<p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p><div dir="ltr">Hi,<br><div><br></div><div>I investigated a little more about the wrong bemforming reconstruction (it was the same with different beamforming methods). </div><div>I imported the source model and the bem from mne to fieldtrip but I load the grad structure directly from Fiedltrip and as you can see in the mne_.jpg they don t have the same coordinates. Then I took the inverse of the transformation matrix ctf_head_t and applied to the headmodel and sourcemodel to get cft_aligned.jpg. I finally performed the DICS beamoforming with exactly the same CSD data and I get the peak on the frontal right hemisphere this time, like I was trying to replicate.</div><div><br></div><div>On the other hand if I apply a different transformation matrix to the grad ( to bring everything aligned with the imported headmodel and sourcemodel from mne) the peak is on the frontal left. So I guess I have a problem with the coordinates and there is not flipping or other issue in the source model or beamforming method.</div><div><br></div><div>Should I bring everything to ctf coordinates in mne ? do you know why this happened?</div><div><br></div><div>thanks</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Il giorno mer 2 dic 2020 alle ore 22:05 Eric Larson <<a href="mailto:larson.eric.d@gmail.com">larson.eric.d@gmail.com</a>> ha scritto:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p><p></p><div dir="ltr"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Do you have another idea where there could be a flip right/ left ? mri conventions, coordinates and so on<br></div></blockquote><div><br></div><div>1. To check these I would use `plot_alignment` in MNE-Python to check to make sure everything is defined properly. Then if you use the same src/trans/bem in make_forward_solution it should all be correct.</div><div>2. It's possible we are hitting some rank bug, see for example <a href="https://secure-web.cisco.com/1o_lH-k4rHSYPhDzjd__shBfyihVFumwSV_W9W_OMpoll5YYDcxtValRvb9okGVShJsvTRZCV6hb00YuaKjRtY-iOGJ3UoWZUpZ-sdLKjb4NlS51yYibeBLjxDpYR8YHYFgdj8D7b7UBs_NcHgjB2mGiF6YU_LykyrQMfZxUsLXBxZm5XvNZJoeOUimYbUdIFjPCJYD8x2jC1QNM1uPhqxnZsey0r8j7ToEQaxHBPbfQgZimyQvYW3T2JOGFQNGTSidhSMqzFkqKwTkLEIgm4ng/https%3A%2F%2Fgithub.com%2Fmne-tools%2Fmne-python%2Fpull%2F8594" target="_blank"><font color="red"><b>MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be</b></font> https://github.com/mne-tools/mne-python/pull/8594</a></div><div>3. You might need to use reduce_rank=True as in <a href="https://secure-web.cisco.com/13MsdCox5KdzEpkrHMoAukWFSeMSbQzGuM0nRfQFGr7oaJ8uyROq_2nFM41F8P2DmnxF03hvqeB8I0Ao6OUFluoTL9Mtka3zYJqHIp8K7eRUGxWXuR5BskgNzlfNwDJ6UK8oEb3tjXAaNlPBQy3X43EbHnN0_YKdHKGexmausx9AJqM_zI3M8iTdyon8qNz_IBnSjLgtOEpgAxgt2Uz4R7JQe4ebaLWv7xbMCT5XU6BZH953ICan7D2pyaeQVFeFQOgG_0jSTj5bNrIUrrEWNHg/https%3A%2F%2Fmne.tools%2Fdev%2Fauto_examples%2Finverse%2Fplot_dics_source_power.html%23sphx-glr-auto-examples-inverse-plot-dics-source-power-py" target="_blank">this example</a>. It's possible FT reduces rank by default and we do not, so make sure parameters match.</div><div>4. Can you also try doing `real_filter=True` to see if it helps? We are looking into orientation selection for the complex filters currently, it seems like FT produces better results for the complex.<br></div><div><br></div><div>Eric</div><div><br></div></div></div>
_______________________________________________<br>
Mne_analysis mailing list<br>
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
<a href="https://secure-web.cisco.com/1t8xxHoBwdbRXXkNebWur4tr3Bb85PILfgviCsaN7en-mhn7BUAiu2_Yl67YGlOmYSCfPj5TKoW-t5iMF4zWIJV3od5hVKZha5T8HQPvAS4r8KupxsDP0tXKIa1bP4VEa5RrXyA287jTllfwOOizOjC7qj3ayEOEs9fUtNEsdAOZfdL5slW0uRFp4h3YxxpVvIx7zT-NGofaB2OsgtFePzPC13ioLtCGr9wh31O1zkjtawBrbf4oWYepc-V1IOkObMATRS89VJmiuGZ7iiO6Ymw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Fmne_analysis" rel="noreferrer" target="_blank"><font color="red"><b>MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be</b></font> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div>