[Mne_analysis] Mne_analysis Digest, Vol 154, Issue 27 {Disarmed}
Stout, Jeff (NIH/NIMH) [C]
jeff.stout at nih.gov
Sat Nov 21 10:03:09 EST 2020
External Email - Use Caution
Hi Mainak,
Thanks for the response.
mne_bids.read_raw_bids(bidspath) << As you expected - fails with the same error regarding channel name matching
--This does work--
extra_params=dict(clean_names=True)
raw=mne_bids.read_raw_bids(bidspath, extra_params=extra_params)
There are several warnings listed, but appear to be specific to the bids file. This does not currently affect the data loading.
<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.
raw=mne_bids.read_raw_bids(bidspath, extra_params=extra_params)
<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.
Thank you for the help.
Jeff Stout [C]
Computer Systems Analyst
NIH/NIMH
Building 10 Room B1D65A
10 Center Dr.
Bethesda, MD 20892-1059
301-402-2362
________________________________
From: mne_analysis-request at nmr.mgh.harvard.edu <mne_analysis-request at nmr.mgh.harvard.edu>
Sent: Friday, November 20, 2020 11:21 PM
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Subject: Mne_analysis Digest, Vol 154, Issue 27
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Today's Topics:
1. Re: BIDS dataset issue - CTF {Disarmed} (Mainak Jas)
----------------------------------------------------------------------
Message: 1
Date: Fri, 20 Nov 2020 23:21:00 -0500
From: Mainak Jas <mainakjas at gmail.com>
Subject: Re: [Mne_analysis] BIDS dataset issue - CTF {Disarmed}
To: Discussion and support forum for the users of MNE Software
<mne_analysis at nmr.mgh.harvard.edu>, Adam Li <adam2392 at gmail.com>,
Stefan Appelhoff <stefan.appelhoff at mailbox.org>, Richard H?chenberger
<richard.hoechenberger at gmail.com>
Message-ID:
<CANzrpG12uBNfs=JCPWeT3ubaq8mm87bK4MxoG6f5VXzVUsWKkA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi Jeff,
I haven?t worked with this particular dataset but I?m guessing that we
might need to expose extra_params
<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>
for this function. Can you confirm if read_raw_bids fails as well but works
if you pass extra_params=dict(clean_names=True) ?
I?m ccing a couple of active developers who might be able to help implement
this soonest.
Best,
Mainak
On Thu, Nov 19, 2020 at 5:33 PM Stout, Jeff (NIH/NIMH) [C]
jeff.stout at nih.gov <http://secure-web.cisco.com/1AfBNSvmycq035OWEs5I1qEZ_VjVfXEP8m9l1uZHM_ZhswAzaC9RmOItzpuk8TuCcq7mKYzTUQCUAV6yFdsiIMqFxb207uCpJlQkbg00F-ar0wqpzso2-Tw-Vf7aqFrkb7iKtQVLlRZtbYqZnh__k8epVJpfnUNO5vSuiSyGujuZhJMIXwZYHZYJFyTvMIhhcn7FyAVkZWd_6oLHqK1uunXIgsd5cp9rIS4WF0GMHmN7iefHRTUf6hP9XpD4FgWaFJIukdbH0ba1mWMJR8ZF1Yw/http%3A%2F%2Fmailto%3Ajeff.stout%40nih.gov> wrote:
External Email - Use Caution
>
> I have downloaded the MOUS MEG dataset in BIDS format from the Donders
> institute. If I try to get the head transform using mne_bids, it throws an
> error on the channel name matching (see below). This has to do with how
> MNE reads the CTF MEG channel names. All of the channels have a number
> after the channel name (I was told this is the site specific serial
> number). This naming convention is different from that in the bids
> channels.tsv file.
>
>
>
> import mne_bids
> import os
> os.chdir('/data/MOUS/BIDS')
>
> bidspath=mne_bids.BIDSPath(subject='A2002',
> task='rest',
> root='/data/MOUS/BIDS',
> datatype='meg')
> mne_bids.get_head_mri_trans(bidspath)
>
>
>
> RuntimeError: Channels do not correspond between raw data and the
> channels.tsv file. For MNE-BIDS, the channel names in the tsv MUST be equal
> and in the same order as the channels in the raw data.
>
> 356 channels in tsv file:
> "/data/MOUS/BIDS/sub-A2002/meg/sub-A2002_task-rest_channels.tsv"
>
> --> ['UDIO001', 'UPPT001', 'UPPT002', 'SCLK01', 'BG1', 'BG2', 'BG3',
> 'BP1', 'BP3', 'BR1', 'BR2', 'BR3', 'G11', 'G12', 'G13', 'G22', 'G23',
> 'P11', 'P12', 'P13', 'P22', 'P23', 'Q11', 'Q12', 'Q13', 'Q22'
>
> ...................
>
>
>
> 356 channels in raw file: "sub-A2002_task-rest_meg.ds"
>
> --> ['UDIO001', 'UPPT001', 'UPPT002', 'SCLK01-177', 'BG1-4304',
> 'BG2-4304', 'BG3-4304', 'BP1-4304', 'BP3-4304', 'BR1-4304', 'BR2-4304',
> 'BR3-4304', 'G11-4304', 'G12-4304', 'G13-4304', 'G22-4304', 'G23-4304',
> 'P11-4304', 'P12-4304', 'P13-4304', 'P22-4304', 'P23-4304', 'Q11-4304',
> 'Q12-4304', 'Q13-4304', 'Q22-4304', 'Q23-4304', 'R11-4304', 'R12-4304',
> 'R13-4304', 'R22-4304', 'R23-4304', 'MLC11-4304', 'MLC12-4304',
> 'MLC13-4304', 'MLC14-4304', 'MLC15-4304'
>
>
>
>
> Not sure if its necessary, but I am using MNE version 0.21 on redhat 8.
>
>
>
> Thank you,
>
> Jeff Stout [C]
> Computer Systems Analyst
> NIH/NIMH
> Building 10 Room B1D65A
> 10 Center Dr.
> Bethesda, MD 20892-1059
> 301-402-2362
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