Error using matlab.internal.math.interp1 and Error using gpuArray/subsref

[kellirestivo]

I'm using Kilosort for NeuroNexus 32 channel linear probes, and I'm getting this error during pre-processing:

Error using matlab.internal.math.interp1
Sample points must be unique and sorted in ascending order.

Error in interp1 (line 188)
VqLite = matlab.internal.math.interp1(X,V,method,method,Xqcol);

Error in shift_batch_on_disk2 (line 14)
shifts = interp1(ysamp, shifts, rez.yc, 'makima', 'extrap');

Error in datashift2 (line 149)
dprev = shift_batch_on_disk2(rez, ibatch, dshift(ibatch, :), yblk, sig, dprev);

Error in ksGUI/runPreproc (line 732)
obj.rez = datashift2(obj.rez, 1);

Error in ksGUI>@(,)obj.runPreproc() (line 333)
'Callback', @(,)obj.runPreproc());

Error while evaluating UIControl Callback.

---

When I work around this error, I get another error during spike sorting:

Error using gpuArray/subsref
Subscript indices must either be real positive integers or logicals.

Error in extractTemplatesfromSnippets (line 56)
wTEMP = dd(:, round(linspace(1, size(dd,2), nPCs)));

Error in extract_spikes (line 42)
[wTEMP, wPCA] = extractTemplatesfromSnippets(rez, NrankPC);

Error in ksGUI/runSpikesort (line 795)
[obj.rez, st3, tF] = extract_spikes(obj.rez);

Error in ksGUI>@(,)obj.runSpikesort() (line 339)
'Callback', @(,)obj.runSpikesort());

Error while evaluating UIControl Callback.

[marius10p]

What are your channel map positions, ycoord and xcoord?

[kellirestivo]

Nchannels = 32; chanMap = 1:Nchannels; xcoords = ones(Nchannels,1); ycoords = (1:Nchannels)';

…

On Sat, May 1, 2021 at 7:30 AM Marius Pachitariu ***@***.***> wrote: What are your channel map positions, ycoord and xcoord? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#390 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALK2BXFHSWCMW4CS2H5HLTLTLPX7BANCNFSM432OWVFQ> .

[neurojaym]

I am having an identical issue!, and same mapping settings

[crewl2]

Same issue. It would be nice to get some assistance on this problem. @marius10p

[joramvanrheede]

I'm having the same issue. What appears to be happening is that there is initially data in temp_wh.dat after preprocessDataSub; however, after running datashift2, in the function shift_batch_on_disk, temp_wh gets overwritten by all zeros.

[joramvanrheede]

I have data sets from tetrodes/hextrodes in different structures and therefore variable numbers of channels per kilosort run. Data sets with 16, 18 and 24 channels worked fine, but the issue came up in a data set with 12 channels.

[joramvanrheede]

Additionally, if I run datashift2 with do_correction set to false the sort completes successfully

[SheinIdelsonMark]

Same error. ysamp has one repeating value and is therefor not unique.

[Magontek]

Same error with a unique tetrode in a square array.
x = [0 25 0 25]
y = [0 0 25 25]
When trying to rotate in this way for the y axis to be in acendent order this way:
x = 0 21.6500000000000 -12.5000000000000 9.15000000000000
y = 0 12.5000000000000 21.6500000000000 34.1500000000000
i get a different error:

Error using matlab.internal.math.interp1
The sample points must be finite.

because the function align_block2 returns NaN

[mik-schutte]

Same issue data from a 16 channel linear probe NeuroNexus. Converted data to .bin file contains 16 channels

xcoords = zeros(16, 1)
ycoords =[250,350,150,550,450,50,650,750,800,700,100,500,600,200,400,300] 16x1

Value of ysamp during error generation:
in datashift2| ysamp= [2.5000 7.5000 12.5000 17.5000 22.5000]
in shift_batch_on_disk2| ysamp= = [2.5, 7.5, 7.5, 12.5, 12.5, 17.5, 17.5, 22.5, 22.5]

With this ysamp interp1 is called which causes the error.

Any help from the team would be greatly appreciated