[Mne_analysis] BIDS dataset issue - CTF {Disarmed}

Mainak Jas mainakjas at gmail.com
Fri Nov 20 23:21:00 EST 2020
Search archives:

        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
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20201120/b7371e8a/attachment-0001.html 


More information about the Mne_analysis mailing list