<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr"><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 style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Hi Mainak, <br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Thanks for the response. <br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
mne_bids.read_raw_bids(bidspath) << As you expected - fails with the same error regarding channel name matching<br>
</div>
<div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
--This does work--<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
extra_params=dict(clean_names=True)
<div>raw=mne_bids.read_raw_bids(bidspath, extra_params=extra_params)</div>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
There are several warnings listed, but appear to be specific to the bids file. This does not currently affect the data loading.<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<ipython-input-41-4e9b69de2f62>:2: RuntimeWarning: The BIDS dataset contains channel types in lowercase spelling. This violates the BIDS specification and will raise an error in the future.
<div> raw=mne_bids.read_raw_bids(bidspath, extra_params=extra_params)</div>
<div><ipython-input-41-4e9b69de2f62>:2: RuntimeWarning: The BIDS dataset contains channel types in lowercase spelling. This violates the BIDS specification and will raise an error in the future.</div>
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Thank you for the help.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div id="Signature">
<div>
<div></div>
<div style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
Jeff Stout [C]</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
Computer Systems Analyst</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
NIH/NIMH</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
Building 10 Room B1D65A</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
10 Center Dr.</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
Bethesda, MD 20892-1059</div>
<div style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
301-402-2362<br>
</div>
</div>
</div>
</div>
<div id="appendonsend"></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> mne_analysis-request@nmr.mgh.harvard.edu <mne_analysis-request@nmr.mgh.harvard.edu><br>
<b>Sent:</b> Friday, November 20, 2020 11:21 PM<br>
<b>To:</b> mne_analysis@nmr.mgh.harvard.edu <mne_analysis@nmr.mgh.harvard.edu><br>
<b>Subject:</b> Mne_analysis Digest, Vol 154, Issue 27</font>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<div class="PlainText">Send Mne_analysis mailing list submissions to<br>
mne_analysis@nmr.mgh.harvard.edu<br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="https://secure-web.cisco.com/1QfHx_Fg2cA1wHXT-9e7TmBcwcL8jzljNo_WyJqPcPwCyHjZZHzCdPo9Z4pBLvSD1eSppvbyf6qadXne84-xl7z53ZEwaQnZmLn5C2xPCwiPk6nd79zvaoOUGl7DFh55D8_XDsOtIlPDKMo_ueO_FC514byaO40xJ9ymoXc6ifxL_hhj3HQbRbYTZTni-i1rHlSE4r6OKf_zQVULDP_yzfG0EXFFOHqwZtrhCc9s9muc-IR9g2YORQYLS7kaMzNFAYB-tAdwhtZiHopcf_J0vng/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Fmne_analysis"><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><br>
or, via email, send a message with subject or body 'help' to<br>
mne_analysis-request@nmr.mgh.harvard.edu<br>
<br>
You can reach the person managing the list at<br>
mne_analysis-owner@nmr.mgh.harvard.edu<br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of Mne_analysis digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Re: BIDS dataset issue - CTF {Disarmed} (Mainak Jas)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 20 Nov 2020 23:21:00 -0500<br>
From: Mainak Jas <mainakjas@gmail.com><br>
Subject: Re: [Mne_analysis] BIDS dataset issue - CTF {Disarmed}<br>
To: Discussion and support forum for the users of MNE Software<br>
<mne_analysis@nmr.mgh.harvard.edu>, Adam Li <adam2392@gmail.com>,<br>
Stefan Appelhoff <stefan.appelhoff@mailbox.org>, Richard H?chenberger<br>
<richard.hoechenberger@gmail.com><br>
Message-ID:<br>
<CANzrpG12uBNfs=JCPWeT3ubaq8mm87bK4MxoG6f5VXzVUsWKkA@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
External Email - Use Caution <br>
<br>
Hi Jeff,<br>
<br>
I haven?t worked with this particular dataset but I?m guessing that we<br>
might need to expose extra_params<br>
<<a href="https://secure-web.cisco.com/1iiWGk5d9MI8HaczNZ5wX5TojCcoystXkIdaNQlmjAhsb8O-jrPmnl2V-EoOXe-TtXSzqXRxLwa_ebQ5jQubsQZZ6oh_0Go3PJJX2HFpHEr6NnE-D2rOOvYp49vtGEMzcf_BIOaBPUGeLuEWn7W5LZJGxRhWVu1xRdIbdqz9vxlqlATgH2tSV1UchRzfMPdODIbpdYc0BVPjPl_Y3NB4SrAsl6LsSdT512MdqUnLDl19VydJop8hdUb3jU13TQsgHALiwuwGHfELqLzqs0-QPJA/https%3A%2F%2Fgithub.com%2Fmne-tools%2Fmne-bids%2Fblob%2Ff16da6a21f6d387eaa4997414eb9ea2dac3f8c37%2Fmne_bids%2Fread.py%23L590">https://secure-web.cisco.com/1iiWGk5d9MI8HaczNZ5wX5TojCcoystXkIdaNQlmjAhsb8O-jrPmnl2V-EoOXe-TtXSzqXRxLwa_ebQ5jQubsQZZ6oh_0Go3PJJX2HFpHEr6NnE-D2rOOvYp49vtGEMzcf_BIOaBPUGeLuEWn7W5LZJGxRhWVu1xRdIbdqz9vxlqlATgH2tSV1UchRzfMPdODIbpdYc0BVPjPl_Y3NB4SrAsl6LsSdT512MdqUnLDl19VydJop8hdUb3jU13TQsgHALiwuwGHfELqLzqs0-QPJA/https%3A%2F%2Fgithub.com%2Fmne-tools%2Fmne-bids%2Fblob%2Ff16da6a21f6d387eaa4997414eb9ea2dac3f8c37%2Fmne_bids%2Fread.py%23L590</a>><br>
for this function. Can you confirm if read_raw_bids fails as well but works<br>
if you pass extra_params=dict(clean_names=True) ?<br>
<br>
I?m ccing a couple of active developers who might be able to help implement<br>
this soonest.<br>
<br>
Best,<br>
Mainak<br>
<br>
On Thu, Nov 19, 2020 at 5:33 PM Stout, Jeff (NIH/NIMH) [C]<br>
jeff.stout@nih.gov <<a href="http://secure-web.cisco.com/1AfBNSvmycq035OWEs5I1qEZ_VjVfXEP8m9l1uZHM_ZhswAzaC9RmOItzpuk8TuCcq7mKYzTUQCUAV6yFdsiIMqFxb207uCpJlQkbg00F-ar0wqpzso2-Tw-Vf7aqFrkb7iKtQVLlRZtbYqZnh__k8epVJpfnUNO5vSuiSyGujuZhJMIXwZYHZYJFyTvMIhhcn7FyAVkZWd_6oLHqK1uunXIgsd5cp9rIS4WF0GMHmN7iefHRTUf6hP9XpD4FgWaFJIukdbH0ba1mWMJR8ZF1Yw/http%3A%2F%2Fmailto%3Ajeff.stout%40nih.gov">http://secure-web.cisco.com/1AfBNSvmycq035OWEs5I1qEZ_VjVfXEP8m9l1uZHM_ZhswAzaC9RmOItzpuk8TuCcq7mKYzTUQCUAV6yFdsiIMqFxb207uCpJlQkbg00F-ar0wqpzso2-Tw-Vf7aqFrkb7iKtQVLlRZtbYqZnh__k8epVJpfnUNO5vSuiSyGujuZhJMIXwZYHZYJFyTvMIhhcn7FyAVkZWd_6oLHqK1uunXIgsd5cp9rIS4WF0GMHmN7iefHRTUf6hP9XpD4FgWaFJIukdbH0ba1mWMJR8ZF1Yw/http%3A%2F%2Fmailto%3Ajeff.stout%40nih.gov</a>>
wrote:<br>
<br>
External Email - Use Caution<br>
><br>
> I have downloaded the MOUS MEG dataset in BIDS format from the Donders<br>
> institute. If I try to get the head transform using mne_bids, it throws an<br>
> error on the channel name matching (see below). This has to do with how<br>
> MNE reads the CTF MEG channel names. All of the channels have a number<br>
> after the channel name (I was told this is the site specific serial<br>
> number). This naming convention is different from that in the bids<br>
> channels.tsv file.<br>
><br>
><br>
><br>
> import mne_bids<br>
> import os<br>
> os.chdir('/data/MOUS/BIDS')<br>
><br>
> bidspath=mne_bids.BIDSPath(subject='A2002',<br>
> task='rest',<br>
> root='/data/MOUS/BIDS',<br>
> datatype='meg')<br>
> mne_bids.get_head_mri_trans(bidspath)<br>
><br>
><br>
><br>
> RuntimeError: Channels do not correspond between raw data and the<br>
> channels.tsv file. For MNE-BIDS, the channel names in the tsv MUST be equal<br>
> and in the same order as the channels in the raw data.<br>
><br>
> 356 channels in tsv file:<br>
> "/data/MOUS/BIDS/sub-A2002/meg/sub-A2002_task-rest_channels.tsv"<br>
><br>
> --> ['UDIO001', 'UPPT001', 'UPPT002', 'SCLK01', 'BG1', 'BG2', 'BG3',<br>
> 'BP1', 'BP3', 'BR1', 'BR2', 'BR3', 'G11', 'G12', 'G13', 'G22', 'G23',<br>
> 'P11', 'P12', 'P13', 'P22', 'P23', 'Q11', 'Q12', 'Q13', 'Q22'<br>
><br>
> ...................<br>
><br>
><br>
><br>
> 356 channels in raw file: "sub-A2002_task-rest_meg.ds"<br>
><br>
> --> ['UDIO001', 'UPPT001', 'UPPT002', 'SCLK01-177', 'BG1-4304',<br>
> 'BG2-4304', 'BG3-4304', 'BP1-4304', 'BP3-4304', 'BR1-4304', 'BR2-4304',<br>
> 'BR3-4304', 'G11-4304', 'G12-4304', 'G13-4304', 'G22-4304', 'G23-4304',<br>
> 'P11-4304', 'P12-4304', 'P13-4304', 'P22-4304', 'P23-4304', 'Q11-4304',<br>
> 'Q12-4304', 'Q13-4304', 'Q22-4304', 'Q23-4304', 'R11-4304', 'R12-4304',<br>
> 'R13-4304', 'R22-4304', 'R23-4304', 'MLC11-4304', 'MLC12-4304',<br>
> 'MLC13-4304', 'MLC14-4304', 'MLC15-4304'<br>
><br>
><br>
><br>
><br>
> Not sure if its necessary, but I am using MNE version 0.21 on redhat 8.<br>
><br>
><br>
><br>
> Thank you,<br>
><br>
> Jeff Stout [C]<br>
> Computer Systems Analyst<br>
> NIH/NIMH<br>
> Building 10 Room B1D65A<br>
> 10 Center Dr.<br>
> Bethesda, MD 20892-1059<br>
> 301-402-2362<br>
> _______________________________________________<br>
> Mne_analysis mailing list<br>
> Mne_analysis@nmr.mgh.harvard.edu<br>
> <a href="https://secure-web.cisco.com/1Yic72ZSKkWd59BwUV5sZxYTKFInbs84fmQrv-i-IdZqe1EvwGsFKXD3DoCjnYc4V2yW4NFhrGUP6J63lOcX7LkWoWqFFjVEkNjC0FjLGxGC7QnkGBhE2vgBeuJRzg9TfSaU-IFDSWl5ggNKWPEtmsSvi297R5GLWfjn-l129HFHgdCPCEXmesSp8XwHPpDo48dVUUQGs1dNugbihGV49YsspLfiwOu6_nTBmELnyNOwFacLGmC2xamINV46L6tiL-UYAP4ejMkxhUep-kcCwKQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Fmne_analysis">
https://secure-web.cisco.com/1Yic72ZSKkWd59BwUV5sZxYTKFInbs84fmQrv-i-IdZqe1EvwGsFKXD3DoCjnYc4V2yW4NFhrGUP6J63lOcX7LkWoWqFFjVEkNjC0FjLGxGC7QnkGBhE2vgBeuJRzg9TfSaU-IFDSWl5ggNKWPEtmsSvi297R5GLWfjn-l129HFHgdCPCEXmesSp8XwHPpDo48dVUUQGs1dNugbihGV49YsspLfiwOu6_nTBmELnyNOwFacLGmC2xamINV46L6tiL-UYAP4ejMkxhUep-kcCwKQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Fmne_analysis</a><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://secure-web.cisco.com/1e4CtlxoAzH6xypneUopUDKMKK0LgZBjXJJMztIvQzaw9lNN9Dj3yW8nTXdaapX1wNWmVAvd6sQA8nMNsph6L3Y6dtciFkYy9IX88R8OfeiFPMDWQmGj8pxNVd1eR3aU-X4N2iDu7alTLxvQKgCKJZ-vzvhmKOKGviz76abymefvkk4COPovACaepaq35Q2icC0UAmCJaMvTL3SbqZo48fGrbanWYw61O8EXKIzo58XJUUez2lf7Z5fizdwdu_oWcZ89NIfDXMgqpjdFwqNAOAA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Fmne_analysis%2Fattachments%2F20201120%2Fb7371e8a%2Fattachment.html"><font color="red"><b>MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be</b></font>
http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20201120/b7371e8a/attachment.html</a>
<br>
<br>
------------------------------<br>
<br>
_______________________________________________<br>
Mne_analysis mailing list<br>
Mne_analysis@nmr.mgh.harvard.edu<br>
<a href="https://secure-web.cisco.com/1QfHx_Fg2cA1wHXT-9e7TmBcwcL8jzljNo_WyJqPcPwCyHjZZHzCdPo9Z4pBLvSD1eSppvbyf6qadXne84-xl7z53ZEwaQnZmLn5C2xPCwiPk6nd79zvaoOUGl7DFh55D8_XDsOtIlPDKMo_ueO_FC514byaO40xJ9ymoXc6ifxL_hhj3HQbRbYTZTni-i1rHlSE4r6OKf_zQVULDP_yzfG0EXFFOHqwZtrhCc9s9muc-IR9g2YORQYLS7kaMzNFAYB-tAdwhtZiHopcf_J0vng/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Fmne_analysis"><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><br>
<br>
End of Mne_analysis Digest, Vol 154, Issue 27<br>
*********************************************<br>
</div>
</span></font></div>
</body>
</html>