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runRS_FIX_NARPS_MGT3_TEMP.m
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runRS_FIX_NARPS_MGT3_TEMP.m
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clear, clc; warning off all
%%%
% EPI preprocessing
%
% Felix Hoffstaedter
% Data and Platforms
% INM-7 - Brain and Behaviour
% March 2018 - Research Centre Juelich
%
% calling: CATsub_all( <path2raw.nii>, <subjectname(_session)>, <targetdir>, force )
%%%
% ---------- define sample to process ----------------------------
sample = 'NARPS';
% ---------- Repition time for band-pass filter TR -----------------------
TR = 1; % get from json !!!
% ---------- smoothing kernel in mm --------------------------------------
FWHM = 5;
% ---------- Define RS scan -----------------------
scan = 'MGT_run-03'; % get from json !!!
% ---------- Define output folder -----------------------
out = 'MGT3'; clean = 'FIX';
% force --- reprocessing of ready subjects [0 = NOT reprocess] -----
force = 0;
% ------ define slurm call with max RAM & wall clock time -------
call_slurm = ['srun -p large -N 1 -n 1 --mem-per-cpu=5500 --time=9:00:00 --job-name=' sample];
% call_slurm = ['srun -p large -N 1 -n 1 --time=6:00:00 --exclude=brainb32a --job-name=' sample];
call_matlab = ' /nfsusr/local/MATLAB/R2016a/bin/matlab -nodisplay -nodesktop -nosplash -r';
% ---------- get subject and sessions ------------------------------
RAWdirs = fullfile('/data/BnB_TEMP/Data_NARPS/', sample);
% scaninfo = jsondecode(fileread(fullfile(Dirs,[scan '.json'])));
% ---------- CAT output folder -------------------------------------
target = fullfile('/data/BnB_TEMP/Data_NARPS/Derivatives');
TMP = fullfile('/data/BnB_TEMP/Data_NARPS/Derivatives/tmp');
CAT = fullfile('/data/BnB_TEMP/Data_NARPS/Derivatives/CAT/12.5');
Si = dir(fullfile(RAWdirs,'*')); Si = Si([Si.isdir]); Si = Si(3:end);
if strfind(Si(3).name,'sub')
Di = Si;
fprintf('Sample "%s" contains ~%d subjects \n', sample, size(Di,1));
cnt=1;
for i=1:size(Di,1)
if strfind(Di(i).name,'sub')
subdir = fullfile(RAWdirs, Di(i).name);
Dii = dir(fullfile(subdir,'*'));
try Dii = Dii([Dii.isdir]); Dii = Dii(3:end); end
if strfind(Dii(1).name,'ses')
for ii=1:size(Dii,1)
if exist(fullfile(subdir, Dii(ii).name, 'func'),'dir')
fil = dir(fullfile(subdir, Dii(ii).name, 'func', ...
[Di(i).name '_' Dii(ii).name '_task-' scan '_bold.nii.gz']));
if numel(fil) > 0
sub_raw{cnt} = fullfile(subdir, Dii(ii).name, 'func', fil(1).name);
xsubs{cnt} = [Di(i).name '_' Dii(ii).name];
TMPdir{cnt} = fullfile(TMP, out, Di(i).name, Dii(ii).name);
cat_dir{cnt} = fullfile(CAT, Di(i).name, Dii(ii).name);
targetdir{cnt} = fullfile(target, out, Di(i).name, Dii(ii).name);
if exist(fullfile(subdir, Dii(ii).name, 'fmap'),'dir')
FMdir_raw{cnt} = fullfile(subdir, Dii(ii).name, 'fmap');
FMdir{cnt} = fullfile(target, 'FM', Di(i).name, Dii(ii).name);
else
FMdir_raw{cnt} = '';
FMdir{cnt} = '';
end
cnt=cnt+1;
end
end
end
else
if exist(fullfile(target, [out '_fsl'], Di(i).name, [clean '_func_data.nii.gz']),'file')
xsubs{cnt} = Di(i).name;
TMPdir{cnt} = fullfile(TMP, [out '_' clean], Di(i).name);
sub_raw{cnt} = fullfile(target, [out '_fsl'], Di(i).name, [clean '_func_data.nii.gz']);
targetdir{cnt} = fullfile(target, [out '_' clean], Di(i).name);
cat_dir{cnt} = fullfile(CAT, Di(i).name);
if exist(fullfile(RAWdirs, Di(i).name, 'fmap'),'dir')
FMdir_raw{cnt} = fullfile(RAWdirs, Di(i).name, 'fmap');
FMdir{cnt} = fullfile(target, 'FM', Di(i).name);
else
FMdir_raw{cnt} = '';
FMdir{cnt} = '';
end
cnt=cnt+1;
end
end
end
end
else
fprintf('%s Sites found \n', num2str(size(Si,1)));
cnt=1;
for s = 1:size(Si,1)
site = Si(s).name;
Di = dir(fullfile(RAWdirs, site, '*')); Di = Di([Di.isdir]); Di = Di(3:end);
fprintf('%s: %d subjects \n', site, size(Di,1));
for i = 1:size(Di,1)
if strfind(Di(i).name,'sub')
subdir = fullfile(RAWdirs, site , Di(i).name);
Dii = dir(fullfile(subdir,'*'));
try Dii = Dii([Dii.isdir]); Dii = Dii(3:end); end
if strfind(Dii(1).name,'ses')
for ii=1:size(Dii,1)
if exist(fullfile(subdir, Dii(ii).name, 'func'),'dir')
fil = dir(fullfile(subdir, Dii(ii).name, 'func', ...
[Di(i).name '_' Dii(ii).name '_task-' scan '_bold.nii.gz']));
if numel(fil) > 0
sub_raw{cnt} = fullfile(subdir, Dii(ii).name, 'func', fil(1).name);
xsubs{cnt} = [Di(i).name '_' Dii(ii).name];
TMPdir{cnt} = fullfile(TMP, site, out, Di(i).name, Dii(ii).name);
cat_dir{cnt} = fullfile(CAT, site, Di(i).name, Dii(ii).name);
targetdir{cnt} = fullfile(target, site, out, Di(i).name, Dii(ii).name);
if exist(fullfile(subdir, Dii(ii).name, 'fmap'),'dir')
FMdir_raw{cnt} = fullfile(subdir, Dii(ii).name, 'fmap');
FMdir{cnt} = fullfile(target, site, 'FM', Di(i).name, Dii(ii).name);
else
FMdir_raw{cnt} = '';
FMdir{cnt} = '';
end
cnt=cnt+1;
end
end
end
else
if exist(fullfile(subdir, 'func'),'dir')
fil = dir(fullfile(subdir, 'func', [Di(i).name '_task-' scan '_bold.nii.gz']));
if numel(fil) > 0
sub_raw{cnt} = fullfile(subdir, 'func', fil(1).name);
xsubs{cnt} = Di(i).name;
TMPdir{cnt} = fullfile(TMP, site, out, Di(i).name);
cat_dir{cnt} = fullfile(CAT, site, Di(i).name);
targetdir{cnt} = fullfile(target, site, out, Di(i).name);
if exist(fullfile(subdir, 'fmap'),'dir')
FMdir_raw{cnt} = fullfile(subdir, 'fmap');
FMdir{cnt} = fullfile(target, site, 'FM', Di(i).name);
else
FMdir_raw{cnt} = '';
FMdir{cnt} = '';
end
cnt=cnt+1;
end
end
end
end
end
end
end
% ---------- check for already processed subjects -----------------------
idx= []; i=0;
if force
idx = 1 : numel(xsubs);
else
for sub = 1:numel(xsubs)
if exist(sub_raw{sub},'file') && exist(cat_dir{sub},'dir') && ...
~exist(fullfile(targetdir{sub}, ['Counfounds_' xsubs{sub} '.mat']),'file')
% if exist(fullfile(TMPdir{sub}, ['Counfounds_' xsubs{sub} '.mat']),'file') && ...
% ~exist(fullfile(targetdir{sub}, ['Counfounds_' xsubs{sub} '.mat']),'file')
i = i + 1;
idx(i) = sub;
end
end
end
if numel(idx) == 0
fprintf('No subjects to process! Aborting.'); return;
else
fprintf('Found %i unprocessed of %i subjects..\n', numel(idx), numel(xsubs));
end
sub_raw = sub_raw(idx);
FMdir_raw = FMdir_raw(idx);
xsubs = xsubs(idx);
cat_dir = cat_dir(idx);
TMPdir = TMPdir(idx);
FMdir = FMdir(idx);
targetdir = targetdir(idx);
pause
% for sub = 1:numel(xsubs)
% fprintf('Submit CAT12 job for subject %s \n', xsubs{sub});
% system([call_slurm ' --error=slurm_log/RS_' xsubs{sub} call_matlab ...
% ' "RSsub_FM_FIX(''' sub_raw{sub} ''' ,' '''' FMdir_raw{sub} ''' ,' '''' ...
% xsubs{sub} ''' ,' '''' cat_dir{sub} ''' ,' '''' TMPdir{sub} ''',' '''' ...
% FMdir{sub} ''',' '''' targetdir{sub} ''', ' '' num2str(TR) ...
% ' ,' '' num2str(FWHM) ' ,' '' num2str(force) ' )" &' ],'-echo');
% end
% for sub = 1:numel(xsubs)
% fprintf('Submit EPI job for subject %s \n', xsubs{sub});
% system([call_matlab ' "RSsub_FM_FIX(''' sub_raw{sub} ''' ,' '''' FMdir_raw{sub} ''' ,' '''' ...
% xsubs{sub} ''' ,' '''' cat_dir{sub} ''' ,' '''' TMPdir{sub} ''',' '''' ...
% FMdir{sub} ''',' '''' targetdir{sub} ''', ' '' num2str(TR) ...
% ' ,' '' num2str(FWHM) ' ,' '' num2str(force) ' )" &' ],'-echo');
% end
parfor sub = 1:numel(xsubs)
% try
RSsub_FM_FIX(sub_raw{sub}, FMdir_raw{sub}, xsubs{sub}, cat_dir{sub}, ...
TMPdir{sub}, FMdir{sub}, targetdir{sub}, TR, FWHM, force);
% end
end