Having Trouble getting started

[meyert11]

Hey guys,

I went through the Neuropixels course (so I have some rudimentary Kilosort experimence). I've been trying to setup a Kilosort Rig from our Convolutional Neural Network Rig. Here are my versions:

After trial and error, I got this to 'work': Matlab 2016a & all needed toolboxes, Visual studio 2012 C++ compiler, CUDA 7.5.

I can run mexGPUall, and mex completes successfully. I acquired example data from: http://data.cortexlab.net/singlePhase3/data/

• specifically rawDataSample.bin

The problem
I open Kilosort, load the selected data file, slect the working and results director. When I get to the channel mapping, regardless of what I select (Phase3A, 3B1, 3B2) there is a matlab error during 'Computing whitening filter...'

The error is:
'Error using -
Matrix dimensions must agree.

Error in ksFilter (line 24)
dataRAW = dataRAW - mean(dataRAW, 1);
'
There are more error lines going up the tree to where the callback in the gui it errored, let me know if that'd be helpful. Needless to say, the Run box never ungrays out. Any suggestions?

Travis

[nsteinme]

Unfortunately this is caused by a change in matlab that happened in 2016b - https://blogs.mathworks.com/loren/2016/10/24/matlab-arithmetic-expands-in-r2016b/ There is not much you can do: you could replace that particular line with the bsxfun equivalent but there are many more instances and there is no way to search to find them all (I have tried this...). Essentially, KS2 is not compatible with matlab prior to 2016b. Sorry :/

…

On Fri, May 31, 2019 at 7:34 AM Travis Meyer ***@***.***> wrote: Hey guys, I went through the Neuropixels course (so I have some rudimentary Kilosort experimence). I've been trying to setup a Kilosort Rig from our Convolutional Neural Network Rig. Here are my versions: After trial and error, I got this to 'work': Matlab 2016a & all needed toolboxes, Visual studio 2012 C++ compiler, CUDA 7.5. I can run mexGPUall, and mex completes successfully. I acquired example data from: http://data.cortexlab.net/singlePhase3/data/ - specifically rawDataSample.bin *The problem* I open Kilosort, load the selected data file, slect the working and results director. When I get to the channel mapping, regardless of what I select (Phase3A, 3B1, 3B2) there is a matlab error during 'Computing whitening filter...' The error is: 'Error using - Matrix dimensions must agree. Error in ksFilter (line 24) dataRAW = dataRAW - mean(dataRAW, 1); ' There are more error lines going up the tree to where the callback in the gui it errored, let me know if that'd be helpful. Needless to say, the Run box never ungrays out. Any suggestions? Travis — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#74>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABZ5IPYWIAV2FRJNEJSVP3DPYEZOXANCNFSM4HR3JBUA> .

[meyert11]

Thanks Nick! It's actually a relief to know it wasn't something I had done :) I'll give a new matlab a try, hopefully it'll be compatible with my combination of CUDA and compilers!

[meyert11]

It worked! I installed 2019a, I had to re-setup the compiler, make a new kilosort-master folder, and reinstall the GUI Layout Toolbox, but it works! Thanks!