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Slepi/Code/Utilities/MyPreprocessing/convert_atlas_wrapper_TB.m
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convert_atlas_wrapper_TB.m
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function [ret, fAtlasfn]=convert_atlas_wrapper_TB(path_f,path_sa,fid,C_SUBJ_ID,atlasType,varargin)
% thin convenience wrapper around convert_atlas - convert structural image atlas
% into functional image atlas, all in native space
%
% v1.0 Oct 2009 Jonas Richiardi
% v1.0.1 Mar 2010 Jonas Richiardi
% - support for structural data bias field corrected
%v2. Sept 2014 Giulia Preti
%- support for Greicius Atlas as well. Changed
%the output fAtlasfn into a cell containing multiple atlases for Greicius
%and just one for AAL
[DEBUGMODE,vExt,regenerateFatlas,pre_s]=process_options_TB(varargin,'DEBUGMODE',false,...
'vExt','nii','regenerateFatlas',false,'pre_s','');
% check output dir exists
if ~exist(path_f,'file')
error(['Output path does not exist: ' path_f]);
end
%HCP: I don't have the mean functional, take first file!
fMeanImgfn=dir([path_f filesep 'meanf*.' vExt]);
if ~isempty(fMeanImgfn)
fMeanImgfn=fullfile(path_f,fMeanImgfn(end).name);
else
fMeanImgfn=dir([path_f filesep 'f*0001*.' vExt]); %select first realigned volume
fMeanImgfn=fullfile(path_f,fMeanImgfn(end).name);
fprintf('mean functional NOT found: selecting first realigned volume (OK for HCP,check for other cases)');
end
if ~(exist(fMeanImgfn,'file'))
error(['Failed to locate mean functional file at ' fMeanImgfn]);
end
%load structural atlas/atlases with respect to the atlas chosen
clear sAtlasfn
if atlasType(1)=='A'%AAL
sAtlasfn=dir([path_sa filesep pre_s '*AAL_90.nii']);
end
if atlasType(1)=='G'%Greicius/other
sAtlasfn=dir([path_sa filesep pre_s '*' atlasType '*']);
end
if strcmp(atlasType,'Craddock_300')
sAtlasfn=dir([path_sa filesep pre_s '*Craddock_300.nii']);
end
if strcmp(atlasType,'Craddock_900')
sAtlasfn=dir([path_sa filesep pre_s '*Craddock_900.nii']);
end
if strcmp(atlasType,'Shen')
sAtlasfn=dir([path_sa filesep pre_s '*Shen_268.nii']);
end
if strcmp(atlasType,'Ordon')
sAtlasfn=dir([path_sa filesep pre_s '*MNI_111.nii']);
end
if strcmp(atlasType,'James')
sAtlasfn=dir([path_sa filesep pre_s '*James_222.nii']);
end
clear sAtlasfn_names
if ~isempty(sAtlasfn)
for sss=1:size(sAtlasfn,1)
sAtlasfn_names{sss}=fullfile(path_sa,sAtlasfn(sss).name);
if ~(exist(sAtlasfn_names{sss},'file'))
error(['Failed to locate structural atlas at ' sAtlasfn]);
end
end
else
error(['No structural atlas in ' path_sa ]);
end
disp('Converting structural into functional atlas.');
%disp(sAtlasfn);
%disp('->');
%disp(fAtlasfn);
clear fAtlasfn
for sss=1:size(sAtlasfn,1)
fAtlasfn{sss}=strcat(sAtlasfn_names{sss}(1:end-4),'_functional.nii');
myOOB=convert_atlas_TB(fMeanImgfn,sAtlasfn_names{sss},fAtlasfn{sss},atlasType,fid);
if DEBUGMODE==true
figure; scatter3(myOOB(:,1),myOOB(:,2),myOOB(:,3));
title(['OOB voxels of ' sAtlasfn_names{sss}],'Interpreter','none');
end
end
%end
ret=0;
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