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RSsub_FM.m
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RSsub_FM.m
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function RSsub_FM(sub_raw, FMdir_raw, xsub, cat_dir, RSdir, FMdir, targetdir, TR, FWHM, force)
cwd = pwd;
addpath /data/BnB2/TOOLS/spm12
addpath /data/BnB2/TOOLS/DVARS-master/
origdir = fullfile(RSdir,'Orig'); % Unprocessed resting-state EPI folder
stdir = fullfile(RSdir,'ST'); % Slicetimed data after realigment
normdir = fullfile(RSdir,'Norm'); % Normalized resting-state EPI folder, 3D
smoothdir = fullfile(RSdir,['Smooth_' int2str(FWHM) 'mm']); % Normalized resting-state EPI folder
T1dir = cat_dir; % 3D CAT folder
% --- delete old data if force = true ---
if force == 1
try rmdir(RSdir,'s'); end
end
%--------------- get RAW ready for SPM preprocessing---------------------
if (numel(dir(origdir)) <3 && ~exist(fullfile(RSdir,['Counfounds_' xsub '.mat']),'file')) ...
|| force == 1
% ---------- split 4D NIFTI ---------------
mkdir(origdir);
if strcmp(spm_file(sub_raw, 'ext'), 'gz')
if ~exist(fullfile(RSdir, [xsub '.nii']), 'file')
copyfile(sub_raw, fullfile(RSdir, [xsub '.nii.gz']))
gunzip(fullfile(RSdir, [xsub '.nii.gz']))
end
spm_file_split(fullfile(RSdir, [xsub '.nii']), origdir)
delete(fullfile(RSdir, [xsub '.nii.gz']))
delete(fullfile(RSdir, [xsub '.nii']))
copyfile(strrep(sub_raw, 'bold', 'sbref'), fullfile(RSdir, [xsub '_sbref.nii.gz']))
gunzip(fullfile(RSdir, [xsub '_sbref.nii.gz']))
delete(fullfile(RSdir, [xsub '_sbref.nii.gz']))
elseif strcmp(spm_file(sub_raw, 'ext'), 'nii')
copyfile(sub_raw, fullfile(RSdir, [xsub '.nii']))
spm_file_split(fullfile(RSdir, [xsub '.nii']), origdir)
delete(fullfile(RSdir, [xsub '.nii']))
elseif exist(sub_raw,'dir')
copyfile(fullfile(sub_raw, '*.nii'), origdir)
else
return
end
% ---------- delete dummys --------------------
fils = dir(fullfile(origdir,'*.nii')); fils = fils(~[fils.isdir]);
for ex = 1:4
delete(fullfile(origdir, fils(ex).name))
end
end
if numel(dir(FMdir_raw)) > 3
if numel(dir(FMdir)) <3 || force == 1
% ---------- split 4D NIFTI ---------------
mkdir(FMdir);
fils = dir(FMdir_raw); fils = fils(~[fils.isdir]);
for i = 1:numel(fils)
if strcmp(spm_file(fullfile(FMdir_raw, fils(i).name),'ext'),'gz')
copyfile(fullfile(FMdir_raw, fils(i).name), FMdir);
gunzip(fullfile(FMdir, fils(i).name));
delete(fullfile(FMdir, fils(i).name));
end
end
end
end
%%% -------- Proceed with pre-processing -------------------
if ~exist(fullfile(RSdir, [xsub '_meanEPI.nii']), 'file') || force == 1
if exist(FMdir)
if isempty(dir(fullfile(FMdir, 'vdm*'))) || force == 1
% ----- create field map (vdm file) -----
if force == 1; try
delete(fullfile(FMdir, 'fpm*'));
delete(fullfile(FMdir, 'vdm*'));
delete(fullfile(FMdir, 'sc*'));
end; end
% Get Magnitude Difference
matlabbatch = {};
matlabbatch{1}.spm.util.imcalc.expression = 'i1-i2';
fils = dir(fullfile(FMdir, '*magnitude*')); fils = fils(~[fils.isdir]);
for i = 1:numel(fils)
matlabbatch{1}.spm.util.imcalc.input{i,1} = fullfile(FMdir, fils(i).name);
end
matlabbatch{1}.spm.util.imcalc.output = fullfile(FMdir, strrep(fils(1).name, 'tude1', 'tudediff'));
spm_jobman('run', matlabbatch)
matlabbatch = {};
% Echo times [short TE long TE]
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.et = [4.92 7.38];
% Blip direction
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.blipdir = -1;
% Total EPI readout time
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.tert = 29.15;
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.maskbrain = 0;
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.epifm = 0;
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.ajm = 0;
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.uflags.method = 'Mark3D';
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.uflags.fwhm = 10;
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.uflags.pad = 0;
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.uflags.ws = 1;
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.mflags.fwhm = 5;
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.mflags.nerode = 2;
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.mflags.ndilate = 4;
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.mflags.thresh = 0.5;
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.mflags.reg = 0.02;
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.matchvdm = 1;
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.sessname = 'vdm5';
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.writeunwarped = 1;
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.matchanat = 1;
% CHECK THE FIELDMAP INPUT & OUTPUT
fils = dir(fullfile(FMdir, '*.*')); fils = fils(~[fils.isdir]);
if numel(fils)==3
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.data.presubphasemag.phase{1} = ...
fullfile(FMdir, fils(3).name);
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.data.presubphasemag.magnitude{1} = ...
fullfile(FMdir, fils(1).name);
elseif numel(fils)==4
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.data.phasemag.shortphase{1} = ...
fullfile(FMdir, fils(3).name);
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.data.phasemag.shortmag{1} = ...
fullfile(FMdir, fils(1).name);
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.data.phasemag.longphase{1} = ...
fullfile(FMdir, fils(4).name);
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.data.phasemag.longmag{1} = ...
fullfile(FMdir, fils(2).name);
end
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.mflags.template{1} = ...
fullfile(spm('dir'), 'toolbox', 'Fieldmap', 'T1.nii');
% fils = dir(fullfile(origdir,'*.nii')); fils = fils(~[fils.isdir]);
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.session.epi{1} = ...
fullfile(RSdir, [xsub '_sbref.nii']);
matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.anat{1} = fullfile(T1dir, [xsub '.nii']);
spm_jobman('run', matlabbatch)
else
fprintf('\n --- Fieldmap already calculated --- \n')
% apply fieldmap to single band reference EPI
matlabbatch = {};
matlabbatch{1}.spm.tools.fieldmap.applyvdm.data.scans{1} = fullfile(RSdir, [xsub '_sbref.nii']);
Fieldmap = dir(fullfile(FMdir,'vdm5*.nii'));
matlabbatch{1}.spm.tools.fieldmap.applyvdm.data.vdmfile{1} = fullfile(FMdir, Fieldmap.name);
matlabbatch{1}.spm.tools.fieldmap.applyvdm.roptions.pedir = 2;
matlabbatch{1}.spm.tools.fieldmap.applyvdm.roptions.which = [2 0];
matlabbatch{1}.spm.tools.fieldmap.applyvdm.roptions.rinterp = 7;
spm_jobman('run', matlabbatch)
end
% ----- realign & unwarp (using the vdm file) -----
try
matlabbatch = {};
matlabbatch{1}.spm.spatial.realignunwarp.eoptions.quality = 0.95;
matlabbatch{1}.spm.spatial.realignunwarp.eoptions.sep = 3;
matlabbatch{1}.spm.spatial.realignunwarp.eoptions.fwhm = 5;
matlabbatch{1}.spm.spatial.realignunwarp.eoptions.rtm = 1;
matlabbatch{1}.spm.spatial.realignunwarp.eoptions.einterp = 7;
matlabbatch{1}.spm.spatial.realignunwarp.eoptions.ewrap = [0 0 0];
matlabbatch{1}.spm.spatial.realignunwarp.eoptions.weight = '';
matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.basfcn = [12 12];
matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.regorder = 1;
matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.lambda = 100000;
matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.jm = 0;
matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.fot = [4 5];
matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.sot = [];
matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.uwfwhm = 4;
matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.rem = 1;
matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.noi = 5;
matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.expround = 'Average';
matlabbatch{1}.spm.spatial.realignunwarp.uwroptions.uwwhich = [1 1];
matlabbatch{1}.spm.spatial.realignunwarp.uwroptions.rinterp = 7;
matlabbatch{1}.spm.spatial.realignunwarp.uwroptions.wrap = [0 0 0];
matlabbatch{1}.spm.spatial.realignunwarp.uwroptions.mask = 1;
matlabbatch{1}.spm.spatial.realignunwarp.uwroptions.prefix = 'u';
fils = dir(fullfile(origdir, '*.nii')); fils = fils(~[fils.isdir]);
for file = 1:size(fils,1)
matlabbatch{1}.spm.spatial.realignunwarp.data.scans{file,1} = ...
fullfile(origdir, fils(file).name);
end
Fieldmap = dir(fullfile(FMdir,'vdm5*.nii'));
matlabbatch{1}.spm.spatial.realignunwarp.data.pmscan{1} = fullfile(FMdir, Fieldmap.name);
spm_jobman('run', matlabbatch)
mEPI = dir(fullfile(origdir, 'mean*.nii'));
movefile(fullfile(origdir, mEPI.name), fullfile(RSdir, [xsub '_meanEPI.nii']))
rptxt = dir(fullfile(origdir, 'rp*.txt'));
copyfile(fullfile(origdir, rptxt.name), fullfile(RSdir, ['rp_' xsub '.txt']))
delete(fullfile(origdir, [xsub '_*.nii'])); % delete unwarped Niftis
% movefile(fullfile(origdir, 'w*.nii'),RSdir); % move warped magnitude image
catch
fprintf('Problem with Fieldmap of %s: %s \n', xsub, err.message);
end
else
% ---------- realignment --------------------
matlabbatch = {};
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.quality = 0.95;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.sep = 3;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.interp = 7;
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.which = [0 1];
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.interp = 7;
fils = dir(fullfile(origdir, '*.nii')); fils = fils(~[fils.isdir]);
for file = 1:size(fils,1)
matlabbatch{1}.spm.spatial.realign.estwrite.data{1}{file,1} = fullfile(origdir, fils(file).name);
end
spm_jobman('run', matlabbatch)
mEPI = dir(fullfile(origdir, 'mean*.nii'));
movefile(fullfile(origdir, mEPI.name), fullfile(RSdir, [xsub '_meanEPI.nii']))
rptxt = dir(fullfile(origdir, 'rp*.txt'));
copyfile(fullfile(origdir, rptxt.name), fullfile(RSdir, ['rp_' xsub '.txt']))
end
end
%%% !!!! CAREFUL: incorporate slice order manually for now !!!!
if TR > 1.5 && ~exist(fullfile(RSdir, [xsub '_st.nii.gz']), 'file') || TR > 1.5 && force == 1
%--------------- slicetiming ----------------
% merge 3D to 4D Nifti
matlabbatch = {};
fils = dir(fullfile(origdir, '*.nii')); fils = fils(~[fils.isdir]);
for file = 1:size(fils,1)
matlabbatch{1}.spm.util.cat.vols{file,1} = fullfile(origdir, fils(file).name);
end
matlabbatch{1}.spm.util.cat.name = fullfile(RSdir, [xsub '.nii']);
matlabbatch{1}.spm.util.cat.dtype = 4;
spm_jobman('run', matlabbatch);
system(['slicetimer -i ' fullfile(RSdir, [xsub '.nii']) ' -o ' fullfile(RSdir, [xsub '_st.nii']) ' -r ' num2str(TR)],'-echo')
gunzip(fullfile(RSdir, [xsub '_st.nii.gz']));
mkdir(stdir);
% delete(fullfile(RSdir, [xsub '_st.nii.gz']));
spm_file_split(fullfile(RSdir, [xsub '_st.nii']), stdir);
delete(fullfile(RSdir, [xsub '_st.nii']));
end
if ~exist(fullfile(RSdir, ['w' xsub '_meanEPI.nii']), 'file') || force == 1
% ---------- Normalise EPIs using Unified Segment -----
if ~exist(fullfile(RSdir, ['u' xsub '_sbref_seg_sn.mat']), 'file') || force == 1
% ---------- Affine registration into MNI space --------------------
% coreg single band EPI to mean EPI
matlabbatch = {};
matlabbatch{1}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';
matlabbatch{1}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];
matlabbatch{1}.spm.spatial.coreg.estimate.eoptions.tol = ...
[0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];
matlabbatch{1}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];
matlabbatch{1}.spm.spatial.coreg.estimate.source{1} = fullfile(RSdir, ['u' xsub '_sbref.nii']);
matlabbatch{1}.spm.spatial.coreg.estimate.ref{1} = fullfile(RSdir, [xsub '_meanEPI.nii']);
spm_jobman('run', matlabbatch)
% coreg single band EPI to gray matter PM
matlabbatch = {};
matlabbatch{1}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';
matlabbatch{1}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];
matlabbatch{1}.spm.spatial.coreg.estimate.eoptions.tol = ...
[0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];
matlabbatch{1}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];
matlabbatch{1}.spm.spatial.coreg.estimate.source{1} = fullfile(RSdir, ['u' xsub '_sbref.nii']);
matlabbatch{1}.spm.spatial.coreg.estimate.ref{1} = fullfile(spm('dir'), 'toolbox', 'OldSeg', 'grey.nii');
if exist(stdir,'dir')
fils = dir(fullfile(stdir, '*.nii')); fils = fils(~[fils.isdir]);
for file = 1:size(fils,1)
matlabbatch{1}.spm.spatial.coreg.estimate.other{file,1} = fullfile(stdir, fils(file).name);
end
else
fils = dir(fullfile(origdir, '*.nii')); fils = fils(~[fils.isdir]);
for file = 1:size(fils,1)
matlabbatch{1}.spm.spatial.coreg.estimate.other{file,1} = fullfile(origdir, fils(file).name);
end
end
matlabbatch{1}.spm.spatial.coreg.estimate.other{file+1,1} = fullfile(RSdir, [xsub '_meanEPI.nii']);
spm_jobman('run', matlabbatch)
% --- Normalise using unified segmentation with cutoff of DCT bases (4x5x4) ---
matlabbatch = {};
matlabbatch{1}.spm.tools.oldseg.data{1} = fullfile(RSdir, ['u' xsub '_sbref.nii']);
matlabbatch{1}.spm.tools.oldseg.output.GM = [0 0 0];
matlabbatch{1}.spm.tools.oldseg.output.WM = [0 0 0];
matlabbatch{1}.spm.tools.oldseg.output.biascor = 0;
matlabbatch{1}.spm.tools.oldseg.opts.warpco = 45; % cutoff
matlabbatch{1}.spm.tools.oldseg.opts.samp = 2;
spm_jobman('run', matlabbatch)
end
if ~exist(fullfile(RSdir, ['w' xsub '_meanEPI.nii']),'file') || force == 1
% ---------- Apply deformations --------------------
mkdir(normdir);
matlabbatch = {};
matlabbatch{1}.spm.util.defs.comp{1}.sn2def.matname{1} = fullfile(RSdir, ['u' xsub '_sbref_seg_sn.mat']);
% matlabbatch{1}.spm.util.defs.comp{1}.sn2def.matname{1} = fullfile(RSdir,[xsub '_meanEPI_seg_sn.mat']);
matlabbatch{1}.spm.util.defs.comp{1}.sn2def.vox = [2 2 2];
if exist(stdir,'dir')
fils = dir(fullfile(stdir,'*.nii')); fils = fils(~[fils.isdir]);
for file = 1:size(fils,1)
matlabbatch{1}.spm.util.defs.out{1}.pull.fnames{file,1} = fullfile(stdir,fils(file).name);
end
else
fils = dir(fullfile(origdir,'*.nii')); fils = fils(~[fils.isdir]);
for file = 1:size(fils,1)
matlabbatch{1}.spm.util.defs.out{1}.pull.fnames{file,1} = fullfile(origdir,fils(file).name);
end
end
matlabbatch{1}.spm.util.defs.out{1}.pull.savedir.saveusr{1} = normdir;
matlabbatch{1}.spm.util.defs.out{1}.pull.interp = 3;
spm_jobman('run',matlabbatch)
matlabbatch{1}.spm.util.defs.out{1}.pull.fnames = {};
matlabbatch{1}.spm.util.defs.out{1}.pull.fnames{1,1} = fullfile(RSdir,['u' xsub '_sbref.nii']);
matlabbatch{1}.spm.util.defs.out{1}.pull.fnames{2,1} = fullfile(RSdir,[xsub '_meanEPI.nii']);
matlabbatch{1}.spm.util.defs.out{1}.pull.savedir.saveusr{1} = RSdir;
spm_jobman('run',matlabbatch)
end
end
if exist(normdir,'dir') && ~exist(smoothdir,'dir') || force == 1
% ---------- Smooth --------------------
matlabbatch = {};
matlabbatch{1}.spm.spatial.smooth.dtype = 0;
matlabbatch{1}.spm.spatial.smooth.im = 0;
matlabbatch{1}.spm.spatial.smooth.prefix = 's';
matlabbatch{1}.spm.spatial.smooth.fwhm = [FWHM FWHM FWHM];
fils = dir(fullfile(normdir,'w*.nii')); fils = fils(~[fils.isdir]);
for file = 1:size(fils,1)
matlabbatch{1}.spm.spatial.smooth.data{file,1} = fullfile(normdir,fils(file).name);
end
spm_jobman('run',matlabbatch)
mkdir(smoothdir);
movefile(fullfile(normdir,'sw*.nii'),smoothdir)
end
if ~exist(fullfile(RSdir,['w' xsub '.nii']),'file')
% merge 3D to 4D Nifti
matlabbatch = {};
fils = dir(fullfile(normdir,'w*.nii'));
for file = 1:size(fils,1)
matlabbatch{1}.spm.util.cat.vols{file,1} = fullfile(normdir,fils(file).name);
end
matlabbatch{1}.spm.util.cat.name = fullfile(RSdir,['w' xsub '.nii']);
matlabbatch{1}.spm.util.cat.dtype = 4;
spm_jobman('run',matlabbatch);
matlabbatch = {};
fils = dir(fullfile(smoothdir,'sw*.nii'));
for file = 1:size(fils,1)
matlabbatch{1}.spm.util.cat.vols{file,1} = fullfile(smoothdir,fils(file).name);
end
matlabbatch{1}.spm.util.cat.name = fullfile(RSdir,['s' num2str(FWHM) 'w' xsub '.nii']);
matlabbatch{1}.spm.util.cat.dtype = 4;
spm_jobman('run',matlabbatch);
end
%%% redo smoothing with 8mm -- MAYBE IMPLEMENT A LOOP with previous
try rmdir(smoothdir,'s'); end
FWHM = FWHM + 3;
smoothdir = fullfile(RSdir,['Smooth_' int2str(FWHM) 'mm']); % smooothed resting-state EPI folder
if exist(normdir,'dir') && ~exist(smoothdir,'dir') || force == 1
% ---------- Smooth --------------------
matlabbatch = {};
matlabbatch{1}.spm.spatial.smooth.dtype = 0;
matlabbatch{1}.spm.spatial.smooth.im = 0;
matlabbatch{1}.spm.spatial.smooth.prefix = 's';
matlabbatch{1}.spm.spatial.smooth.fwhm = [FWHM FWHM FWHM];
fils = dir(fullfile(normdir,'w*.nii')); fils = fils(~[fils.isdir]);
for file = 1:size(fils,1)
matlabbatch{1}.spm.spatial.smooth.data{file,1} = fullfile(normdir,fils(file).name);
end
spm_jobman('run',matlabbatch)
mkdir(smoothdir);
movefile(fullfile(normdir,'sw*.nii'),smoothdir)
end
if ~exist(fullfile(RSdir,['s' num2str(FWHM) 'w' xsub '.nii']),'file')
% merge 3D to 4D Nifti
matlabbatch = {};
fils = dir(fullfile(smoothdir,'sw*.nii'));
for file = 1:size(fils,1)
matlabbatch{1}.spm.util.cat.vols{file,1} = fullfile(smoothdir,fils(file).name);
end
matlabbatch{1}.spm.util.cat.name = fullfile(RSdir,['s' num2str(FWHM) 'w' xsub '.nii']);
matlabbatch{1}.spm.util.cat.dtype = 4;
spm_jobman('run',matlabbatch);
end
if exist(fullfile(T1dir,'mri',['wp0' xsub '.nii']),'file') && ...
~exist(fullfile(RSdir,['wp0' xsub '.nii']),'file')
% resample partial volume label image to 2x2x2mm
matlabbatch = {};
matlabbatch{1}.spm.spatial.coreg.write.ref = ...
{fullfile(RSdir,['w' xsub '_meanEPI.nii'])};
matlabbatch{1}.spm.spatial.coreg.write.source = ...
{fullfile(T1dir,'mri',['wp0' xsub '.nii'])};
matlabbatch{1}.spm.spatial.coreg.write.roptions.interp = 0;
matlabbatch{1}.spm.spatial.coreg.write.roptions.wrap = [0 0 0];
matlabbatch{1}.spm.spatial.coreg.write.roptions.mask = 0;
matlabbatch{1}.spm.spatial.coreg.write.roptions.prefix = 'r';
spm_jobman('run',matlabbatch)
movefile(fullfile(T1dir,'mri',['rwp0' xsub '.nii']),fullfile(RSdir,['wp0' xsub '.nii']))
end
if exist(fullfile(T1dir,'mri',['mwp1' xsub '.nii']),'file') && ...
~exist(fullfile(RSdir,['mwp1' xsub '.nii']),'file')
% resample modulated GM segment image to 2x2x2mm
matlabbatch = {};
matlabbatch{1}.spm.spatial.coreg.write.ref = ...
{fullfile(RSdir,['w' xsub '_meanEPI.nii'])};
matlabbatch{1}.spm.spatial.coreg.write.source = ...
{fullfile(T1dir,'mri',['mwp1' xsub '.nii'])};
matlabbatch{1}.spm.spatial.coreg.write.roptions.interp = 7; % 7th degree B-Spline
matlabbatch{1}.spm.spatial.coreg.write.roptions.wrap = [0 0 0];
matlabbatch{1}.spm.spatial.coreg.write.roptions.mask = 0;
matlabbatch{1}.spm.spatial.coreg.write.roptions.prefix = 'r';
spm_jobman('run',matlabbatch)
movefile(fullfile(T1dir,'mri',['rmwp1' xsub '.nii']),fullfile(RSdir,['mwp1' xsub '.nii']))
end
if ~exist(fullfile(RSdir,['Counfounds_' xsub '.mat']),'file') || force == 1 || force == 2
clear pXYZ tX tY tZ gx gx2 rp rpp A dat msk gx2 reg y
% getting & computing movement parameter (FD & sqrt) from realignment parameter
txt = dir(fullfile(RSdir,'rp_*.txt'));
rp = load(fullfile(RSdir,txt.name));
[FDts,FD_Stat]=FDCalc(rp);
rp = rp-repmat(mean(rp),size(rp,1),1);
drp = [zeros(1,6); diff(rp)];
move = sqrt(sum(drp(:,1:3).^2,2));
% compute root mean squared movement & frame wise displacement
euler = zeros(size(rp,1),1);
for ii=1:size(rp,1)
euler(ii) = 50*acos((cos(drp(ii,4))*cos(drp(ii,5)) + cos(drp(ii,4))*cos(drp(ii,6)) + ...
cos(drp(ii,5))*cos(drp(ii,6)) + sin(drp(ii,4))*sin(drp(ii,6))*sin(drp(ii,5)) - 1)/2);
end
RMS = sqrt(nanmean([move+euler].^2));
tmp = sum(abs([drp(:,1:3) drp(:,4:6)*50]),2);
FD = sqrt(nanmean(tmp.^2));
% data file
% Vi = spm_vol(fullfile(fsmoothdir,['sw' xsub '.nii']));
Vi = spm_vol(fullfile(RSdir,['w' xsub '.nii']));
% computing global, GM, WM, CSF, mean signals
% getting partial volume mask
msk = spm_read_vols(spm_vol(fullfile(RSdir,['wp0' xsub '.nii'])));
% msk: min 0.0157; max 2.9961; 1=CSF, 2=GM, 3=WM
idxGM = find(msk>1.99 & msk<2.01);
% GMmsk = msk;
% GMmsk(msk<1.99 | msk>2.01) = 0;
% GMmsk = spm_erode(GMmsk); % erode once
% % GMmsk = spm_erode(spm_erode(GMmsk)); % erode twice
% idxGM = find(GMmsk>0);
% idxWM = find(msk>2.99);
idxCSF = find(msk>0.99 & msk<1.01);
gx = nan(4,numel(Vi));
% i.e. aCompCor does >.99 WM 2x erode & >.99 CSF NN clustering criteria
% WMmsk = msk;
WMmsk(msk<2.99) = 0;
WMmsk = spm_erode(WMmsk); % erode once
% WMmsk = spm_erode(spm_erode(WMmsk)); % erode twice
idxWM = find(WMmsk>0);
datWM = zeros(length(idxWM),numel(Vi));
datCSF = zeros(length(idxCSF),numel(Vi));
datALL = zeros(length(find(msk>0)),numel(Vi));
for i=1:numel(Vi)
dat = spm_read_vols(Vi(i));
gx(1,i) = mean(dat(idxGM));
datWM(:,i) = dat(idxWM); % WM voxels only
gx(2,i) = mean(datWM(:,i));
datCSF(:,i) = dat(idxCSF); % CSF voxels only
gx(3,i) = mean(datCSF(:,i));
datALL(:,i) = dat(msk>0); % All brain voxels
gx(4,i) = mean(dat(msk>0));
end
PCA_WM = pca(datWM - repmat(mean(datWM),size(datWM,1),1));
PCA_CSF = pca(datCSF - repmat(mean(datCSF),size(datCSF,1),1));
gx2(1,:) = gx(1,:)-mean(gx(1,:));
gx2(2,:) = gx(2,:)-mean(gx(2,:));
gx2(3,:) = gx(3,:)-mean(gx(3,:));
gx2(4,:) = gx(4,:)-mean(gx(4,:));
reg = [gx2' gx2'.^2 rp rp.^2 drp drp.^2 PCA_WM(:,1:7) PCA_CSF(:,1:7)];
reg = reg-repmat(mean(reg),size(reg,1),1);
reg = reg./repmat(std(reg),size(reg,1),1);
[DVARS,DVARS_Stat]=DVARSCalc(datALL,'scale',1/100,'RDVARS');
badTP=find(DVARS_Stat.pvals<0.05./(numel(DVARS)));
[V,DSE_Stat]=DSEvars(datALL,'scale',1/100);
% FIGURE with BOLD intensity carpet-plot
% fMRIDiag_plot(V,DVARS_Stat,'BOLD',datALL,'ColRng',[-3 3],'FD',FDts,'AbsMov',[FD_Stat.AbsRot FD_Stat.AbsTrans]);
% Diagnosis plot based on stored variables
% f_hdl=figure('position',[50,500,600,600]);
% fMRIDiag_plot(V,DVARS_Stat,'FD',FDts,'AbsMov',[FD_Stat.AbsRot FD_Stat.AbsTrans],'TickScaler',0.5,'figure',f_hdl);
save(fullfile(RSdir,['Counfounds_' xsub '.mat']),'reg','rp','drp','gx',...
'gx2','TR','RMS','FD','DVARS','DVARS_Stat','V','DSE_Stat','FDts','FD_Stat','badTP')
end
if exist(fullfile(RSdir,['w' xsub '.nii']),'file')
try rmdir(origdir,'s'); end
try rmdir(stdir,'s'); end
try rmdir(normdir,'s'); end
try rmdir(smoothdir,'s'); end
end
if exist(fullfile(RSdir,['Counfounds_' xsub '.mat']),'file')
mkdir(targetdir);
movefile(fullfile(RSdir,'*'),targetdir);
rmdir(RSdir);
end
% exit
end