sEEG electrods coordinates

ArthurP · March 6, 2025, 5:55pm

Hello,

I'm trying to import coordinate files for different subjects in sEEG, but the problem is that the coordinates are not fully detected (link in the message). Specifically, I should have 131 electrodes, but only 39 are detected…

Here is the sEEG channel file that I have on Brainstorm:

Could you help me understand why?

Thanks in advance,
Arthur

LYONNEURO_2013_VACj_ACPC.pts (5.2 KB)
LYONNEURO_2013_VACj_MNI.pts (5.1 KB)
LYONNEURO_2013_VACj_T1Post_2013-10-9.pts (5.2 KB)
LYONNEURO_2013_VACj.csv (37.0 KB)
LYONNEURO_2013_VACj.pts (5.0 KB)

tmedani · March 11, 2025, 4:38am

@chinmay.chinara can you please check this

chinmay.chinara · March 11, 2025, 8:06pm

@ArthurP thank you for reaching out to us.

Can you tell me more about the software/instrument used to create these files ?
Also I just opened the files you sent in a text editor and the channel names in the screenshot do not match with the channel names in the files you sent. Can you verify them ?

ArthurP · March 12, 2025, 10:33am

Hi,

First of all, the coordinates are incorrect. You're right, so here is the correct data:

LYONNEURO_2014_SIEj_ACPC.pts (3.3 KB)
LYONNEURO_2014_SIEj_MNI.pts (3.5 KB)
LYONNEURO_2014_SIEj_T1Post_2014-10-3.pts (3.5 KB)
LYONNEURO_2014_SIEj.csv (24.2 KB)
LYONNEURO_2014_SIEj.pts (3.4 KB)

Regarding the rest of your message, I can't provide you with the exact name of the material used to create the data because I just received it as is.

I would like to know how Brainstorm detects the coordinates and the names of the electrodes, and if there are any issues with the detection in these files.

For the importation, I use IntraAnat, MNI space, with the MNI files in .pts.

Thank you in advance,
Arthur

chinmay.chinara · March 12, 2025, 7:45pm

I did the same for the files you provided above and it seems to be importing correctly.

Note: This still does not match the initial screenshot you shared.

When you Import Channel File with file type EEG: IntrAnat, MNI space (pts;csv), import_channel.m gets called. As you can see, in_channel_ascii.m then handles the parsing of this .pts file. It expects a .pts file with four columns ('Name','X','Y','Z' ), 3 header lines and [mm] as units.

github.com/brainstorm-tools/brainstorm3

toolbox/io/import_channel.m

c113225a8


      
                  ChannelMat = AllChannelMats{1};

                  % Convert coordinates: MRI => SCS

                  fcnTransf = @(Loc)cs_convert(sMri, 'mri', 'scs', Loc')';

                  AllChannelMats = channel_apply_transf(ChannelMat, fcnTransf, [], 1);

                  ChannelMat = AllChannelMats{1};

              end

              

          case {'INTRANAT', 'INTRANAT_MNI'}

              switch (fExt)

                  case 'pts'

                      ChannelMat = in_channel_ascii(ChannelFile, {'name','X','Y','Z'}, 3, .001);

                  case 'csv'

                      if strcmpi(FileFormat, 'INTRANAT_MNI')

                          ChannelMat = in_channel_tsv(ChannelFile, 'contact', 'MNI', .001);

                      else

                          ChannelMat = in_channel_tsv(ChannelFile, 'contact', 'T1pre Scanner Based', .001);

                      end

              end

              ChannelMat.Comment = 'Contacts';

              FileUnits = 'mm';

              [ChannelMat.Channel.Type] = deal('SEEG');

github.com/brainstorm-tools/brainstorm3

toolbox/io/in_channel_ascii.m

master

function ChannelMat = in_channel_ascii(ChannelFile, Format, nSkipLines, Factor)
% IN_CHANNEL_ASCII:  Read 3D cartesian positions for a set of electrodes from an ASCII file.
%
% USAGE:  ChannelMat = in_channel_ascii(ChannelFile, Format={'X','Y','Z'}, nSkipLines=0, Factor=0.1(cm))
%
% INPUTS: 
%     - ChannelFile : Full path to the file
%     - Format      : Cell-array describing the columns in the ASCII file (assumes that 1 row = 1 electrode)
%                     => 'X','Y','Z' : 3D electrode position (float)
%                     => 'indice'    : electrode indice (integer)
%                     => 'name'      : electrode name (string)
%                     => otherwise   : do not use this column
%     - nSkipLines  : Number of lines to skip before starting to read values (for files with headers)
%     - Factor      : Factor to convert the positions values in meters.

% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
% 
% Copyright (c) University of Southern California & McGill University

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