GetSegCoords.m

The current code for this custom MATLAB function are provided below for convenient dissemination.

GetSegCoords.m

function [xyz, hemi, segnames] = getSegCoords(varargin)
% Given a set of label file names, parse the label files and return the mean XYZ coordinate of each label
% Can be called with a list of parameters for easy scripting, or interactively without parameters, which will 
% generate a series of ui dialog boxes.
%
% returns:
% xyz, a nx3 array of XYZ coordinates, where n is the number of labels parsed
% hemi, a nx1 binary vector indicating the corresponding label is left (1) or right (0) hemisphere
% segnames: a nx1 cell array of label strings.
%
% (C) 2018 Chris McNorgan
%  Use at your own risk.
%
 
%% Part 1: Parse arguments
options = struct( ...
   'lhsegdir',, ...
   'rhsegdir',, ...
   'lsegnames', , ...
   'rsegnames', , ...
   'automatch', true, ...
   'hemi', 'lhrh', ...
   'directory', pwd() );

% read the acceptable names
optionNames = fieldnames(options);

% count arguments
nArgs = length(varargin);
if round(nArgs/2)~=nArgs/2
   error('TSExtractor needs propertyName/propertyValue pairs')
end

for pair = reshape(varargin,2,[]) % pair is {propName;propValue}
   inpName = lower(pair{1}); % make case insensitive
   
   if any(strcmp(inpName,optionNames))
       % overwrite options. If you want you can test for the right class here
       % Also, if you find out that there is an option you keep getting wrong,
       % you can use "if strcmp(inpName,'problemOption'),testMore,end"-statements
       options.(inpName) = pair{2};
   else
       error('%s is not a recognized parameter name',inpName)
   end
end

lh=~isempty(strfind(options.hemi, 'lh'));
rh=~isempty(strfind(options.hemi, 'rh'));
 
%% Part 2: Determine folders
%If we want lh coords and we haven't already provided a directory, open
%dialog box
if (lh && isempty(options.lhsegdir))
   options.lhsegdir = uigetdir(options.directory,'Select LH labels directory');
end
if (rh && isempty(options.rhsegdir))
   if(options.automatch)
       options.rhsegdir = strrep(options.lhsegdir, 'lh', 'rh');
   else
       options.rhsegdir = uigetdir(options.directory,'Select RH labels directory');
   end
end

%% Part 3: Verify segment names
% If segment names were not specified, call to parseFSSegments
if (lh && isempty(options.lsegnames))
   %If you've indicated you want lh segment info but haven't provided the
   %names, prompt for them
   warntxt=sprintf('You have not specified the names of the lh segments.\nYou will now be prompted to locate an appropriate file (LEFT HEMISPHERE).');
   d=warndlg(warntxt,'!! Warning !!');
   uiwait(d);
   options.lsegnames=parseFSSegments();
end
if (rh && isempty(options.rsegnames))
   %If you've indicated you want rh segment info but haven't provided the
   %names, prompt for them
   warntxt=sprintf('You have not specified the names of the rh segments.\nYou will now be prompted to locate an appropriate file (RIGHT HEMISPHERE).');
   d=warndlg(warntxt,'!! Warning !!');
   uiwait(d);
   options.rsegnames=parseFSSegments();
end

%% Part 4: Iterate through files associated with segments
xyz=nan(length(options.lsegnames)+length(options.rsegnames),3);
hemi=[repmat('lh',length(options.lsegnames),1);repmat('rh',length(options.rsegnames),1)];
segnames=[(options.lsegnames);(options.rsegnames)];
i=0;
if(lh)
   for i=1:length(options.lsegnames)
       fname=fullfile(options.lhsegdir, ['lh.' options.lsegnames{i} '.label']);
       xyz(i,:)=getMeanLabelCoords(fname);
   end
end
rstart=i;
if(rh)
   for i=1:length(options.rsegnames)
       fname=fullfile(options.rhsegdir, ['rh.' options.rsegnames{i} '.label']);
       xyz(rstart+i,:)=getMeanLabelCoords(fname);
   end
end

%% Helper function: Find mean XYZ of named file
   function [xyz]=getMeanLabelCoords(labelfile)
        
       %First line is a header, second line is nvertices. Skip those two
       %and read the rest of the file: 5 columns, x y z are columns 2, 3,
       %and 4 (except when dlmread interprets it, the 2-space delimiters
       %between the columns is read as an extra column of zeros)
       M=dlmread(labelfile, ' ', 2, 0);
       x=mean(M(:,3));
       y=mean(M(:,5));
       z=mean(M(:,7));
       xyz=[x y z];
   end
end