[FieldTrip] importing data from blackrock

Wed Feb 3 08:57:46 CET 2016

Hi Andre,

Thanks for thinking along and this contribution. I am aware of these functions, and these are essentially already built into fieldtrip, although not fully functional yet. Have a look at ft_read_data and ft_read_header, and search for ‘blackrock’. It’s just the internal data bookkeeping that needs to be sorted out, as well as some potential data scaling issues. If you have some insights in this regard, please do sign up for bug 2964 and chime in.

Cheers,
JM

On Feb 2, 2016, at 6:17 PM, André Bastos <andrembastos at gmail.com<mailto:andrembastos at gmail.com>> wrote:

Hey JM,

I just handed Andreas some code to read in the data to MATLAB using the openNSx.m (for importing continuous raw data) and openNEV (for spikes and event codes), and then a Fieldtrip data structure can be created by hand relative to events of interest or for the whole length of the session.

I know this is probably not the ideal solution from a FT development point of view, but it's working for us which means also limited urgency to change.

I would be able to eventually work towards a more aesthetically pleasing solution, especially if Andreas can help!

Cheers,
Andre

On Tue, Feb 2, 2016 at 1:55 AM, Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>> wrote:
Hi Andreas,

At this moment the code that uses the NPMK toolbox for fileio is not yet functional. I have started working on this a bit, but did not have time (and urgency) to complete this yet.
The neuroshare code is based on very outdated (windows support only) mex-code, and it does not surprise me that it does not work for you.

If you specify ‘headerformat’ and ‘dataformat’ to be ‘blackrock_nsx’ the code should take the correct turn, and end up at a portion of the m-file that is calling the NPMK functions.
However, you will hit a keyboard statement right away, so you would need to provide some additional code, that is reformatting the output of the lower-level NPMK function into the shape that FieldTrip can work with. I think you could get some inspiration from the documentation about the support for different data formats as well as some examples from the various dataformats as implemented in ft_read_data. If you can provide me with some functional code, I will be happy to plug it into the release version of FieldTrip. I also suggest you to create an account on our bugzilla server: bugzilla.fieldtriptoolbox.org<http://bugzilla.fieldtriptoolbox.org/>, and assign yourself to the CC-list of bug 2964. Any progress you make, code suggestions, as well as questions regarding to the implementation of this dataformat can be posted here.

Since I don’t have dedicated time to work on this right now, the easiest way forward would be if you investigate a bit more yourself and come up with good suggestions. This will expedite the process greatly.

Thanks, and best wishes,

Jan-Mathijs

On Feb 1, 2016, at 11:36 PM, Andreas Gerhard Wutz <andreas.wutz-1 at unitn.it<mailto:andreas.wutz-1 at unitn.it>> wrote:

Dear Fieldtrip community,

I am trying to read in LFP data from a blackrock system. I started out with the sample code provided here: http://www.fieldtriptoolbox.org/getting_started/blackrock

I use Windows 7 (64-bit), Matlab 2011b (32-bit), downloaded and installed the latest version of Fieldtrip (20160128) and of the NPMK toolbox.

Unfortunately, I didn't come very far.
Here is my code:

filename = 'my_data.ns2';
data = ft_read_data(filename, 'headerformat', 'neuroshare');

Immediately exits with the following error message:
"Invalid MEX-file" pointing to "fieldtrip/external/neuroshare/mexprog.dll": The specified procedure could not be found.

Error in ns_SetLibrary (line 39)
Error in read_neuroshare (line 82)
Error in ft_read_header (line 2056)
Error in ft_read_data (line 197)

What options do I have to get this going?
Thank you very much for your help.
Best,
Andreas

--
Andreas Wutz, PhD
Post-doctoral researcher
Center for Mind/Brain Sciences (CiMeC)
University of Trento
Rovereto, Italy
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