[Mne_analysis] Mne_analysis Digest, Vol 154, Issue 27 {Disarmed}

Sat Nov 21 11:43:32 EST 2020

        External Email - Use Caution        

Hi Jeff,

Get the development version once this pull request is merged:
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

The warnings are expected as the files do not conform to the specification
fully.

Hope this helps,
Mainak

On Sat, Nov 21, 2020 at 10:03 AM Stout, Jeff (NIH/NIMH) [C] <
jeff.stout at nih.gov> wrote:

>         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
> *To:* mne_analysis at nmr.mgh.harvard.edu <mne_analysis at nmr.mgh.harvard.edu>
> *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
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
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