channel.Loc semicolon

abdallahqusaibe · August 19, 2020, 8:28am

Hi BST community,

hope you are fine

I have a simple question but I do not have an answer
In channel.Loc there is semicolon between the numbers as: [0.0410;0.1061;0.0045]

I would like to insert new coordinates that I have in this form:
0.0207485655421089 0.0829486401560343 0.0124883096586798

How can I replace those new coordinates in the channel.Loc but included the semicolon?

Thank you!

Best regards
Abdallah

Francois · August 19, 2020, 8:48am

https://www.mathworks.com/matlabcentral/answers/69274-the-difference-between-semicolon-and-comma

abdallahqusaibe · August 19, 2020, 10:08am

yes but I am asking how can I re save them again with semicolon,
the values are saved with space or coma but not with semicolon
so is there a syntax I can used?

abdallahqusaibe · August 19, 2020, 10:04am

Hi, why saving in the form of eeglab xyz the channel.Loc: [0.0410;0.1061;0.0045]

gives different values: -10.608866 4.099918 0.454515 ?

Francois · August 19, 2020, 1:17pm

yes but I am asking how can I re save them again with semicolon,
the values are saved with space or coma but not with semicolon
so is there a syntax I can used?

Space is the same as a comma => separates columns
Semi-colon => separates rows
If you are expecting to write scripts with Brainstorm, you would probably save some time by reading some generic Matlab tutorials explaining how to manipulate arrays and matrices.

Hi, why saving in the form of eeglab xyz the channel.Loc: [0.0410;0.1061;0.0045]
gives different values: -10.608866 4.099918 0.454515 ?

Exporting what, from where, how, to where?
Please be more specific: add descriptions of what you're doing and screen captures.

abdallahqusaibe · August 19, 2020, 1:35pm

I original channel.Loc is with semicolon is look like that:

I want to replace the above with:

My question is how to put them with semiclon, because when I put them it appear in the channel.Loc with coma or with space but not with semicolon that seems with BST it should worked jut with semicolon

abdallahqusaibe · August 19, 2020, 1:40pm

when I export those channel to eeglab format in BST:

the save file is look like:

comparing the both they have different values

Francois · August 19, 2020, 2:26pm

In Brainstorm, the ChannelMat.Channel(i).Loc field should be [3 x Nintegration_points].
For EEG, you have one integration point only, it should therefore be [3 x 1].
https://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile#Edit_the_channel_file

If you want to modify these values, I recommend you directly edit the Matlab structures. Load the channel.mat with ChannelMat=load('/.../channel.mat'), modify the values you want, save it back with save('/.../channel.mat', '-struct', ChannelMat). I am not familiar with any other reliable solution for editing Matlab structures.

Read the Scripting tutorial for more help with scripting with Brainstorm:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting

Francois · August 19, 2020, 2:28pm

When exporting as "EEGLAB-XYZ", th X and Y coordinates are swapped and the coordinates are converted from meters to centimeters:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/export_channel.m#L159


      
                  error(['The SCS and MNI transformations must be defined for this subject' 10 'in order to load sensor positions in MNI coordinates.']);

              end

              % Pass the entire MRI structure for conversions to MNI space

              Transf = sMri;

          % World transformation (vox2ras/nii)

          elseif isWorldTransf

              % Check that the transformation is available

              if ~isfield(sMri, 'InitTransf') || isempty(sMri.InitTransf) || ~ismember('vox2ras', sMri.InitTransf(:,1))

                  error(['The world/vox2ras transformations must be defined for this subject' 10 'in order to export sensor positions in world coordinates.']);

              end

              % Compute the transformation SCS => WORLD

              Transf = cs_convert(sMri, 'scs', 'world');

              % If exporting to BIDS format AND there are transformations that were applied to MRI after it was imported to Brainstorm

              iTransfReg = find(strcmpi(sMri.InitTransf(:,1), 'reg'), 1);

              if ~isempty(iTransfReg) && isRevertReg

                  Transf = inv(sMri.InitTransf{iTransfReg,2}) * Transf;

              end

          else

              Transf = [];

          end

abdallahqusaibe · August 19, 2020, 2:36pm

Yes the issue is here, how to save the number with semicolon?,
the idea appear to be simple but I block on it ,
But anyway thank you Francois!

Francois · August 19, 2020, 3:06pm

The values are not save "with or without semicolon", they are saved "as row vectors or column vectors".
If you are not familiar with Matlab syntax and matrix manipulation, you may have to teach yourself a bit about this before being able to write Matlab scripts...