[FieldTrip] Issue reading data from old sqd file version

[Schoffelen, J.M. (Jan Mathijs)]

Dear Mrugank,

The coregistration procedure in kit/yokogawa/ricoh systems is notoriously complicated. I am not sure whether your troubles are related to that fact, rather than to a software incompatibility. That is, if there’s some MATLAB code that manages to read in the HPI’s and fiducials, I have no reason to assume that the other (non-functional) code would yield different information.

I assume that you have found this piece of documentation? https://www.fieldtriptoolbox.org/getting_started/meg/yokogawa/<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Fgetting_started%2Fmeg%2Fyokogawa%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cf3adcc3b17d24118435508dd751d2fde%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638795490393032730%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=hG9b6PCnOOo6uL4PKrt7AYH3FFGTRFf6enjMzWwXcBU%3D&reserved=0>

BW,
JM


On 5 Apr 2025, at 19:40, Mrugank Dake via fieldtrip <fieldtrip at science.ru.nl> wrote:

Hi everyone,

I am reading MEG data from .sqd for data collected at NYU using the MEG-KIT 160 system back in 2009. I believe there are multiple versions of sqd file and the current sqd file I am loading is an old version. I faced issues reading data from these sqd files using MNE python basically warning me that the file is old and the data read was indeed corrupt with neural channels and trigger channels all messed up in order. I switched to Fieldtrip and have been successfully able to read the data and do all the sensor-level analyses but I never really bothered wondering what goes inside the sqd files and what has changed over the versions.

Currently, I am trying out source reconstruction and from the looks of it, the HPI and fiducials I have recorded for the subjects back in 2009 don't look at all aligned with the gradiometer positions. I am unsure if this problem goes with the version of sqd file itself, but that's definitely on my mind and would be open to know if anyone here knows more about this.

Secondly, fieldtrip (the latest versions), provides two reading options for the Yokogawa MEG system: "external/yokogawa" and "external/yokogawa_meg_reader". By default Fieldtrip resorts to using yokogawa_meg_reader, but if I force fieldtrip to use "yokogawa", I get the following error:
"
    hdr = read_yokogawa_header(rawSqdPath)
         The P-code file
         /System/Volumes/Data/d/DATD/hyper/software/fieldtrip-20250318/external/yokogawa/GetMeg160SystemInfoM.p
         was generated prior to MATLAB version 7.5 (R2007b) and is no longer supported.  Use
         pcode to regenerate the file using MATLAB R2007b or later.

         Error in read_yokogawa_header (line 62)
         [id, ver, rev, sys_name] = GetMeg160SystemInfoM(fid);
"

And since I am working on a Mac with an M1 chip, I do not have an option to install MATLAB 2007b. Is there any other workaround? Or am I going in the wrong direction? What is the difference between these two reading options from Yokogawa?

Thanks in advance for taking time to read this long spiel and helping find a solution.

Best,
--
Mrugank Dake,
PhD Student,
Curtis Lab,
NYU Department of Psychology
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