GUI: Spikesorting of Neuropixels Sample Data Fails

[AGenews]

Dear Folks,
first of all, thanks for this great piece of software!

However, I have some problems running KiloSort2 on the admittedly huge sample data set Hopkins_20160722_g0_t0.imec.ap_CAR.bin from UCL found here.

My system:
Windows 10 Education, Intel i7-8700K, MATLAB 2016b, CUDA 7.5, GeForce RTX2080, 32GB RAM

I am using the GUI and the preprocessing works fine, however after ~10 min of spikesorting it fails telling me:
Error running kilosort! Undefined function 'zscore' for input arguments of type 'gpuArray'.

I hope this is not MATLAB 2016b related ...

Yours sincerely and many thanks!
Andreas

UPDATE:
... so I've just tested my install with the "not-drifting" sample data sim_binary.dat generated by KiloSort1 master_eMouse.m and this works nicely with KiloSort2!
I'll try to get the drifting version to run ....

[nsteinme]

I think you need "statistics & machine learning" toolbox, and parallel computing toolbox. https://www.mathworks.com/help/stats/zscore.html

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On Tue, Jul 23, 2019 at 3:42 AM Andreas Genewsky ***@***.***> wrote: Dear Folks, first of all, thanks for this great piece of software! However, I have some problems running KiloSort2 on the admittedly huge sample data set *Hopkins_20160722_g0_t0.imec.ap_CAR.bin* from UCL found here <http://data.cortexlab.net/singlePhase3/data/>. *My system:* Windows 10 Education, Intel i7-8700K, MATLAB 2016b, CUDA 7.5, GeForce RTX2080, 32GB RAM I am using the GUI and the preprocessing works fine, however after ~10 min of spikesorting it fails telling me: Error running kilosort! Undefined function 'zscore' for input arguments of type 'gpuArray'. I hope this is not MATLAB 2016b related ... Yours sincerely and many thanks! Andreas — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#92>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABZ5IP7O44ROLEDNK6SXCBLQA3OC5ANCNFSM4IGC2CFA> .

[AGenews]

Dear Nick,
thank' lot for the quick reply! Indeed I had to install the "statistics & machine learning" toolbox for the eMouse simulation, and running Kilosort2 with the master_kilosort.m works nicely now.
However, the GUI still fails in part, but now with a different error:
Error saving data for phy! Reference to non-existent field 'Wphy'.

Yours sincerely and many thanks,
Andreas

[KBillel]

Hi I think it's because you need to have the folder npy-matlab-master in your path. You can find it here : https://github.com/kwikteam/npy-matlab

[xintangg]

Hi

Have you solved this problem?

[AGenews]

Hi there ...
well I had all the respective software packages installed all along, so I figured I simply use the matlab script which works nicely. But with the GUI it didn't work and I haven't tried since then.
Best,
A.

[marius10p]

My guess is that 2016b does not support z-score on the GPU, which the GUI uses but not the main code. You could write a little z-score function of your own and replace it in the code? I'd be happy to check any pull requests on this.

[jvschweim]

Dear Nick,
thank' lot for the quick reply! Indeed I had to install the "statistics & machine learning" toolbox for the eMouse simulation, and running Kilosort2 with the master_kilosort.m works nicely now.
However, the GUI still fails in part, but now with a different error:
> Error saving data for phy! Reference to non-existent field 'Wphy'.
Yours sincerely and many thanks,
Andreas

On that issue, I sometimes get the same error message when I run kilosort2 on several files after each other. Clearing the .phy folder usually helps to get around the issue.

[erc84]

I'm also receiving the same error when using the GUI. I've made sure to add the npy-matlab-master folder to the path, have all the toolboxes otherwise properly installed, and I at least don't see any .phy folder in the kilosort directory to clear or modify. I'm also running R2019a. Any other suggestions?

[nsteinme]

This is an error that happens in the saving step *when a previous step has failed to complete*. You can look in the status bar at the bottom of the GUI for more information about what went wrong at the previous step.

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On Wed, Oct 30, 2019 at 3:14 PM erc84 ***@***.***> wrote: I'm also receiving the same error when using the GUI. I've made sure to add the npy-matlab-master folder to the path, have all the toolboxes otherwise properly installed, and I at least don't see any .phy folder in the kilosort directory to clear or modify. I'm also running R2019a. Any other suggestions? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#92>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZ5IP44IO4Q34K3JZZFJ6DQRIBMFANCNFSM4IGC2CFA> .