Can't read the .bin file with error: Index exceeds the number of array elements. Index must not exceed 4.

[AmaranthCao]

Hello,
I am using KS to analyze my data from tetrode recording, and meet the error with: Index exceeds the number of array elements. Index must not exceed 4.

I used following code to create my .bin file(samples is a 4xN matrix, which is my[nchannel x ntimepoints] matrix):
dat = int16(samples.*1e6);
fidout = fopen("samplestry0517.bin","w")
fwrite(fidout,dat(:),'*int16');
fclose(fidout);

and my probe layout is bellow:
X-coordinates of each sites:
ones(4,1)
Y-coordinates of each sites:
1:4
ChannelMap:
1:4
and the other 2 rows are blank;

and when I input my file and create new probe layout, it return with following errors:

Index exceeds the number of array elements. Index must not exceed 4.
Error ksGUI/updateDataView (line 891)
Dat = datAll (obj) P.c hanMap. ChanMap (chList), :);
Error ksGUI/computeWhitening (line 782)
Obj. UpdateDataView;
Error ksGUI/updateProbeView (line 1222)
Obj.com puteWhitening ()
Error ksGUI> @(,)obj.updateProbeView('reset') (line 273)
'Callback' @ (~, ~) obj. UpdateProbeView (' reset '));

Error calculating UIControl Callback.

Could anyone please support any kind of help? Thanks a lot!

[GrimmSnark]

So if you are using the GUI to run kilosort I think it by default tries to display 8 channels in the probe view and the data window. Your data not having enough channels may cause it to crash. I had something similar happen to me, and had to use the 'old' script method to run kilosort on my data.

[AmaranthCao]

Thanks a lot for your help! Could you please supply your code to transfer your tetrode ep file to .bin file? I guess I have some wrongs with .bin file transformation. When I doubled my date to 8 channels and rearrange a 8 channel probe map, I met a new error: Index exceeds the number of array elements. Index must not exceed 8...

Thanks again for your help!

[GrimmSnark]

Here is my code snippet for reading and writing the data into the .bin file. My data is saved per channel in individual files. Hope this helps!

% read in files and convert to mV

for chan = 1:length(fileList)

    % open and read file
    f=fopen(fileList(chan),'r');
    d=fread(f,'int16');
    d = d';
    fclose(f);
    
    trace_uV = d * 1/6400/3000*1e6; % uV conversion
    
    % place into matrix
    grandTraces(chan,:) = trace_uV;

end

% save the files
fid = fopen([kilosortFolder,'/','raw.bin'], 'w');
fwrite(fid, grandTraces, 'int16');
fclose(fid);

[AmaranthCao]

Thanks a lot! Really helpful.

[marius10p]

Please reopen if necessary.