Spike Sorting on Brainstorm Install w/o Matlab

Requests
1

I am a brand new user to Brainstorm, I just installed it to test it out as an alternative to spike sort/view/analyize my electrophysiology data. I did the install without Matlab license (MCR 2015b 9.0 version).

I try to run any of the 3 pre-instlaled spike sorters (Wave_clus/UltraMegaSort2000/Kilosort) and they all give the same error.

[process_spikesorting-waveclus] Electrophysiology > Unsupervised Sorting > WaveClus

This function is not available in the compiled version of Brainstorm.

Is there any chance of having this avilable in the compiled version, or do I need a Matlab license to access this feature?

2

Hello,

Sorry, we have no plans of supporting the compiled versions for these processes. You will need a Matlab license. The reason is that we are using existing external libraries for spike sorting and it would be a nightmare to start compiling them all every time either we update Brainstorm or these libraries are updated and then packaging everything together, notwithstanding the potential licensing issues and increase in file size of our installer.

Sorry for the inconvenience,
Martin

3

Hi Martin, I am using BrainStorm in MATLAB interface, but I don't see the option electrophysiology to run spike sorting. Help me out. Thanks.

4

Hi, check that your Brainstorm version is the latest.

You can find information related to the electrophysiology functions in Brainstorm in the e-phy tutorial:
https://neuroimage.usc.edu/brainstorm/e-phys/Introduction

5

Thank you so much for your reply. I went through the E-Phys page before. This is what I see:
image

6

Within the /process/functions I see the following codes for spike sorting:
image

But when I look at the plugins, I don't see the electrophysiology options.
image

So I don't know how to access the spike sorting functions.

7

Those processes are located within the Pipeline editor in the Electrophysiology category.

ephy
ephy754×984 46.9 KB

9

Thank you so much. When I am running with the test data provided with brainstorm, the options seem to show up. When I load my own data, this option does not show up. The only difference I am able to see is that in the test example the data is loaded as "Link to raw file". When I load preselected channel data the spike sorting option doesn't show up. How do I troubleshoot this?

Thanks.

10

Hello,

So I figured that spike sorting toolboxes only work if the data is loaded in as raw (even if the epochs are clipped based on markers). I was able to get past that roadblock. I was able to run UltraMegaSort, but I get this error:
image

Kindly help.

Thanks.

11

We recommend that before trying to use the tools from the e-phys toolbox, you start by learning how to use Brainstorm with the introduction tutorials (section "Get started"), following them at least until #19.
https://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile#Review_vs_Import

I was able to run UltraMegaSort, but I get this error:

This function was written by @mpompolas, I have never used it myself.
In order to fix this error, I would need your help in order to reproduce it on my computer first.
Could you please share a short example file, and detailed step-by-step instructions from the "Review raw file" needed to reproduce the error.

You can find a recent example of bug resolution here: