   - cpython=3.12.13=py312hd8ed1ab_0
   - cycler=0.12.1=pyhcf101f3_2
-  - cyclopts=4.7.0=pyhcf101f3_0
+  - cyclopts=4.10.1=pyhcf101f3_0
   - cyrus-sasl=2.1.28=hd9c7081_0
   - dav1d=1.2.1=hd590300_0
   - dbus=1.16.2=h24cb091_1
@@ -67,19 +66,19 @@ dependencies:
   - fonts-conda-forge=1=hc364b38_1
   - fonttools=4.62.0=py312h8a5da7c_0
   - fqdn=1.5.1=pyhd8ed1ab_1
-  - freetype=2.14.2=ha770c72_0
+  - freetype=2.14.3=ha770c72_0
   - fribidi=1.0.16=hb03c661_0
   - frozenlist=1.7.0=py312h447239a_0
   - fslpy=3.27.0=pyhd8ed1ab_0
   - gdk-pixbuf=2.44.4=h2b0a6b4_0
   - giflib=5.2.2=hd590300_0
-  - gl2ps=1.4.2=hae5d5c5_1
+  - gl2ps=1.4.2=h36e74d4_2
   - gmp=6.3.0=hac33072_2
   - gnutls=3.8.11=h18acefa_1
   - graphite2=1.3.14=hecca717_2
   - h11=0.16.0=pyhcf101f3_1
   - h2=4.3.0=pyhcf101f3_0
-  - h5io=0.2.5=pyhecae5ae_0
+  - h5io=0.2.5=pyhc455866_0
   - h5py=3.13.0=nompi_py312hedeef09_100
   - harfbuzz=12.2.0=h15599e2_0
   - hdf4=4.2.15=h2a13503_7
@@ -92,9 +91,9 @@ dependencies:
   - idna=3.11=pyhd8ed1ab_0
   - imagecodecs=2026.1.14=py312h40df4bb_1
   - imageio=2.37.0=pyhfb79c49_0
-  - importlib-metadata=8.7.0=pyhe01879c_1
+  - importlib-metadata=8.8.0=pyhcf101f3_0
   - importlib_resources=6.5.2=pyhd8ed1ab_0
-  - intel-gmmlib=22.9.0=hb700be7_0
+  - intel-gmmlib=22.10.0=hb700be7_0
   - intel-media-driver=25.3.4=hecca717_0
   - ipyevents=2.0.4=pyhbbac1ac_0
   - ipykernel=7.2.0=pyha191276_1
@@ -107,7 +106,7 @@ dependencies:
   - joblib=1.5.3=pyhd8ed1ab_0
   - json5=0.13.0=pyhd8ed1ab_0
   - jsoncpp=1.9.6=hf42df4d_1
-  - jsonpointer=3.0.0=pyhcf101f3_3
+  - jsonpointer=3.1.1=pyhcf101f3_0
   - jsonschema=4.26.0=pyhcf101f3_0
   - jsonschema-specifications=2025.9.1=pyhcf101f3_0
   - jsonschema-with-format-nongpl=4.26.0=hcf101f3_0
@@ -132,7 +131,7 @@ dependencies:
   - lazy-loader=0.5=pyhd8ed1ab_0
   - lazy_loader=0.5=pyhd8ed1ab_0
   - lcms2=2.18=h0c24ade_0
-  - ld_impl_linux-64=2.45.1=default_hbd61a6d_101
+  - ld_impl_linux-64=2.45.1=default_hbd61a6d_102
   - lerc=4.1.0=hdb68285_0
   - level-zero=1.28.2=hb700be7_0
   - libabseil=20250512.1=cxx17_hba17884_0
@@ -144,7 +143,7 @@ dependencies:
   - libbrotlicommon=1.2.0=hb03c661_1
   - libbrotlidec=1.2.0=hb03c661_1
   - libbrotlienc=1.2.0=hb03c661_1
-  - libcap=2.77=h3ff7636_0
+  - libcap=2.77=hd0affe5_1
   - libcblas=3.11.0=5_h0358290_openblas
   - libclang-cpp21.1=21.1.0=default_h99862b1_1
   - libclang13=21.1.0=default_h746c552_1
@@ -158,8 +157,8 @@ dependencies:
   - libexpat=2.7.4=hecca717_0
   - libffi=3.5.2=h3435931_0
   - libflac=1.5.0=he200343_1
-  - libfreetype=2.14.2=ha770c72_0
-  - libfreetype6=2.14.2=h73754d4_0
+  - libfreetype=2.14.3=ha770c72_0
+  - libfreetype6=2.14.3=h73754d4_0
   - libgcc=15.2.0=he0feb66_18
   - libgcc-ng=15.2.0=h69a702a_18
   - libgfortran=15.2.0=h69a702a_18
@@ -181,7 +180,7 @@ dependencies:
   - liblzma=5.8.2=hb03c661_0
   - libmicrohttpd=1.0.2=hc2fc477_0
   - libnetcdf=4.9.2=nompi_h00e09a9_116
-  - libnghttp2=1.67.0=had1ee68_0
+  - libnghttp2=1.68.1=h877daf1_0
   - libnsl=2.0.1=hb9d3cd8_1
   - libntlm=1.8=hb9d3cd8_0
   - libogg=1.3.5=hd0c01bc_1
@@ -212,11 +211,11 @@ dependencies:
   - libssh2=1.11.1=hcf80075_0
   - libstdcxx=15.2.0=h934c35e_18
   - libstdcxx-ng=15.2.0=hdf11a46_18
-  - libsystemd0=257.10=hd0affe5_4
+  - libsystemd0=257.13=hd0affe5_0
   - libtasn1=4.21.0=hb03c661_0
   - libtheora=1.1.1=h4ab18f5_1006
   - libtiff=4.7.1=h9d88235_1
-  - libudev1=257.10=hd0affe5_4
+  - libudev1=257.13=hd0affe5_0
   - libunistring=0.9.10=h7f98852_0
   - libunwind=1.8.3=h65a8314_0
   - liburing=2.12=hb700be7_0
@@ -234,7 +233,7 @@ dependencies:
   - libxml2=2.13.9=h04c0eec_0
   - libxslt=1.1.43=h7a3aeb2_0
   - libzip=1.11.2=h6991a6a_0
-  - libzlib=1.3.1=hb9d3cd8_2
+  - libzlib=1.3.2=h25fd6f3_2
   - libzopfli=1.0.3=h9c3ff4c_0
   - llvmlite=0.46.0=py312h7424e68_0
   - loguru=0.7.3=pyh707e725_0
@@ -270,7 +269,7 @@ dependencies:
   - notebook-shim=0.2.4=pyhd8ed1ab_1
   - numba=0.64.0=py312hd1dde6f_0
   - ocl-icd=2.3.3=hb9d3cd8_0
-  - opencl-headers=2025.06.13=h5888daf_0
+  - opencl-headers=2025.06.13=hecca717_0
   - openh264=2.6.0=hc22cd8d_0
   - openjpeg=2.5.4=h55fea9a_0
   - openjph=0.26.3=h8d634f6_0
@@ -326,7 +325,7 @@ dependencies:
   - rav1e=0.7.1=h8fae777_3
   - readline=8.3=h853b02a_0
   - referencing=0.37.0=pyhcf101f3_0
-  - requests=2.32.5=pyhcf101f3_1
+  - requests=2.33.0=pyhcf101f3_0
   - rfc3339-validator=0.1.4=pyhd8ed1ab_1
   - rfc3986-validator=0.1.1=pyh9f0ad1d_0
   - rfc3987-syntax=1.1.0=pyhe01879c_1
@@ -358,14 +357,14 @@ dependencies:
   - tinycss2=1.4.0=pyhd8ed1ab_0
   - tk=8.6.13=noxft_h366c992_103
   - tomli=2.4.0=pyhcf101f3_0
-  - tornado=6.5.3=py312h4c3975b_0
+  - tornado=6.5.5=py312h4c3975b_0
   - tqdm=4.67.3=pyh8f84b5b_0
   - traitlets=5.14.3=pyhd8ed1ab_1
   - trame=3.12.0=pyhd8ed1ab_0
-  - trame-client=3.11.3=pyhd8ed1ab_0
-  - trame-common=1.1.2=pyhd8ed1ab_0
+  - trame-client=3.11.4=pyhd8ed1ab_0
+  - trame-common=1.1.3=pyhd8ed1ab_0
   - trame-server=3.10.0=pyhd8ed1ab_0
-  - trame-vtk=2.11.1=pyh932262d_0
+  - trame-vtk=2.11.5=pyh3504b2d_0
   - trame-vuetify=3.2.1=pyhd8ed1ab_0
   - typing-extensions=4.15.0=h396c80c_0
   - typing_extensions=4.15.0=pyhcf101f3_0
@@ -378,7 +377,7 @@ dependencies:
   - vtk=9.3.1=osmesa_py312hf4758c4_116
   - vtk-base=9.3.1=osmesa_py312hc9bc066_116
   - vtk-io-ffmpeg=9.3.1=osmesa_py312hf4758c4_116
-  - wayland=1.24.0=hd6090a7_1
+  - wayland=1.25.0=hd6090a7_0
   - wayland-protocols=1.47=hd8ed1ab_0
   - wcwidth=0.6.0=pyhd8ed1ab_0
   - webcolors=25.10.0=pyhd8ed1ab_0
@@ -419,7 +418,7 @@ dependencies:
   - zeromq=4.3.5=h387f397_9
   - zfp=1.0.1=h909a3a2_5
   - zipp=3.23.0=pyhcf101f3_1
-  - zlib=1.3.1=hb9d3cd8_2
+  - zlib=1.3.2=h25fd6f3_2
   - zlib-ng=2.3.3=hceb46e0_1
   - zstd=1.5.7=hb78ec9c_6
   - pip:
@@ -435,6 +434,8 @@ dependencies:
       - libclang==18.1.1
       - markdown==3.10.2
       - ml-dtypes==0.5.4
+      - mne-icalabel==0.8.1
+      - mpmath==1.3.0
       - namex==0.1.0
       - numpy==2.1.3
       - nvidia-cublas-cu12==12.5.3.2
@@ -449,15 +450,17 @@ dependencies:
       - nvidia-cusparse-cu12==12.5.1.3
       - nvidia-nccl-cu12==2.23.4
       - nvidia-nvjitlink-cu12==12.5.82
+      - onnxruntime==1.24.4
       - opt-einsum==3.4.0
       - optree==0.19.0
       - protobuf==5.29.6
+      - sympy==1.14.0
       - tensorboard==2.19.0
       - tensorboard-data-server==0.7.2
       - tensorflow==2.19.0
       - tensorflow-probability==0.25.0
       - termcolor==3.3.0
       - tf-keras==2.19.0
-      - werkzeug==3.1.6
+      - werkzeug==3.1.7
       - wrapt==2.1.2
       - osl-dynamics

envs/fsl.yml

@@ -31,5 +31,6 @@ dependencies:
   - trame-vtk
   - trame-vuetify
   - pip:
+    - mne-icalabel[onnx]
     - tensorflow==2.19
     - tensorflow-probability[tf]==0.25