Cannot read headshape for Yokogawa recordings


I have Yokogawa (160-channel) MEG recordings, which I have preprocessed and analyzed in the frequency domain using Fieldtrip.
I would like to use Brainstorm for source analysis, and I do not have MRI scans for my participants, but 3D head shape recordings obtained with a Polhemus system. However, when importing my MEG files into Brainstorm (review RAW files), I can only choose between .con (raw recordings) and .mrk (marker measurements), but not .hsp files (which contain the digitized headshape) – therefore I get an error about the absence of digitized head points and cannot continue. Is there a way to add these files in?

Thank you,


Where these files saved directly by the Yokogawa system?
The only way of using the with the MEG recordings would be to have them registered with the MEG sensors positions (all these 3D points should be in the same coordinate system).

Could you please share a small example dataset (short MEG recordings + hsp file)?
Upload the file somewhere and post the download link here.

Thanks a lot, Francois. Yes, the .con files are the raw Yokogawa recordings.
Here is a folder with an example.
Unfortunately, the recording file (.con) isn't super short, but I hope it's alright. I have added other files that might be relevant.
Thank you!

Yes, the .con files are the raw Yokogawa recordings.

Are the hsp saved by the Yokogawa software?
How is it coregistered with the MEG sensors positions saved in the Yokogawa recordings?

No, the hsp files come from the digitizer. The mrk and mri files are from the Yokogawa system and are those coming from the coregistration procedure. Thanks.

I could find two functions reading these hsp/elp files together with the .con file:

But I could not find any proper documentation on how those files are generated.
What is the procedure you are using to generate these files?
Does this come from any user documentation from the Yokogawa company?
I need some more information about the protocol you are using to get these two undocumented extra files, to understand how to use them correctly. The more details the better...


Thank you.
Unfortunately, I am not able to provide much more information than this, as I was in the lab for just a limited amount of time and followed some established procedures, so I am not extremely familiar with these matters, and I should probably ask others about this.
I did know of the resources you linked, especially the second one, which I have already used. I was just wondering whether I was missing something obvious as I was trying to move to Brainstorm for this analysis, but I guess there might not be a very straightforward way of implementing all the required information because of how it was acquired.

If it's in MNE-Python, it can be implemented in Brainstorm as well.
I'm just not sure what is the correct way of doing this: which priority to give to which type of information, what to show in the interactive messages...
This does not seem to be a procedure documented by Yokogawa. Where are the "established procedures" you mention coming from? Are they related with only one lab?

I realized this actually corresponds to a mechanism that had been implemented a while ago to co-register NYU recordings, but with different file names and formats. I guess the Polhemus digitizer was upgraded and the acquisition procedure too?

I updated the Yokagawa/KIT reader to support the "new" hsp/elp files:

Please update Brainstorm and try again.
Double-check carefully the registrations you obtain, as I may have left some bugs in there, I don't have anything to compare the results I get with.

Thank you so much, Francois! I will be able to give it a try in the next weeks and come back to you. In the meantime, I really appreciate your help and support.

Hi all,

I would assuming that my question is a follow-up on this topic, but correct me if I am wrong...

We performed MEG-recordings with a Yokogawa system, in which the "Third-party export" function is not available. We have both patient-specific MRI scans as well as digitized headshapes. However, the latter were not aquired using a Polhemus but a Zebris system, resulting in sfp-files. Taken together we end up with a folder containing:

  • .con file (MEG data of 1 recording run)
  • .mrk file (marker position of that run)
  • .sfp file (with headhsape/fiducial information)

Unfortunately, we still get the Brainstorm error message that "This file has not been exported properly from the Yokogawa software. The MEG/MRI co-registration information is missing. [...]"

Given that in the alternative startegy it is mentioned that the following files - .mrk, .con, .txt/.elp/.hsp = Polhemus file - have to be included in the same folder and that Zebris provides us with .sfp/.epf/.cms files, we thought tht this might be the source of the problem?

Of note, the error message remains even if we change those file formats to .txt ...

Thanks for your help and greetings from the Brainstorm-Workshop at PracticalMEEG!


Sorry for the response delay...

Can you please share a short example file?
Zip a folder with all the files together, upload it somewhere and post the download link here.
(please make use a recording duration as short as possible)


I tried to add the support for reading your .sfp file instead of the .elp file, but I'm not sure what I did is correct.

Please update Brainstorm and let me know if this seem any better.
Note that you have to remove one of the two .mrk files from the folder that you shared.

Hi Francois,

I tried it with 3 different data sets now and it seems to work.
Thank you so much for your help!!

Greetings from Berlin :slight_smile:

Dear Francois & Brainstorm Team:

Following up on this: I have a Yokogawa dataset without individual .sfp or .elp files and the data was not exported from the acquisition system as described in the tutorial. So, ultimately, I only have .con and .mrk files for each of the runs as well as a subject MRI for each of the subjects. Is there a way - even though of course much less accurate - to still perform source reconstruction for these files ?
Thank you very much in advance!


Hi @BahneBahners, is it possible for you to share one example of the files you have?
If so, update it in any cloud storage service and share the link (either in the post or as direct message)

Hi @Raymundo.Cassani, Thank you so much for your reply. I sent you a direct method. Let me know, if you need further information. Thanks again, Bahne

Do you have any information regarding the points in the Yokogawa_file-coregis.txt file?

It has the location for 5 points, however, they do not seen to be the locations for the 5 Head Position Indicators (HPI)

  • LPA : Left PreAuricular
  • RPA : Right PreAuricular
  • CPF : Center PreFrontal
  • LPF: Left PreFrontal
  • RPF: Right PreFrontal

Hi @Raymundo.Cassani

I asked my colleague who was involved with data acquisition. The -coregis.txt file is apparently only a *.txt file version of the *.mrk file. He says that only coils 1-3 are relevant and that they are in the following order: LPA, RPA, NA.


Hi @Raymundo.Cassani , anything new on your end? I am trying to move forward with that project.
What happens, if I just review the raw file without the required files ? Does Brainstorm take some kind of "Yokogawa standard coordinates" for nasion, lpa and rpa and coregisters these with the MRI fiducials? Do you think, I could use the information in the txt file/ .mrk file for the co-registration in addition to improve the co-registration? Thank you so much for your support, Bahne