# ica.find\_bads\_exg components does not return the same components if using raw used for fitting or same raw with components excluded. **URL:** \ **Category:** Support & Discussions\ **Tags:** preprocessing, eeg, ica\ **Created:** [October 13, 2021, 11:42am UTC](https://mne.discourse.group/t/ica-find-bads-exg-components-does-not-return-the-same-components-if-using-raw-used-for-fitting-or-same-raw-with-components-excluded/3803 "2021-10-13T11:42:02Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![mscheltienne](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/mscheltienne/32/827_2.png) [@mscheltienne](https://mne.discourse.group/u/mscheltienne)\ **Post date:** [October 13, 2021, 11:42am UTC](https://mne.discourse.group/t/ica-find-bads-exg-components-does-not-return-the-same-components-if-using-raw-used-for-fitting-or-same-raw-with-components-excluded/3803/1 "2021-10-13T11:42:03Z")
Hello, I was trying to assess how the adaptative z-scoring of `ica.find_bads_eog` and `ica.find_bads_ecg` was performing, and I now face a behavior that I can not explain. I start by loading one of my `-raw.fif` file and I apply filters/rereferencing. The file include 64 EEG channels + 1 EOG channel and 1 ECG channel. I fit an ICA with this `raw` instance. I look for the components correlating with the EOG and ECG channel (`ica.find_bads_exg` methods) and I exclude them. I copy the `raw` instance and apply the ICA to it. I look for the components correlating with the EOG and ECG channel of the copied instance. I was expecting to find exactly the same, as the EOG and ECG channels are not modified by `ica.apply`. Am I wrong in assuming the methods `ica.find_bads_eog` and `ica.find_bads_ecg` are correlating with the EOG and ECG channel? Reproducible example: ```python import mne import numpy as np # Load fname = 'sample-raw.fif' raw = mne.io.read_raw_fif(fname, preload=True) mne.rename_channels(raw.info, {"AUX7": "EOG", "AUX8": "ECG"}) raw.set_channel_types(mapping={"ECG": "ecg", "EOG": "eog"}) mapping = { "FP1": "Fp1", "FPZ": "Fpz", "FP2": "Fp2", "FZ": "Fz", "CZ": "Cz", "PZ": "Pz", "POZ": "POz", "FCZ": "FCz", "OZ": "Oz", "FPz": "Fpz", } for key, value in mapping.items(): try: mne.rename_channels(raw.info, {key: value}) except Exception: pass # Filter and montage raw.filter(l_freq=1., h_freq=40., picks=['eog', 'ecg'], phase="zero-double", pad="edge") raw.notch_filter(np.arange(50, 151, 50), picks=['eog', 'ecg']) # Yes, not necessary raw.add_reference_channels(ref_channels='CPz') raw.set_montage('standard_1020') raw.set_eeg_reference( ref_channels="average", ch_type="eeg", projection=True) raw.filter(l_freq=1., h_freq=40., picks='eeg', phase="zero-double", pad="edge") # ICA ica = mne.preprocessing.ICA(method='picard', max_iter='auto', random_state=101) ica.fit(raw, picks='eeg', reject_by_annotation=False) # No annotations # Correlation eog_idx_raw, eog_scores_raw = ica.find_bads_eog(raw) ecg_idx_raw, ecg_scores_raw = ica.find_bads_ecg(raw) ica.exclude = eog_idx_raw + ecg_idx_raw # Apply ICA raw_ica_applied = raw.copy() ica.apply(raw_ica_applied) # Correlation with applied ICA ica.exclude = list() eog_idx_raw_ica_applied, eog_scores_raw_ica_applied = ica.find_bads_eog(raw_ica_applied) ecg_idx_raw_ica_applied, ecg_scores_raw_ica_applied = ica.find_bads_ecg(raw_ica_applied) ``` File to run: (available 24h, ask for re-upload). [https://file.re/2021/10/13/sample-raw/](https://file.re/2021/10/13/sample-raw/) Running 0.23.0. Output: ```python eog_idx_raw Out[15]: [0] ecg_idx_raw Out[16]: [26, 19] eog_idx_raw_ica_applied Out[17]: [0, 26, 19] ecg_idx_raw_ica_applied Out[18]: [] ``` Mathieu ---
**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\ **Post date:** [October 13, 2021, 12:39pm UTC](https://mne.discourse.group/t/ica-find-bads-exg-components-does-not-return-the-same-components-if-using-raw-used-for-fitting-or-same-raw-with-components-excluded/3803/2 "2021-10-13T12:39:46Z")
> [@mscheltienne](#): > > I was expecting to find exactly the same, as the EOG and ECG channels are not modified by `ica.apply` . This is true and therefore, `mne.preprocessing.find_ecg_events()` and `find_eog_events()` (which are both used under the hood by `ICA.find_bads_eXg()`) should yield the exact same event arrays for both the pre- and post-ICA data. However, for the actual pattern matching, the EEG channels will be used. I’m actually surprised you still get somewhat similar results after cleaning the data with ICA – I would have assumed that the artifacts would have been reduced so much that the pattern matching would fail. My bet would be that the “eog” components you find in `eog_idx_raw_ica_applied` are actually mostly physiological brain data you’d want to keep. ---
**Author:** ![mscheltienne](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/mscheltienne/32/827_2.png) [@mscheltienne](https://mne.discourse.group/u/mscheltienne)\ **Post date:** [October 13, 2021, 12:53pm UTC](https://mne.discourse.group/t/ica-find-bads-exg-components-does-not-return-the-same-components-if-using-raw-used-for-fitting-or-same-raw-with-components-excluded/3803/3 "2021-10-13T12:53:43Z")
Ok, so this is actually very surprising to me. I assumed that to determine the EOG and ECG related components, the algo would look for the correlation between each component and the EOG/ECG channel. Why is it using the EEG channels for pattern matching/correlation? * * * As you can see above, I excluded simultaneously both EOG and ECG components with `ica.exclude = eog_idx_raw + ecg_idx_raw`. I then saved to disk both the `ICA` and the `raw_ica_applied` instances, but not the intermediate filtered/rereferenced `raw`. **From these 2 saved objects, how can I recover which component was excluded and with which correlation (score)?** `ica.exclude` will include both EOG and ECG related components, but it won’t tell me which is which. Using `ica.find_bads_eXg` with the `raw_ica_applied` instance will not return the same output as when it is called with `raw` instance. Any ideas? ---
**Author:** ![mscheltienne](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/mscheltienne/32/827_2.png) [@mscheltienne](https://mne.discourse.group/u/mscheltienne)\ **Post date:** [October 13, 2021, 1:08pm UTC](https://mne.discourse.group/t/ica-find-bads-exg-components-does-not-return-the-same-components-if-using-raw-used-for-fitting-or-same-raw-with-components-excluded/3803/4 "2021-10-13T13:08:19Z")
I am looking a bit more into the documentation. for `ica.find_bads_ecg`: ```python Detect ECG related components. Cross-trial phase statistics (default) or Pearson correlation can be used for detection. .. note:: If no ECG channel is available, routine attempts to create an artificial ECG based on cross-channel averaging. ``` To me, this clearly indicates that the method correlates with an ECG channel. This docstring doesn’t include the role of the EEG (data to be more general) channels. ---
**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\ **Post date:** [October 13, 2021, 1:16pm UTC](https://mne.discourse.group/t/ica-find-bads-exg-components-does-not-return-the-same-components-if-using-raw-used-for-fitting-or-same-raw-with-components-excluded/3803/5 "2021-10-13T13:16:12Z")
I just had a look at the code and it appears what I stated above is, in fact, incorrect. I was mislead by some similarly incorrect bits in the docstring, which I’ll fix. Another remark that doesn’t answer your question 🙂 > [@mscheltienne](#): > > ```python > eog_idx_raw, eog_scores_raw = ica.find_bads_eog(raw) > ecg_idx_raw, ecg_scores_raw = ica.find_bads_ecg(raw) > > ``` This is not “how it’s usually done”. Instead, the “good” practice is to create EOG and ECG epochs and run `find_bads_eXG()` on those epochs. Like I said, it doesn’t answer your question, but I just wanted to leave it here anyway. ---
**Author:** ![mscheltienne](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/mscheltienne/32/827_2.png) [@mscheltienne](https://mne.discourse.group/u/mscheltienne)\ **Post date:** [October 13, 2021, 1:20pm UTC](https://mne.discourse.group/t/ica-find-bads-exg-components-does-not-return-the-same-components-if-using-raw-used-for-fitting-or-same-raw-with-components-excluded/3803/6 "2021-10-13T13:20:55Z")
There is definitely some confusion coming from both the docstring and from the tutorial: [https://mne.tools/stable/auto\_tutorials/preprocessing/40\_artifact\_correction\_ica.html#using-an-eog-channel-to-select-ica-components](https://mne.tools/stable/auto_tutorials/preprocessing/40_artifact_correction_ica.html#using-an-eog-channel-to-select-ica-components) Btw, the tutorial does use the `raw` instance and not epochs created around `EOG` or `ECG` artifacts. And if what you stated above is incorrect, do you mean it does not use the EEG data for the correlation? In which case, why the difference? ---
**Author:** ![mscheltienne](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/mscheltienne/32/827_2.png) [@mscheltienne](https://mne.discourse.group/u/mscheltienne)\ **Post date:** [October 13, 2021, 1:47pm UTC](https://mne.discourse.group/t/ica-find-bads-exg-components-does-not-return-the-same-components-if-using-raw-used-for-fitting-or-same-raw-with-components-excluded/3803/7 "2021-10-13T13:47:03Z")
For my particular need, I found part of what I was looking for: `ica.labels_` It is documented, I didn’t pay enough attention. It gives me at least which components was excluded because it was related to EOG, and which was excluded because it was related to ECG. However, I am still missing the `scores`… ---
**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\ **Post date:** [October 13, 2021, 2:46pm UTC](https://mne.discourse.group/t/ica-find-bads-exg-components-does-not-return-the-same-components-if-using-raw-used-for-fitting-or-same-raw-with-components-excluded/3803/8 "2021-10-13T14:46:36Z")
My “good practices” reference is the MNE-BIDS-Pipeline. Here’s the relevant (granted, somewhat lengthy) code we use there: >