GetSegCoords.m - Revision history

Chris at 17:17, 6 November 2018

2018-11-06T17:17:12Z

← Older revision		Revision as of 13:17, 6 November 2018
Line 1:		Line 1:
	The current code for this custom MATLAB function ~~are~~ provided below for convenient dissemination.		The current code for this custom MATLAB function is provided below for convenient dissemination.

	=GetSegCoords.m=		=GetSegCoords.m=

Chris: /* GetSegCoords.m */

2018-11-06T17:15:33Z

GetSegCoords.m

← Older revision		Revision as of 13:15, 6 November 2018
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	'hemi', 'lhrh', ...		'hemi', 'lhrh', ...
	'directory', pwd() );		'directory', pwd() );

	% read the acceptable names		% read the acceptable names
	optionNames = fieldnames(options);		optionNames = fieldnames(options);
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	error('TSExtractor needs propertyName/propertyValue pairs')		error('TSExtractor needs propertyName/propertyValue pairs')
	end		end

	for pair = reshape(varargin,2,[]) % pair is {propName;propValue}		for pair = reshape(varargin,2,[]) % pair is {propName;propValue}
	inpName = lower(pair{1}); % make case insensitive		inpName = lower(pair{1}); % make case insensitive
Line 51:		Line 51:
	lh=~isempty(strfind(options.hemi, 'lh'));		lh=~isempty(strfind(options.hemi, 'lh'));
	rh=~isempty(strfind(options.hemi, 'rh'));		rh=~isempty(strfind(options.hemi, 'rh'));

	%% Part 2: Determine folders		%% Part 2: Determine folders
	%If we want lh coords and we haven't already provided a directory, open		%If we want lh coords and we haven't already provided a directory, open

Chris: /* GetSegCoords.m */

2018-11-06T17:14:46Z

GetSegCoords.m

← Older revision		Revision as of 13:14, 6 November 2018
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	=GetSegCoords.m=		=GetSegCoords.m=

	function [xyz, hemi, segnames] = getSegCoords(varargin)		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		% 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		% Can be called with a list of parameters for easy scripting, or interactively without parameters, which will
	% generate a series of ui dialog boxes.		% generate a series of ui dialog boxes.
	%		%
	% returns:		% returns:
	% xyz, a nx3 array of XYZ coordinates, where n is the number of labels parsed		% 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		% hemi, a nx1 binary vector indicating the corresponding label is left (1) or right (0) hemisphere
	% segnames: a nx1 cell array of label strings.		% segnames: a nx1 cell array of label strings.
	%		%
	% (C) 2018 Chris McNorgan		% (C) 2018 Chris McNorgan
	% Use at your own risk.		% Use at your own risk.
	%		%

	%% Part 1: Parse arguments		%% Part 1: Parse arguments
	options = struct( ...		options = struct( ...
	'lhsegdir','', ...		'lhsegdir','', ...
	'rhsegdir','', ...		'rhsegdir','', ...
Line 27:		Line 27:
	'directory', pwd() );		'directory', pwd() );

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

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

	for pair = reshape(varargin,2,[]) % pair is {propName;propValue}		for pair = reshape(varargin,2,[]) % pair is {propName;propValue}
	inpName = lower(pair{1}); % make case insensitive		inpName = lower(pair{1}); % make case insensitive

Line 47:		Line 47:
	error('%s is not a recognized parameter name',inpName)		error('%s is not a recognized parameter name',inpName)
	end		end
	end		end

	lh=~isempty(strfind(options.hemi, 'lh'));		lh=~isempty(strfind(options.hemi, 'lh'));
	rh=~isempty(strfind(options.hemi, 'rh'));		rh=~isempty(strfind(options.hemi, 'rh'));

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

	%% Part 3: Verify segment names		%% Part 3: Verify segment names
	% If segment names were not specified, call to parseFSSegments		% If segment names were not specified, call to parseFSSegments
	if (lh && isempty(options.lsegnames))		if (lh && isempty(options.lsegnames))
	%If you've indicated you want lh segment info but haven't provided the		%If you've indicated you want lh segment info but haven't provided the
	%names, prompt for them		%names, prompt for them
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	uiwait(d);		uiwait(d);
	options.lsegnames=parseFSSegments();		options.lsegnames=parseFSSegments();
	end		end
	if (rh && isempty(options.rsegnames))		if (rh && isempty(options.rsegnames))
	%If you've indicated you want rh segment info but haven't provided the		%If you've indicated you want rh segment info but haven't provided the
	%names, prompt for them		%names, prompt for them
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	uiwait(d);		uiwait(d);
	options.rsegnames=parseFSSegments();		options.rsegnames=parseFSSegments();
	end		end

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

	%% Helper function: Find mean XYZ of named file		%% Helper function: Find mean XYZ of named file
	function [xyz]=getMeanLabelCoords(labelfile)		function [xyz]=getMeanLabelCoords(labelfile)

	%First line is a header, second line is nvertices. Skip those two		%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 read the rest of the file: 5 columns, x y z are columns 2, 3,
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	xyz=[x y z];		xyz=[x y z];
	end		end
	end		end

Chris: Created page with "The current code for this custom MATLAB function are provided below for convenient dissemination. =GetSegCoords.m= function [xyz, hemi, segnames] = getSegCoords(varargin) %..."

2018-11-06T17:13:16Z

Created page with "The current code for this custom MATLAB function are provided below for convenient dissemination. =GetSegCoords.m= function [xyz, hemi, segnames] = getSegCoords(varargin) %..."

New page

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