Hello,
I am using the review raw file option inorder to import my NEV data that are saved as
as a .mat file, but I keep getting the message "no valid recording field".
Could you guide me through this?
Thanks much.
Best,
Kostas
How are you trying to import this data?
If the recordings were saved using a Blackrock or Neuralynx devices you should use the original files format instead of exports as .mat files.
The Matlab .mat file format is not really "an EEG data format" but a "container". It can be used to store any arbitrary list of variables. There is very little chance that you can import into Brainstorm a random collection of variables from a .mat.
If you can't get access to the original recordings, please share a small example .mat file here (upload it somewhere and post the download link here), I might be able to suggest a solution for rewriting the file into something that Brainstorm can interpret.
Thanks.
The original recording files were saved using Open Ephys and are in *.continuous or *.spikes format,
so I loaded a NEV version (using Blackrock's NPMK scripts) in MatLab and saved it as a .mat.
Any suggestions?
Thanks again.
The NEV file was actually created from an older .nev file recorded with Blackrock device where the original data were removed and data from an Ephys .spikes file were pasted.
Sure, I can send a .mat file example, is a link for WeTransfer ok?
Thanks again.
Open Ephys binary file format is supported natively in Brainstorm, do not convert it to anything before linking the continuous files to your Brainstorm database. Select menu "Review raw file" and file format "Open Ephys flat binary".
These files are expected to have .dat extensions: rename the files before trying to open then in Brainstorm.
https://open-ephys.github.io/gui-docs/User-Manual/Recording-data/Binary-format.html
The Blackrock files (.nev) are also supported natively in Brainstorm (Review raw file > Blackrock Neuroport). The NPMK library is available as a Brainstorm plugin, imported automatically when need. If you can't link the Open Ephys files, use the .nev files.
Do not try to convert manually these files to .mat, this would make the import in Brainstorm much more complicated.
We are not familiar with the Open Ephys binary format, our files are saved in .continuous, .spikes format.
Is there a way to covert them to binary?
Thanks.
Unfortunately we are not familiar with this either...
@mpompolas ?
This is the file format we record at Open Ephys:
https://open-ephys.github.io/gui-docs/User-Manual/Recording-data/Open-Ephys-format.html
My other question is whether files that contain spike sorted data can be processed.
Here is an example:
https://we.tl/t-tU8p2Dgokm
It looks like there is a Matlab function readily available for reading this file format (analysis-tools/load_open_ephys_data.m at master · open-ephys/analysis-tools · GitHub), so it should not be too complicated to add the support for it in Brainstorm easily.
Please share one or more (short) example files that include continuous signals and event markers.
If possible, try first that you can actually load them with the Matlab function above.
My other question is whether files that contain spike sorted data can be processed.
The Plexon .plx are supported for continuous signals only.
At the moment, it is not possible to import anything but continuous signals into the Brainstorm database. Spike waveforms and clustering results are not supported.
Here is an example file .continuous that I have already loaded in Matlab using the load_ephys_data.m function:
After saving it as .mat file I was able to import it in Brainstorm, but only as timestamps and when I try to view the content it looks like it's empty.
I managed to load the data part of the .mat file and I am doing spike sorting using WaveClus.
It is not clear how the threshold value can be modified in the set parameters file.
The red line running along my raw data is set at +2 , whereas is negative (~-3) in the tutorial example.
One more thing, this time regarding the events file:
I have opened your example .csv file from the Pack lab paper and it seems that there are 96 times for each of the 9 experiment conditions, but is not clear to what they correspond and they seem completely random.
Thanks.
Unfortunately, I can't help you with WavClus.
I have opened your example .csv file from the Pack lab paper and it seems that there are 96 times for each of the 9 experiment conditions, but is not clear to what they correspond and they seem completely random.
"9 new types of events at the end of the events list (Stim On 1-9) that correspond to the screen location of the presented stimulus"
https://neuroimage.usc.edu/brainstorm/e-phys/Introduction#Import_events
I have tried also the the other two spike sorting algorithms but I get the following errors:
1)Ultramegasort2000
"Error: Line 406: plot_waveforms
** Too many input arguments."
2)Kilosort
When using it wihout GPU acivated
Error: [process_spikesorting_kilosort] Electrophysiology > Unsupervised Spike Sorting > KiloSort
** Error with Kilosort while training on the CPU
Ok, that but in the link's page, the numbers in the events matrix what do they correspond to?
Adding the reading for this file format is more complicated than reading only this single .continuous file, as according to the description of the file format, the entire folder should be read as one entity, one file per channel.
The simplest approach is probably to convert these recordings to the multiplexed "binary" format.
Have you tried the library documented here?
https://groups.google.com/g/open-ephys/c/OAvY0Ln0YA4?pli=1
I don't know.
@mpompolas @Sylvain?
Sorry, I don't understand.
I read the single .continuous file that I shared here and then I was able to to import it as raw data file in Brainstorm.
Yes, one file can be read independently, one channel per file, and this single signal could be made accessible in the Brainstorm database.
But one .continuous file does not represent a recording session. A recording session is the entire folder, with multiple .continuous files, a .events file, a .openephys file...
If implementing the support for this file format in Brainstorm, we should include all this, including the possibility to import the demultiplexed .continuous data as a single multiplexed file. Otherwise it wouldn't be possible to process or display multiple channels together in Brainstorm.
This requires more work than what I can dedicate to this topic at the moment. Unfortunately, the person who coded this e-phys toolbox is not working with us anymore.
Can you please try to convert your dataset to a binary file that can be imported in Brainstorm?
Ok, I will try to convert them in .dat.
If you know any MatLab library that does the conversion, I would be grateful.
Thanks.