Write a getting started with QuSpin OPM data

[robertoostenveld]

I am now discussing this with @dbobela406 and details will follow here. Note that this is not only about writing some documentation, but the supporting code should of course also be implemented.

[robertoostenveld]

See also mne-tools/mne-python#8671

[dbobela406]

Hi Robert et al.

Dave Bobela here from QuSpin. To kick things off on this thread, I'm uploading some example data from the QuSpin Neuro-1 system, so that users can understand the formatting, and begin writing importer scripts for your application. This should cover the use case of saving data directly from QuSpin user interface.

I'm also uploading a pdf file that documents the data formatting--please refer to this for a general overview. If I've forgotten something, or if you need clarification, please reach out.

Briefly, the QuSpin N1 user interface generates two files when saving data: one file that contains sensor measurement data (a labview ".lvm" file), and one file containing sensor and system level information. Here are the example files (note, I had to attach a .txt extension to the .lvm file to satisfy GitHub's requirements. Remove this extension):

QuSpin Example N1 Dataset_10-14-24_array1.lvm.txt

QuSpin Example N1 Dataset_10-14-24_array1_calibrations.txt

QuSpin_Data_File_Format_Description.pdf

[Mettphysik]

To kick things off on this thread, I'm uploading some example data from the QuSpin Neuro-1 system, so that users can understand the formatting, and begin writing importer scripts for your application. This should cover the use case of saving data directly from QuSpin user interface.

Is it possible that the .lvm file is corrupted? I am using lvm-read (https://pypi.org/project/lvm-read/) which works fine with my own Neuro-1 data, but not with the provided file. It looks like there are 5 data points for the channels X1 to Y62 but only 4 data points for the remaining channels.

I'm not directly working on this issue, but I guess this might still be of interest here.

[dbobela406]

Thanks Mettphysik for pointing this out and indeed you were correct about the file. I updated the links from my September 26th post, above, with valid data that can be opened using lvm-read (https://pypi.org/project/lvm-read/).

[robertoostenveld]

Dear Dave,

Sorry for not following this up as planned. At the moment I am sick at home and not able to work on this. I hope to be back to work soon and will then pick this up again.

best
Robert

[dbobela406]

Hi Robert, No worries at all. Hope it’s not serious , and that a full recovery is on the horizon! Best regards, Dave David C. Bobela Physicist, QuSpin Inc., 331 South 104th Street, Suite 130 Louisville, CO 80027 Ph: 720-982-8807 Email: ***@***.*** ***@***.***> Website: http://www.quspin.com/

…

On Tue, Oct 15, 2024 at 2:37 AM Robert Oostenveld ***@***.***> wrote: Dear Dave, Sorry for not following this up as planned. At the moment I am sick at home and not able to work on this. I hope to be back to work soon and will then pick this up again. best Robert — Reply to this email directly, view it on GitHub <#807 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BLLYAB5T4WX3EHG6LPJ2HW3Z3TH2XAVCNFSM6AAAAABOSGUBLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJTGI2DMNJVGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[robertoostenveld]

It has been some time that we initiated worked on this, but now with the QuSpin system installed in Aarhus we have renewed motivation to get this resolved. @laurabpaulsen, @ualsbombe and @sarangnemo have shared some of their data with me and I will work with them on implementing the getting started documentation.