Hi. trying to use kilosort for the unsupervised spike sorting it gives me the error of "not having the signal processing toolbox" in MATLAB even if I've already installed it. Did i do something wrong?
It says : "not having the signal processing toolbox"
The error above happened when we tried to run it in our server.
When I ran it locally in my laptop, there was no such an issue.
However, just when it was about to finish I got thes
e messages
Thanks much.
Kostas
Sorry i thought i attached the screenshot but i didn't. It's Just saynig "you don't have the signal processing toolbox" without writing down the line of the error. We tried ti use that toolbox in MATLAB and It actually runs without any problem
Indeed, this is a problem with the Kilosort2Neurpsuite.m script, part of KilosortWrapper which is needed to use Kilosort in Brainstorm.
From the Kilosort2Neurpsuite.m documentation
% The script has a high memory usage as all waveforms are loaded into
% memory at the same time. If you experience a memory error, increase
% your swap/cashe file, and increase the amount of memory MATLAB can use.
@GianlucaGamberinu, beside having installed the Signal Processing Toolbox, you need to tell Brainstorm that it should use it. Got to Brainstorm preferences ( File > Edit preferences) and check the Use Signal Processing Toolbox (Matlab) option:
Thanks.
K
Hello @Raymundo.Cassani
After running successfully Kilosort we found several problems on installing the Linux version Klusters on our server and decided to use Phy that is compatible with Kilosort 3
Are there any libraries available that can be used to import Kilosort 1 files on Phy?
Thanks much.
Klusters is not detected automatically in Linux, you would need to indicate the executable with the option Pick executable in the dialog window. In the case Brainstorm is run on a Server, you can define the path for Klusters before using it with:
bst_set('KlustersExecutable', KlustersExecutableFullPath);
This questions seems more appropriated for the phy developers
Any suggestion @mpompolas?
1 Like
We had a converter to phy AFAIR in the code, but the integration to phy was never completed.
I would suggest to check if that conversion still exists in the kilosort spike sorter function we have, and if not, i would suggest you try to check the neurosuite library or kilosort library themselves for converters to phy to use outside of brainstorm
2 Likes
Thanks very much both of you.
Kostas
Hello,
I have installed the phy plugin but I am not sure how I launch it to convert the Kilosort spike sorter result.
Should I do it from phython?
What is phy AFAIR?
Thanks,
Kostas
The phy plugin is installed as dependency of Kilosort. I checked the code, and it does not seem that the conversion from Kilosort to Phy was implemented in any process in Brainstorm.
"As Far as I Remember"