BIDS dataset issue - CTF

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20201119/b92b3dd2/attachment.html

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

        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