# trying to use ica.plot\_overlay **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [October 2, 2017, 10:55pm UTC](https://mne.discourse.group/t/trying-to-use-ica-plot-overlay/1323 "2017-10-02T22:55:40Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 2, 2017, 10:55pm UTC](https://mne.discourse.group/t/trying-to-use-ica-plot-overlay/1323/1 "2017-10-02T22:55:40Z")
Hi all, I'm having trouble following the tutorial for Artifact Correction with ICA. [http://martinos.org/mne/stable/auto\_tutorials/plot\_artifacts\_correction\_ica.html?highlight=ica%20fit](http://martinos.org/mne/stable/auto_tutorials/plot_artifacts_correction_ica.html?highlight=ica%20fit) I have epoched data where my artifact is timed to the event; I'm not investigating EOG artifact. I am able to use ica.plot\_properties and ica.plot\_sources fine. But when I try to do ica.plot\_overlay, it looks like it's not excluding my bad component. Since artifact is timed to event, average is just the averaged epochs. Attached: images from ica.plot\_properties, ica.plot\_sources, and ica.plot\_overlay. I'm not exactly clear on what picks and exclude expects (list, array, int?). Commands used are below. Thanks very much for any help! Megan random\_state = 23 n\_components =50 # if float, select n\_components by explained variance of PCA method = 'fastica' # for comparison with EEGLAB try "extended-infomax" here decim = 3 # we need sufficient statistics, not all time points -\> saves time reject=None # artifact is rather large, so don't want to reject it... ica = ICA(n\_components=n\_components, method=method, random\_state=random\_state) ica.fit(epochs, picks=picks\_meg, decim=decim, reject=reject) ica.plot\_sources(epochs) epoch\_avg= epochs.average() ica.plot\_sources(epoch\_avg, exclude=['35']) ica.plot\_properties(epochs, picks=35, psd\_args={'fmax': 35.},                     image\_args={'sigma': 1.}) # Following lines included with input and output: In [72]: ica.plot\_overlay(epoch\_avg, exclude=['35'], show=False) Transforming to ICA space (50 components) /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/lib/python3.5/site-packages/numpy/lib/arraysetops.py:375: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison   mask &= (ar1 != a) Zeroing out 0 ICA components Out[72]: \ In [74]: mne.\_\_version\_\_ Out[74]: '0.14.dev0' MEG Technician The Mind Research Network 1101 Yale Blvd. NE Albuquerque, New Mexico 87106 -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20171002/46125eae/attachment-0001.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20171002/46125eae/attachment-0001.html) -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2017-10-02 at 4.47.15 PM.png Type: image/png Size: 416492 bytes Desc: not available Url : [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20171002/46125eae/attachment-0003.png](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20171002/46125eae/attachment-0003.png) -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2017-10-02 at 4.14.55 PM.png Type: image/png Size: 610496 bytes Desc: not available Url : [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20171002/46125eae/attachment-0004.png](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20171002/46125eae/attachment-0004.png) -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2017-10-02 at 3.51.50 PM.png Type: image/png Size: 646946 bytes Desc: not available Url : [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20171002/46125eae/attachment-0005.png](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20171002/46125eae/attachment-0005.png) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 3, 2017, 8:15am UTC](https://mne.discourse.group/t/trying-to-use-ica-plot-overlay/1323/2 "2017-10-03T08:15:19Z")
hi Megan, can you try with: ica.plot\_sources(epoch\_avg, exclude=[35]) exclude should be in an int not a string. Alex ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 3, 2017, 9:40pm UTC](https://mne.discourse.group/t/trying-to-use-ica-plot-overlay/1323/3 "2017-10-03T21:40:24Z")
Thank you, Alex! That was my problem. Megan MEG Technician The Mind Research Network 1101 Yale Blvd. NE Albuquerque, New Mexico 87106