-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathrunRS_XX_TEMP.m
205 lines (194 loc) · 9.31 KB
/
runRS_XX_TEMP.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
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-01'; % get from json !!!
% ---------- Define output folder -----------------------
out = 'MGT1';
% 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');
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(TMP, '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, out, Di(i).name);
cat_dir{cnt} = fullfile(CAT, Di(i).name);
targetdir{cnt} = fullfile(target, out, Di(i).name);
if exist(fullfile(subdir, 'fmap'),'dir')
FMdir_raw{cnt} = fullfile(subdir, 'fmap');
FMdir{cnt} = fullfile(TMP, 'FM', Di(i).name);
else
FMdir_raw{cnt} = '';
FMdir{cnt} = '';
end
cnt=cnt+1;
end
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(TMP, 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(TMP, 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') && ...
if exist(sub_raw{sub},'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(''' 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(''' 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)
try
RSsub_FM(sub_raw{sub}, FMdir_raw{sub}, xsubs{sub}, cat_dir{sub}, ...
TMPdir{sub}, FMdir{sub}, targetdir{sub}, TR, FWHM, force);
end
end