Importing a flat binary file format to brainstorm

Requests
1

I am using the open ephys aquisition board to record spontaneous and evoked LFP and spikes with linear neuronexus probes. i have recorded data in a flat binary format (more details about the format in the links below). Is there a way to import the raw data into brainstorm? i am not a coding expert and your help will be much appreciated...

flat binary format

load open ephys binary into matlab

Thanks ahead

2

We can add a native support in Brainstorm for this file format. The reference to the code and documentation you shared should be sufficient for me to write a reader.

However, I would need a short example dataset for developing and testing these new functions.
Could you upload an example file somewhere (as small as possible) and post the download link here?

Thanks
Francois

3

Thank you Francois for your quick reply
attached are 2 sample files containing 1 minute of spontaneous activity in the visual cortex followed by 1 minute of evoked response to visual stimuli. it was recorded with a 32 channel linear neuronexus probe, intan amplifier and open ephys aquisition box. the stimuli were also recorded in the aquisition via a ttl signal.

google drive link to files

Thanks

4

Thank you for the example files.

I wrote a first draft of a reader for the Open Ephys flat binary format:
IO: Support for Open Ephys flat binary file (.dat/.oebin) · brainstorm-tools/brainstorm3@ca16e96 · GitHub

I could not read the TEXT event labels, because the library matlab-npy does not support reading arrays of strings yet. I opened an issue about this on the github repository:
Support for arrays of strings? · Issue #13 · kwikteam/npy-matlab · GitHub

Simply update Brainstorm to get this update.
To load a file, right-click on a subject > Review raw file, select the file format "Open Ephys flat binary", then any continuous.dat file.

I am not familiar with this type of data, therefore there are probably things to fix.
Please share all your comments about this reader here (eg. event names should be changed, folder name should be changed, channel types should be grouped differently, missing events, etc.)

image
image1074×449 85.1 KB

5

Thank you vert much! this has been a huge help for me
regarding the channels - i'm trying to re-order the channels so i can visualize the traces in an anatomical order, but when i change the index number, it doesn't move the trace to the desired location, instead it moves only the "CH" label. i've attached pictures that show what happens

channel map after change channel map before change

for example, this is the order of the linear edge 32 channel neuronexus probe i would like to use:
[20, 21, 29, 22, 28, 27, 31, 23, 18, 24, 26, 25, 30, 19, 32, 17,...
1, 16, 3, 14, 9, 4, 8, 13, 10, 5, 7, 12, 2, 6, 11, 15, 33 : 40];

6

By default, Brainstorm always displays the channels in the order in which they are saved in the files.
This is not always convenient for reviewing the data.

The easier solution for changing the order in which the channels appear in the time series figures is to create a custom montage:
https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor#Custom_montage