/
s_fe_fit_and_cat.m
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s_fe_fit_and_cat.m
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function fe = s_fe_fit_and_cat(subjects2run,bval)
%
% This function:
% - Initializes a LIFE structure from a candidate connectome
% - Generates an optimized connectome from a cadidate connectome using
% LIFE method
% - Eliminates the 0-weight fibers
% - Concatenates several connectomes together
%
% fe = s_fe_fit_and_cat()
%
% INPUTS: none
% OUTPUTS: fe structure the optimized life structure
%
% Copyright Franco Pestilli (2013) Vistasoft Stanford University
% Get the base directory for the data
if strcmpi(deblank(evalc('!hostname')),'marcovaldo') || ...
strcmpi(deblank(evalc('!hostname')),'black')
datapath = '/marcovaldo/frk/2t1/predator';
elseif strcmpi(deblank(evalc('!hostname')),'celadon')
datapath = '/marcovaldo/frk/2t1/predator';
else datapath = '/hsgs/projects/wandell/frk/life';
end
fprintf('\n datapath: %s \n',datapath)
subjects = {...
'JW_96dirs_b2000_1p5iso', ...
'KK_96dirs_b2000_1p5iso', ...
'KW_96dirs_b2000_1p5iso', ...
'MP_96dirs_b2000_1p5iso', ...
'HT_96dirs_b2000_1p5iso', ...
'FP_96dirs_b2000_1p5iso', ...
};
if notDefined('subjects2run');
subjects2run = 1:length(subjects);
end
for isbj = subjects2run
fprintf('\n\n\n subject: %s \n\n\n\n',subjects{isbj})
% Build the file names for the diffusion data, the anatomical MR, the fiber
% group containing the connectome and the
dwiPath = fullfile(datapath,subjects{isbj},'diffusion_data');
if ~isempty(bval)
dwiFiles = dir(fullfile(dwiPath,sprintf('*%s*.gz',num2str(bval))));
else
dwiFiles = dir(fullfile(dwiPath,sprintf('run*.gz')));
end
dwiFile = fullfile(dwiPath,dwiFiles(1).name);
dwiFileRepeat = fullfile(dwiPath,dwiFiles(2).name);
t1File = fullfile(datapath,subjects{isbj},'anatomy','t1.nii.gz');
% Directory where to save the fe structures
savedir = fullfile(datapath,subjects{isbj},'connectomes');
% Now find all the fiber files that we will analyze
fibersPath = fullfile(datapath,subjects{isbj},'fibers');
if ~isempty(bval)
fgFiles = dir(fullfile(fibersPath,sprintf('*%s*.pdb',num2str(bval))));
else
fgFiles = dir(fullfile(fibersPath,sprintf('*.pdb')));
end
keyboard
% We build one modelper fiber group, whole brain fiber group
for iFib = [5 1 3 4 2] %length(fgFiles):-1:1
% The final connectome and dat astructure will be saved with this name:
[~,feFileName] = fileparts(fgFiles(iFib).name);
diary_file = fullfile(datapath,sprintf('diary-%s-%s-%s-%s.txt', ...
mfilename,subjects{isbj},feFileName,date));
if ~(exist([diary_file],'file') == 2)
diary(diary_file)
% Build a full-file of the fibers and the FE structure
fgFileName = fullfile(fibersPath,fgFiles(iFib).name);
feTempPath = fullfile(savedir,feFileName);
if ~(exist([feTempPath,'.mat'],'file') == 2)
% Initialize the Connectome
fe = feConnectomeInit(dwiFile,fgFileName,feFileName,savedir,dwiFileRepeat,t1File);
feConnectomeSave(fe);
M = feGet(fe,'mfiber');
dSig = feGet(fe,'dsigdemeaned');
clear fe
% Fit the model and cull. This will take some time...
fit = feFitModel(M,dSig,'bbnnls');
clear M dSig
fe = feSet(fe,'fit',fit);
clear fit
% Save it
feConnectomeSave(fe);
else
fprintf('\n[%s] Found FE file not re-computing...\n\n%s\n\n',mfilename, feTempPath)
end
else
fprintf('\n\nFOUND DIARY FILE: \n%s \n\n\n',diary_file)
end
fprintf('\n\n\n\n\nDONE processing: %s ...\n\n\n\n',diary_file)
diary off
end
fprintf('\n\n\n DONE subject: %s \n\n\n\n',subjects{isbj})
end
% Exit matlab
exit