Comments (11)
Using load_open_ephys_binary.m
, the following code should create a memory map of the .dat file, rather than loading it into memory (the 2
indicates the index of the recorded file, which is likely 1 for the AP band, and 2 for the LFP band):
D = load_open_ephys_binary(<path_to_oebin_file>, 'continuous', 2, 'mmap')
Then, you can select a range of electrodes or samples with the following line:
D.Data.Data(1).mapped(startChannel:endChannel, startSample:endSample)
Let me know if that works, and if not we can keep trying to troubleshoot!
from analysis-tools.
It's working!!!
I missed '' for the mmap. It is quite embarrassing.
Thanks.
from analysis-tools.
Glad it worked! Just keep in mind that the memory-mapped values are 16-bit integers, and must be multiplied by 0.195 in order to convert to the true sample values in microvolts. This will automatically change the data type to "double" (which takes up 4x more memory), so you should only do this on a small subset of the data at a time.
from analysis-tools.
I'm trying to load the 'continuous.dat' file, but I can't locate the structure.oebin file-what could have gone wrong/can I just import a standard oebin file for these recordings?
from analysis-tools.
I'm not sure what might have gone wrong in this case. But this file shouldn't change between experiments, so you can just re-use one from a previous recording.
from analysis-tools.
I actually can't find one from any of the recordings I've done- can you think of another work around?
from analysis-tools.
Have you been using the NPX extractor or recording directly to the Binary format?
Either way, let me know how many probes are in your experiment, and I can send you an .oebin file that will work.
from analysis-tools.
NPX extractor, just 1. thank you!
from analysis-tools.
Ok, try this one!
from analysis-tools.
hmm ok now I'm getting this error:
Error using load_open_ephys_binary (line 74)
Data folder not found
And it looks like the script is looking for a file called Neuropix-PXI-100.1 which I also don't have in my output from NPX extractor, did I do something wrong during the extraction?
from analysis-tools.
If the folder names are different, just replace the folder_name
entries in the .oebin file to match with the names of your actual data directories. The first one is the AP Band, the second one is the LFP Band
from analysis-tools.
Related Issues (20)
- Splitting and Merging .dat Files HOT 3
- Trouble loading events data in matlab when saving in flat binary format with the updated GUI: load_open_ephys_binary.m looks for channels.npy HOT 3
- Binary dat files to Plexon Offline sorter HOT 7
- Failing to read metadata.npy for TTL events in this specific setup HOT 4
- Converting continuous.dat into SpikeGLX flat binary HOT 4
- data and timestamp length unequal using load_open_ephys_binary HOT 4
- Session? HOT 1
- Flat binary file has more/less samples than expected HOT 4
- How to convert .continuous format to flat binary for using in Klusta HOT 1
- How to display the specific time point for spikes ? HOT 1
- load_open_ephys_data_faster.m memory error HOT 5
- Opening the binary data HOT 4
- issue running TT openephys data recorded in binary to Mclust
- Using analysis tools in Jupyter Notebook HOT 4
- Merging multiple OpenEphys binary (continuous.dat) files HOT 1
- Info Channel Header Location HOT 2
- Missing Probeinterface file for Neuropixel 1.0 (Open Ephys)
- recovering timestamps HOT 1
- OEP v0.6.2 Python KeyError: 'source_processor_sub_idx HOT 3
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