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Published 20 hours ago • verified publisher icon SpikeInterface

Trouble loading Intan Data

Open congcong96 opened this issue 3 years ago • 5 comments

Hi,

I've been using Intan system for my recordings and have trouble importing data to SpikeInterface.

When I use the IntanExtractor, it expects a data format with .rhd extension. However, my data from the Intan acquisition system is saved in a folder, including time series with .dat extension and only information about the recording, e.g. acquisition frequency, is saved in a info.rhd file. The data is saved as one file per channel, which is supported by the Intan software.

How should I import Intan files saved in this format to SpikeInterface?

congcong96 avatar Jul 16 '21 23:07 congcong96

Hi @congcong96

Is the .dat file saved directly from Intan? I though it only saved .rhd or .rhs files. Which acquisition system are you using? And which version of the Intan software? Also, what version of SpikeInterface are you using?

In your case, you could parse the information needed for a BinaryRecordingExtractor (sampling frequency, number of channels, type of the data) form the info.rhd file and import the dat file directly using the BinaryRecordingExtractor.

alejoe91 avatar Jul 19 '21 07:07 alejoe91

Hi, I have heard that intan recently included also a binary format also. Maybe there is a small header and we could implement to read it. I am not sure that the header is in rhd.

samuelgarcia avatar Jul 19 '21 11:07 samuelgarcia

@congcong96 would you be able to gathe a short 1-second data file and share it with us so we can test it?

alejoe91 avatar Jul 19 '21 11:07 alejoe91

The .dat file is saved directly from Intan. I used both Intan RHD2000 and RHX software (RHX is the newer version). The SpikeInterface version is 0.10.0

The time series from each channel are saved in .dat files, one file per channel (int16, to convert to electrode voltage in microvolts, first subtract 32768 then multiply by 0.195). Information about the recording is saved in the info.rhd file. It can be read by pyintan, just without the time series as they are saved in .dat files.

The test data is a short blank recording from a 64-channel probe. Thanks! SpikeInterface_Intan_test_210719_110554.zip

congcong96 avatar Jul 19 '21 18:07 congcong96

Could you open an issue on neo side ? https://github.com/NeuralEnsemble/python-neo The reader has to be implemented there and then wrapped in spikeinterface.

samuelgarcia avatar Oct 29 '21 07:10 samuelgarcia

Did you ever solve your problem @congcong96 ?

h-mayorquin avatar Mar 06 '23 19:03 h-mayorquin

We have fixed this at the neo level. So this can be done with an install of neo from source.

zm711 avatar Apr 01 '24 19:04 zm711