<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"><div dir="ltr"><div>Hi Jeff,</div><div><br></div><div>Get the development version once this pull request is merged: <a href="https://secure-web.cisco.com/1-Ri8AtByEDiLNiyyV_2x9elDLcCbcU6fWmT3I-iIBMhyM-13OcHuK6j7qCO5AV_TrOfVn_pLmLpNUAgKc5Jx_cttEavgl6QrA0kEzvSlibTKS9u1jkSUP2C58hiSyE5KtbY5Mx7x3_07151f6syiJip-F0Nr1mKG9WIfgtqmCVtu64YqsAxpxGyWnM3-4U64EEe1-L5kwEB_KdkHRgD-E7X6NvLySXwQ29UI890hyfnQS5N5Y7wNs22YtZExhPcYGe3-vIPjYMqHezGDF9qUlQ/https%3A%2F%2Fgithub.com%2Fmne-tools%2Fmne-bids%2Fpull%2F638%2F"><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-bids/pull/638/</a></div></div><div><br></div><div>The warnings are expected as the files do not conform to the specification fully.</div><div><br></div><div>Hope this helps,</div><div>Mainak</div><div><br></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Nov 21, 2020 at 10:03 AM Stout, Jeff (NIH/NIMH) [C] <<a href="mailto:jeff.stout@nih.gov">jeff.stout@nih.gov</a>> wrote:<br></div><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"><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 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="gmail-m_2845131657444506060Signature">
<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>
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<b>Subject:</b> Mne_analysis Digest, Vol 154, Issue 27</font>
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Today's Topics:<br>
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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 <<a href="mailto:mainakjas@gmail.com" target="_blank">mainakjas@gmail.com</a>><br>
Subject: Re: [Mne_analysis] BIDS dataset issue - CTF {Disarmed}<br>
To: Discussion and support forum for the users of MNE Software<br>
<<a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.harvard.edu</a>>, Adam Li <<a href="mailto:adam2392@gmail.com" target="_blank">adam2392@gmail.com</a>>,<br>
Stefan Appelhoff <<a href="mailto:stefan.appelhoff@mailbox.org" target="_blank">stefan.appelhoff@mailbox.org</a>>, Richard H?chenberger<br>
<<a href="mailto:richard.hoechenberger@gmail.com" target="_blank">richard.hoechenberger@gmail.com</a>><br>
Message-ID:<br>
<CANzrpG12uBNfs=<a href="mailto:JCPWeT3ubaq8mm87bK4MxoG6f5VXzVUsWKkA@mail.gmail.com" target="_blank">JCPWeT3ubaq8mm87bK4MxoG6f5VXzVUsWKkA@mail.gmail.com</a>><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" target="_blank">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>
<a href="mailto:jeff.stout@nih.gov" target="_blank">jeff.stout@nih.gov</a> <<a href="http://secure-web.cisco.com/1AfBNSvmycq035OWEs5I1qEZ_VjVfXEP8m9l1uZHM_ZhswAzaC9RmOItzpuk8TuCcq7mKYzTUQCUAV6yFdsiIMqFxb207uCpJlQkbg00F-ar0wqpzso2-Tw-Vf7aqFrkb7iKtQVLlRZtbYqZnh__k8epVJpfnUNO5vSuiSyGujuZhJMIXwZYHZYJFyTvMIhhcn7FyAVkZWd_6oLHqK1uunXIgsd5cp9rIS4WF0GMHmN7iefHRTUf6hP9XpD4FgWaFJIukdbH0ba1mWMJR8ZF1Yw/http%3A%2F%2Fmailto%3Ajeff.stout%40nih.gov" target="_blank">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>
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