37 lines
1.7 KiB
(Stored with Git Annex)
Matlab
37 lines
1.7 KiB
(Stored with Git Annex)
Matlab
function [rfunc_file, rp_file] = realignment_byrun(func_vols,out_path)
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% Expand func filenames. A single 4D Nifti file is expected per run. An
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% SPM-style list of volumes is returned.
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% [func_p,func_n,func_e] = fileparts(func_file);
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% func_vols{i} = cellstr(spm_select('ExtFPList',func_p,['^' func_n func_e '$'],inf));
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%func_vols = cellstr(spm_select('ExtFPList',func_file,filt,inf)); %Not sure if it's different sessions (##########)
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% SPM job
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matlabbatch = [];
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tag = 1;
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matlabbatch{tag}.spm.spatial.realign.estwrite.data = {func_vols};
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matlabbatch{tag}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;
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matlabbatch{tag}.spm.spatial.realign.estwrite.eoptions.sep = 4;
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matlabbatch{tag}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;
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matlabbatch{tag}.spm.spatial.realign.estwrite.eoptions.rtm = 1;
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matlabbatch{tag}.spm.spatial.realign.estwrite.eoptions.interp = 2;
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matlabbatch{tag}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];
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matlabbatch{tag}.spm.spatial.realign.estwrite.eoptions.weight = '';
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matlabbatch{tag}.spm.spatial.realign.estwrite.roptions.which = [0 1];
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matlabbatch{tag}.spm.spatial.realign.estwrite.roptions.interp = 4;
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matlabbatch{tag}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];
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matlabbatch{tag}.spm.spatial.realign.estwrite.roptions.mask = 1;
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matlabbatch{tag}.spm.spatial.realign.estwrite.roptions.prefix = 'r';
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tag = tag + 1;
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matlabbatch{tag}.spm.util.print.fname = fullfile(out_path,'realignment.png');
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matlabbatch{tag}.spm.util.print.fig.figname = 'Graphics';
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matlabbatch{tag}.spm.util.print.opts = 'png';
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%save(fullfile(func_p,'batch_realignment.mat'),'matlabbatch')
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spm_jobman('run',matlabbatch)
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rfunc_file = func_vols;
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[file_p,file_n]=fileparts(func_vols{1});
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rp_file=[file_p '/rp_' file_n '.txt'];
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