search

cortex-lab / neuropixels

Information about Neuropixels electrode arrays
83 stars 15 forks source link

CAR issue with probes 3B2 - sync channel 385 #27

Open PierreLeMerre opened 5 years ago

PierreLeMerre commented 5 years ago

Hi,

I had a couple of issues with the "applyCARtoDat.m" script applied to the binary files obtained from the latest SpikeGLX (Release v.20190327) and the imec PXI card with neuropixel probes 3B2.

First, a small error appears while loading "imec.ap.bin" due to the fact that the latest release of SpikeGLX change the file name to "imecX.ap.bin" where X is the probe port number on the imec PXI card. I guess this just need to be updated and can easily be solved by renaming the file as a temporary fix.

Second, the binary file contains 385 channels where channel number 385 is the sync channel acquired through the SMA connector. I think this channel shouldn't be included in the CAR loop. It is not matching the current channel map file (found here) and it creates error while reading the traces and the waveforms from the binary in Phy later on.

I fixed the second issue by creating CAR binary files with 384 channels by modifying the "applyCARtoDat.m" and saving it elsewhere as a temporay fix.

Anybody having similar issues?

nsteinme commented 5 years ago

Yes, but since it takes the median of 385 channels, one bogus/noisy channel does not make any difference in practice...

On Thu, May 16, 2019 at 8:30 PM PierreLeMerre notifications@github.com wrote:

Hi,

I had a couple of issues with the "applyCARtoDat.m" script applied to the binary files obtained from the latest SpikeGLX (Release v.20190327) and the imec PXI card with neuropixel probes 3B2.

First, a small error appears while loading "imec.ap.bin" due to the fact that the latest release of SpikeGLX change the file name to "imecX.ap.bin" where X is the probe port number on the imec PXI card. I guess this just need to be updated and can easily be solved by renaming the file as a temporary fix.

Second, the binary file contains 385 channels where channel number 385 is the sync channel acquired through the SMA connector. I think this channel shouldn't be included in the CAR loop. It is not matching the current channel map file (found here https://github.com/cortex-lab/neuropixels) and it creates error while reading the traces and the waveforms from the binary in Phy later on.

I fixed the second issue by creating CAR binary files with 384 channels by modifying the "applyCARtoDat.m" and saving it elsewhere as a temporay fix.

Anybody having similar issues?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/cortex-lab/neuropixels/issues/27?email_source=notifications&email_token=ABZ5IP5YOR2SYEDNM3AETDDPVWR5XA5CNFSM4HNPDJZ2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4GUHVXVQ, or mute the thread https://github.com/notifications/unsubscribe-auth/ABZ5IP6OMTKD7366DS3NOX3PVWR5XANCNFSM4HNPDJZQ .