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Overflow of timestamps in KS4 #715
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Hello, Spike times are already saved as int64 by Kilosort. Can you please try checking the spike times in a script / notebook instead of looking at Phy? It does look like an overflow is happening, but that might be happening in Phy. Something like this should confirm if the values are stored correctly:
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Thanks, looking into it. |
@seto0425 Sorry for the delay, this has been a difficult one. I fixed a related overflow in an earlier part of the pipeline, but I have still not found the source of this. Every variable assignment and intermediate computation I can find that deals with spike times uses a 64-bit data type so far as I can tell. So, I have a couple follow-up questions:
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Thank you for your reply.
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Thank you! These would be the steps to follow, please let me know if you need any clarifications: Download repository and install in editable mode in a new kilosort environment (modifying the last line if needed for your cuda version):
Checkout branch for this issue:
Then run Kilosort4 however you did before. After sorting, there should be a |
I will send you the Kilosort4.log file. Is this okay with you? Also, I recently noticed that there were no issues related to overflow in the drift plot displayed during Kilosort running. |
Was that the correct log file? It looks like that one stopped with an error very quickly, during drift correction. |
I apologize for the delayed response due to another issue. After updating from KS4.0.10 to the new version, the program no longer runs correctly and encounters an error, even though I am using the same recording data files as before. I have tried KS4.0.12 and 4.0.14, but both seem to stop with the same error. I am attaching the 'kilosort.log' file and the contents of the ‘Message log box’ obtained from the GUI (Kilosort version 4.0.14.dev2) for your reference. I am currently trying to resolve this issue on my end as well. Although it deviates from the main topic of this thread, if you have any solutions for this error, could you please let me know? kilosort4_0_14_dev_20240731.log |
@seto0425 Sorry for the delay. I just pushed a fix for this, it will be live on pypi later today as v4.0.16. |
Describe the issue:
Hi! I am using Kilosort 4.0.10 to perform spike sorting on data recorded with a 64-channel silicon probe for over 40 hours (sampling rate: 20k). During this process, I encountered an issue with the timestamps, as seen in the Amplitude View, Feature View, and Firing Rate View (probably due to overflow). It seems that this issue is caused by settings of the data type in KS4, and I believe it can be improved by changing to a larger data type (int64 or uint32). However, I am not sure where to modify the code to fix this issue. Could you please guide me on which part of the code should be changed?
![time_stamp_issue](https://private-user-images.githubusercontent.com/52811950/338819006-c45adf41-b465-43c1-8966-b9248dec09d2.jpg?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.wnO_lexBJL0aSOtpGCYp2KGtS9HyFJaPe9yLivSK34Q)
Thank you in advance!
Reproduce the bug:
No response
Error message:
No response
Version information:
Kilosort 4.0.10
Context for the issue:
No response
Experiment information:
No response
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