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flatironinstitute / mountainsort

Spike sorting software
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Converting multiple .ncs files into 1 .mda file #19

Open baoloc10 opened 6 years ago

baoloc10 commented 6 years ago

Hi,

I was wondering if there is any built in tools that can help me convert multiple (8) .ncs files (they are Neuralynx data) into 1 .mda file? Or is there a tutorial on how I can achieve this?

I've try using the built in mdaconvert program to directly convert .ncs to .mda, but it seems like it can only convert 1 .ncs to 1 .mda.

Each of my .ncs file is data for a single channel. So I need to combine them into 1 .mda file to do the sorting algorithm.

Thank you.

magland commented 6 years ago

There is no built-in tool for doing this yet. Are you more comfortable in matlab or python? I can help guide you in doing this using a script.

baoloc10 commented 6 years ago

I was able to concatenate and convert the .ncs files to .mda in matlab. However, I don't think the data is correct. I would really appreciate it if you could also provide me with the script, in either matlab or python.

After running the mountain sort with the built-in pipeline and comparing it with the raw data, it seems like mountain sort is has a very low threshold for what is considered a spike in the data. When I tried to edit the built-in pipeline and changing the min frequency in the sort pipeline, for some odd reason, as I increased the min frequency, the amount of timepoints in the firings.mda file increases. This seems very counter-intuitive to me. I could also be editing the wrong parameter. For us, spikes are those that surpasses ~100microV's. Where we would edit that?

Could you please guide me through how to increase the threshold or just filter and sort out better spikes?

Thank you.

baoloc10 commented 6 years ago

Also, the cluster metrics view in mountain view shows a blank screen for some reason. Any idea what could've caused it?

What are the Y-axis for "Timeseries-Data" and "Cluster Detail" views in mountain view? I can't seem to find documentations on it.

Edit: It's because I don't have a cluster_metrics.json. What is the format for the cluster metrics?

magland commented 6 years ago

Sorry for the delay, did you resolve this?