Creating custom raw file import

Discussions
1

Hi,
I have datasets recorded in a binary file format which is not included in the BrainStorm’s list of supported file formats.
The publisher of the software that created the file has kindly provided me with a means to read this file into matlab
but I want to read the file as a raw file directly from BrainStorm.
What can I do to include this file format as another BrainStorm supported formats?

Nir

2

Hi Nir,

If you have Matlab code to read your file format, it is not too complicated. You need to write two functions:

  1. in_fopen_yourformat.m: Reads the file header, returns a structure sFile, as described here:
    http://neuroimage.usc.edu/brainstorm/Tutorials/EventMarkers#On_the_hard_drive
  2. in_fread_yourformat.m: Reads a block a recordings in the file

If you can provide me with these two functions, I would finish the work and add references to these new functions in in_fopen.m, in_fread.m and bst_get.m.
Note that the code used to read the files must be open: please check with the manufacturer that we will be able to redistribute the code as part of Brainstorm (we would include the code in the folder brainstorm3/external).
Is this for a specific EEG acquisition system?

Cheers,
Francois

3

Hi Francois
Thank you for the reoly
I will check with the manufacturer if the code he provided me with can be distributed.
The recordings are captured by DeyMed acquisition system (http://www.deymed.com/)
We have another acquisition system for which we created our own code to convert the native files to matlab.
given that this is an in-house code can it be integrated to BrainStorm as well?
the manufacturer of this system do not support matlab import.

Nir

4

If you can read the file in Matlab and the file format is not “too proprietary”, there is a way to read it in Matlab.
Send me one pair of in_fopen_xxx/in_fread_xxx functions for each format you want to include.

5

Ok thanx
I will send those files to you.

6

Ok
The manufacturer of one aquisition system has asked me directly not to publish the matlab code he provided me with.
The other file types I can read from python and matlab by means of file structure hacking. Therefore I presume it is not a good candidate for shering either.

Thenak you for your suggestions
Nir

7

For the file formats you cannot share: you can write a matlab script to re-write the files in a format that brainstorm can read (text-based, very simple binary like the EGI .raw file format). You can also directly write Brainstorm structures, as documented here (data file + channel file):
http://neuroimage.usc.edu/brainstorm/Tutorials/Epoching#On_the_hard_drive
http://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile#On_the_hard_drive

For the format you can share: it could still be interesting to format the code in Brainstorm format (in_fopen/in_fread functions) for an easier access for you, and for other users who share the same acquisition device.

Francois