Suite 2P not converging. about suite2p HOT 7 CLOSED

For now, use ops.stopSourcery to stop it earlier. The default value is 1/20. Sourcery stops on the first iteration which finds less than this fraction of the number of ROIs found on the first iteration.

I will come back with a more robust solution later.

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I think I am getting a similar error - is it related (see below) there is also a warning. I tried adding in ops.stopSourcery but it did not do anything - what kind of value would be good to set it to?
Matlab output:
...
635 total ROIs, err 1.4406, thresh 0.0048
672 total ROIs, err 1.4373, thresh 0.0048
698 total ROIs, err 1.4350, thresh 0.0048
719 total ROIs, err 1.4335, thresh 0.0048

In sourcery (line 137)
In run_pipeline (line 76)
In master_file(line 67)
Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 3.007762e-10.
734 total ROIs, err 1.4325, thresh 0.0048

UPDATE: I did manage to get the threshold to work but I left this comment here in case the warning message was of any use for you - thanks :-)

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What's your SNR like? I've found that this error is normally associated with my lower SNR recordings (more prevalent in deep recordings). A stopSourcery of around 1/10 is usually good enough to alleviate issues.

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@geffenlab I see that you fixed it by increasing the threshold. It might have been an issue with the conditioning of the matrix inversion in line 137 of sourcery, which I had turned off (what the warning refers to). I turned that back on, so you could try it again.

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I tried 1/10 and I got the same warning (if you leave it going it does not find any ROIs, or just a few weird looking ones). What actually worked was to set the stopSourcery as 1/40...
Marius, I will try with the fix you have implemented on Monday - thanks!

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A recent update fixes this problem. Closing this issue. Please reopen if there are still problems?

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Hi @marius10p, I've recently run into this problem myself on some older data (using Suite2P downloaded today, and on the 15th). Setting stopSourcery to 1/10 fixed it, but I thought it would be good to mention in case the issue pops up for other people.

-Matteo A

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