-
Notifications
You must be signed in to change notification settings - Fork 24
/
FCPROCESS_MSC.m
1915 lines (1635 loc) · 73.8 KB
/
FCPROCESS_MSC.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
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
function [allends switches] = FCPROCESS_MSC(datafile,tdir,tmasktype,cleanup,roilist,varargin)
% jdp 2/22/2012
%
% IMPORTANT: fcp_process removes the /newtargetdir/vcdir/ folder when it
% begins processing a subject, so DO NOT set the targetdir to the directory
% where your 333 BOLD data exist - use a new directory, specific to FC
% data. Since fcp_initial_process is a wrapper for fcp_process, this goes
% for that script too.
%
% This script is the fcprocessing script for the Petersen lab.
%
% The datalist specifies the data to process, and is a 5-column file:
% srcdir vcnum prmfile TR skipframes
% e.g.:
% /data/src/ vc11111 /data/prms/vc11111.prm 2.5 5
% /data/src/ vc22222 /data/prms/vc22222.prm 2.2 5
%
% We presume the file structure for fMRI data:
% /srcdir
% /vcnum
% /boldX
% /boldY
% /atlas
%
% Where the bold# for resting runs are specified in the prmfile, which
% contains the single line:
% set boldruns = (X Y whatever the bold run numbers are)
% e.g: set boldruns = (2 4 6)
%
% The srcdir and prmfile need to be hard paths
%
% The TR is obvious, and the skipframes are the number of frames to skip at
% the beginning of each run (5 is generous but common).
%
% targetdir: where to write files to
% tmasktype can be one of two things:
% 'ones' - just skips the skipframes at the start of each run
% tmasklist - a tmasklist from COHORTSELECOR.m
% cleanup: delete all files but QC files and final fcimage (0=no. 1=yes)
% freesurferlist: a file with 2 columns, the first the subject ID, the second
% where the freesurfer segmentation exists that was used for MAKE_FS_MASKS.csh
% e.g.,
% vc11111 /data/cn4/segmentation/freesurfer5_supercomputer
% vc22222 /data/cn4/segmentation/freesurfer5_supercomputer
%
% The processing order is:
% demean/detrend (mask)
% extract nuisance signals
% multiple regression (mask)
% *interpolate* (mask)
% temporal filter (butter1 filtfilt low-pass)
% demean/detrend (mask)
% spatial blur (gauss_4dfp)
%
%
%
% IMPORTANT: FCPROCESS removes the /newtargetdir/vcdir/ folder when it
% begins processing a subject, so DO NOT set the newtargetdir to the directory
% where your 333 BOLD data exist - use a new directory, specific to FC
% data.
%
% FCPROCESS(datalist,targetdir,tmasktype,cleanup,roilist,freesurferlist)
% FCPROCESS('datalist.txt','/put/data/here/','ones',1,'bigbrain264.txt','fsinfo.txt');
% FCPROCESS('datalist.txt','/put/data/here/','specificmasks.txt',1,'fab5roiz.txt','fsinfo.txt');
%% IMPORTANT VARIABLES
avidir = '/data/cninds01/data2/nil-tools';
releasedir = '/data/petsun4/data1/solaris';
roidir='/home/usr/fidl/lib/';
startdir=pwd;
FDoutlier=0.25; % flag frames over this
GLMoutlierlim=2; % flag frames over this z-score of global signal
GREYoutlierlim=2;
voxdim='333';
switches.WMero=4;
switches.CSFero=1;
set(0, 'DefaultFigureVisible', 'off');
% [rois x y z] = textread(roilist,'%s%f%f%f');
% roimasks = zeros(147456,size(rois,1));
% %roimasks = zeros(147456,size(rois,1));
% for i=1:size(rois,1)
% i
% roimasks_orig(:,i)=read_4dfpimg_HCP(rois{i,1});
% end
[rois] = textread(roilist,'%s');
roimasks_orig = read_4dfpimg_HCP(rois{1});
switches.doregression=0;
switches.regressiontype=1;
switches.motionestimates=1;
switches.WM=0;
switches.V=0;
switches.GS=0;
switches.dointerpolate=0;
switches.dobandpass=0;
switches.temporalfiltertype=3;
switches.lopasscutoff=0;
switches.hipasscutoff=0;
switches.order=0;
switches.doblur=0;
switches.blurkernel=0;
%% CHECK THAT BASIC FILES ARE ACTUALLY THERE
% read in the subject data including location, vcnum, and boldruns
[df.filepath df.vcnum df.prmfile df.TR df.TRskip] = textread(datafile,'%s%s%s%f%d');
fprintf('CHECKING THAT DATA EXIST\n');
pause(2);
numsubs=size(df.vcnum,1);
for i=1:numsubs
QC(i).vcnum=df.vcnum{i,1};
QC(i).TR=df.TR(i,1);
QC(i).TRskip=df.TRskip(i,1);
end
%% CHECK TEMPORAL MASKS
fprintf('CHECKING TEMPORAL MASKS\n');
switch tmasktype
case 'ones'
otherwise
[tm.vcnum tm.tmaskfiles]=textread(tmasktype,'%s%s');
if ~isequal(tm.vcnum,df.vcnum)
error('masklist vcnumbers do not match datalist vcnumbers');
end
end
%% READ IN FREESURFER
if ~isempty(varargin)
[FSfile.vc FSfile.dir]=textread(varargin{1,1},'%s%s');
end
errorout=0;
for i=1:numsubs
found=1;
%for j=1:length(FSfile.dir)
%if isequal(FSfile.vc{j,1},QC(i).vcnum) || isequal([FSfile.vc{j,1} '_2'],[QC(i).vcnum])
QC(i).fsdir=[FSfile.dir{1} '/' FSfile.vc{1}];
% found=found+1;
% end
% end
% if found==1
% elseif found>1
% errorout=1;
% fprintf('%s has multiple matches to FSdirs\n',QC(i).vcnum);
% elseif found<1
% errorout=1;
% fprintf('%s has zero matches to FSdirs\n',QC(i).vcnum);
% end
end
% if errorout
% error();
% end
%% SET SWITCHES
needcorrectinput=1;
while needcorrectinput
switches.doregression=input('Do you want to regress nuisance signals? (1=y; 0=no): ');
switch switches.doregression
case 1
needcorrectinput=0;
needcorrectinput2=1;
while needcorrectinput2
switches.regressiontype=input('Regression: 1 - Freesurfer seeds: ');
switch switches.regressiontype
% classic or freesurfer seeds
case {1}
needcorrectinput2=0;
needcorrectinput1=1;
while needcorrectinput1
switches.motionestimates=input('Do you want to regress motion estimates and derivatives? (0=no; 1=R,R`; 2=FRISTON; 20=R,R`,12rand; 3:volt3): ');
switch switches.motionestimates
case {0,1,2,20,3}
needcorrectinput1=0;
end
end
needcorrectinput1=1;
while needcorrectinput1
switches.WM=input('Do you want to regress white matter signals and derivatives? (1=y; 0=no): ');
switch switches.WM
case {0,1}
needcorrectinput1=0;
end
end
needcorrectinput1=1;
while needcorrectinput1
switches.V=input('Do you want to regress ventricular signals and derivatives? (1=y; 0=no): ');
switch switches.V
case {0,1}
needcorrectinput1=0;
end
end
needcorrectinput1=1;
while needcorrectinput1
switches.GS=input('Do you want to regress global signal and derivative? (1=y; 0=no): ');
switch switches.GS
case {0,1}
needcorrectinput1=0;
end
end
% user seeds
case 2
needcorrectinput2=0;
switches.nus4dfplistfile=input('Enter the hard path to the list of nuisance regressor 4dfps ','s');
[switches.nus4dfpvcnum switches.nus4dfplist] = textread(switches.nus4dfplistfile,'%s%s');
if ~isequal(switches.nus4dfpvcnum,prepstem)
error('Nusiance 4dfp vcnums do not match the vc ordering of the datalist');
end
needcorrectinput1=1;
while needcorrectinput1
switches.motionestimates=input('Do you want to also regress motion estimates and derivatives? (1=y; 0=no): ');
switch switches.motionestimates
case {0,1}
needcorrectinput1=0;
end
end
% user txt file
case 3
needcorrectinput2=0;
switches.nustxtlistfile=input('Enter the hard path to the list of nuisance regressor files ','s');
[switches.nustxtvcnum switches.nustxtlist] = textread(switches.nustxtlistfile,'%s%s');
if ~isequal(switches.nustxtvcnum,prepstem)
error('Nusiance txt vcnums do not match the vc ordering of the datalist');
end
needcorrectinput1=1;
while needcorrectinput1
switches.motionestimates=input('Do you want to also regress motion estimates and derivatives? (1=y; 0=no): ');
switch switches.motionestimates
case {0,1}
needcorrectinput1=0;
end
end
case 9
needcorrectinput=0;
needcorrectinput2=0;
switches.motionestimates=1;
switches.WMV=1.
switches.GS=1;
switches.dicesize=input('What size dice to use? (# voxels): ');
switches.mindicevox=input('What is minimum # voxels needed in cubes?: ');
switches.tcchop=input('What size timeseries to use? (TRs): ');
switches.varexpl=input('How much variance should SVD explain?: ');
switches.WMero=input('How many WM erosions (4 recommended)?: ');
switches.CSFero=input('How many CSF erosions (1 recommended)?: ');
switches.sdval=input('What s.d. threshold to form nuisance mask? ');
end
end
case 0
needcorrectinput=0;
end
end
% interpolate
needcorrectinput=1;
while needcorrectinput
switches.dointerpolate=input('Do you want to interpolate over motion epochs? (1=y; 0=no): ');
switch switches.dointerpolate
case {0,1}
needcorrectinput=0;
end
end
% temporal filter lowpass
needcorrectinput=1;
while needcorrectinput
switches.dobandpass=input('Do you want to temporally filter the data (1=y; 0=no): ');
switch switches.dobandpass
case 1
needcorrectinput=0;
case 0
needcorrectinput=0;
end
end
if switches.dobandpass
needcorrectinput=1;
while needcorrectinput
switches.temporalfiltertype=input('What type of filter: (1) lowpass, (2) highpass (3) bandpass: ');
switch switches.temporalfiltertype
case {1,2,3}
needcorrectinput=0;
end
end
if switches.temporalfiltertype
switch switches.temporalfiltertype
case 1
needcorrectinput1=1;
while needcorrectinput1
switches.lopasscutoff=input('What low-pass cutoff is desired (in Hz; .08 is standard): ');
if isnumeric(switches.lopasscutoff)
needcorrectinput1=0;
end
end
case 2
needcorrectinput1=1;
while needcorrectinput1
switches.hipasscutoff=input('What high-pass cutoff is desired (in Hz; .009 is standard): ');
if isnumeric(switches.hipasscutoff)
needcorrectinput1=0;
end
end
case 3
needcorrectinput1=1;
while needcorrectinput1
switches.lopasscutoff=input('What low-pass cutoff is desired (in Hz; .08 is standard): ');
if isnumeric(switches.lopasscutoff)
needcorrectinput1=0;
end
end
needcorrectinput1=1;
while needcorrectinput1
switches.hipasscutoff=input('What high-pass cutoff is desired (in Hz; .009 is standard): ');
if isnumeric(switches.hipasscutoff)
needcorrectinput1=0;
end
end
if switches.lopasscutoff <= switches.hipasscutoff
fprintf('Low-pass cutoff must be higher than the high-pass cutoff\n');
end
end
needcorrectinput1=1;
while needcorrectinput1
switches.order=input('What filter order is desired (1 is standard): ');
if isnumeric(switches.order)
needcorrectinput1=0;
end
end
end
end
% blurring
needcorrectinput=1;
while needcorrectinput
switches.doblur=input('Do you want to spatially blur the data (1=y; 0=no): ');
switch switches.doblur
case 1
needcorrectinput=0;
needcorrectinput1=1;
while needcorrectinput1
switches.blurkernel=input('What blurring kernel do you want (in mm; 6 is standard): ');
if isnumeric(switches.blurkernel)
needcorrectinput1=0;
fprintf('Blur kernel is %d mm\n',switches.blurkernel);
end
end
case 0
needcorrectinput=0;
end
end
if switches.doblur
blursize=2*log(2)/pi*10/switches.blurkernel;
fprintf('gauss_4dfp set to blur at %d; default is .735452\n',blursize);
end
fprintf('\n\n\n\n*** HERE ARE YOUR SETTINGS ***:\n')
fprintf('switches.doregression (1=yes;0=no): %d\n',switches.doregression);
fprintf('switches.regressiontype (1=freesurfer): %d\n',switches.regressiontype);
fprintf('switches.motionestimates (0=no; 1=R,R`; 2=FRISTON; 20=R,R`,12rand): %d\n',switches.motionestimates);
fprintf('switches.WM (1=regress;0=no): %d\n',switches.WM);
fprintf('switches.V (1=regress;0=no): %d\n',switches.V);
fprintf('switches.GS (1=regress;0=no): %d\n',switches.GS);
fprintf('switches.dointerpolate (1=yes;0=no): %d\n',switches.dointerpolate);
fprintf('switches.dobandpass (1=yes;0=no): %d\n',switches.dobandpass);
fprintf('switches.temporalfiltertype (1=lowpass;2=hipass;3=bandpass): %d\n',switches.temporalfiltertype);
fprintf('switches.lopasscutoff (in Hz; 0.08 is typical): %g\n',switches.lopasscutoff);
fprintf('switches.hipasscutoff (in Hz; 0.009 is typical): %g\n',switches.hipasscutoff);
fprintf('switches.order (1 is typical): %g\n',switches.order);
fprintf('switches.doblur (1=yes;0=no): %d\n',switches.doblur);
fprintf('switches.blurkernel (in mm; 6 is typical): %d\n',switches.blurkernel);
cont=input('\nDo you wish to continue with these settings? (1=yes) ' );
if cont~=1
error('Quitting');
end
tic
%% CHECK FOR PRESENCE OF STRUCTURAL AND BOLD FILES
% CHECK FOR BOLD DATA
for i=1:numsubs
fprintf('CHECKING BOLD RUNS\t%d\t%s\n',i,QC(i).vcnum);
% determine which BOLD runs are rest runs
clear tempruns; [trash tempruns] = system([ 'awk -F "(" ''{print$2}'' ' df.prmfile{i,1} ' | awk -F ")" ''{print $1}''' ]);
QC(i).restruns = strread(tempruns,'%s','delimiter',' ');
% cycle through each BOLD run
for j=1:size(QC(i).restruns,1)
% set original data
boldmat{i,j} = cell2mat(strcat(df.filepath{i,1},'/',QC(i).vcnum,'/bold',QC(i).restruns(j,:),'/',QC(i).vcnum,'_b',QC(i).restruns(j,:),'_faln_dbnd_xr3d.mat'));
boldimg{i,j} = cell2mat(strcat(df.filepath{i,1},'/',QC(i).vcnum,'/bold',QC(i).restruns(j,:),'/',QC(i).vcnum,'_b',QC(i).restruns(j,:),'_faln_dbnd_xr3d_uwrp_atl.4dfp.img'));
boldifh{i,j} = cell2mat(strcat(df.filepath{i,1},'/',QC(i).vcnum,'/bold',QC(i).restruns(j,:),'/',QC(i).vcnum,'_b',QC(i).restruns(j,:),'_faln_dbnd_xr3d_uwrp_atl.4dfp.ifh'));
% check that original data is present
if ~exist(boldmat{i,j})
error('\t%s is not found\n',boldmat{i,j});
end
if ~exist(boldimg{i,j})
error('\t%s is not found\n',boldimg{i,j});
end
if ~exist(boldifh{i,j})
error('\t%s is not found\n',boldifh{i,j});
end
end
anataveimg{i,1} = [ df.filepath{i,1} '/' QC(i).vcnum '/unwarp_mean/' QC(i).vcnum '_faln_dbnd_xr3d_uwrp_atl_ave.4dfp.img'];
anataveifh{i,1} = [ df.filepath{i,1} '/' QC(i).vcnum '/unwarp_mean/' QC(i).vcnum '_faln_dbnd_xr3d_uwrp_atl_ave.4dfp.ifh'];
mprimg{i,1}=[ df.filepath{i,1} '/' QC(i).vcnum '/atlas/' QC(i).vcnum '_mpr_n1_' voxdim '_t88.4dfp.img'];
mprifh{i,1}=[ df.filepath{i,1} '/' QC(i).vcnum '/atlas/' QC(i).vcnum '_mpr_n1_' voxdim '_t88.4dfp.ifh'];
% mprimg{i,1}(end)=[];
% mprifh{i,1}(end)=[];
if ~exist(anataveimg{i,1})
error('\t%s is not found\n',anataveimg{i,1});
end
if ~exist(mprimg{i,1})
error('\t%s is not found\n',mprimg{i,1});
end
end
%% LINKING TO BOLD DATA
% prepare output directory
if ~exist(tdir)
mkdir(tdir)
end
fprintf('PREPARING OUTPUT DIRECTORIES\n');
fprintf('LINKING BOLD DATA\n');
pause(2);
for i=1:numsubs
% prepare target subject directory
QC(i).subdir=[tdir '/' QC(i).vcnum ];
if exist(QC(i).subdir)
rmdir(QC(i).subdir,'s');
end
mkdir(QC(i).subdir);
% make links to atlas and seed data
QC(i).subatlasdir=[QC(i).subdir '/atlas/'];
if ~exist(QC(i).subatlasdir)
mkdir(QC(i).subatlasdir);
end
% set symbolic link to structural data
tanataveimg{i,1} = [ QC(i).subatlasdir '/' QC(i).vcnum '_faln_dbnd_xr3d_uwrp_atl_ave.4dfp.img'];
tanataveifh{i,1} = [ QC(i).subatlasdir '/' QC(i).vcnum '_faln_dbnd_xr3d_uwrp_atl_ave.4dfp.ifh'];
system([ 'ln -s ' anataveimg{i,1} ' ' tanataveimg{i,1}]);
system([ 'ln -s ' anataveifh{i,1} ' ' tanataveifh{i,1}]);
tmprimg{i,1} = [ QC(i).subatlasdir '/' QC(i).vcnum '_mpr_n1_' voxdim '_t88.4dfp.img'];
tmprifh{i,1} = [ QC(i).subatlasdir '/' QC(i).vcnum '_mpr_n1_' voxdim '_t88.4dfp.ifh'];
system([ 'ln -s ' mprimg{i,1} ' ' tmprimg{i,1}]);
system([ 'ln -s ' mprifh{i,1} ' ' tmprifh{i,1}]);
system([ 'cp ' df.prmfile{i,1} ' ' QC(i).subdir '/fc.params' ]);
QC(i).MPRAGE=read_4dfpimg_HCP(mprimg{i,1});
QC(i).ANATAV=read_4dfpimg_HCP(anataveimg{i,1});
% cycle through each BOLD run
for j=1:size(QC(i).restruns,1)
% prepare and enter targetsubbolddir
QC(i).subbolddir{j}=cell2mat(strcat(QC(i).subdir,'/bold',QC(i).restruns(j,:)));
if ~exist(QC(i).subbolddir{j})
mkdir(QC(i).subbolddir{j});
end
cd(QC(i).subbolddir{j});
% set symbolic link to original data
tboldmat{i,j} = cell2mat(strcat(QC(i).subbolddir{j},'/',QC(i).vcnum,'_b',QC(i).restruns(j,:),'_faln_dbnd_xr3d.mat'));
tboldimg{i,j} = cell2mat(strcat(QC(i).subbolddir{j},'/',QC(i).vcnum,'_b',QC(i).restruns(j,:),'_faln_dbnd_xr3d_uwrp_atl.4dfp.img'));
tboldifh{i,j} = cell2mat(strcat(QC(i).subbolddir{j},'/',QC(i).vcnum,'_b',QC(i).restruns(j,:),'_faln_dbnd_xr3d_uwrp_atl.4dfp.ifh'));
system([ 'ln -s ' boldmat{i,j} ' ' tboldmat{i,j}]);
system([ 'ln -s ' boldimg{i,j} ' ' tboldimg{i,j}]);
system([ 'ln -s ' boldifh{i,j} ' ' tboldifh{i,j}]);
end
end
%% SET UP DUMMY HOLDING VARIABLE FOR LAST PROCESSED DATA
%%%% To make this modular, we are using LASTIMG to index the previous
%%%% processed image. This allows us to pick and move processing steps
stage=1;
LASTCONC{stage}= '333';
allends='333';
% initialize LASTIMG to the 333 image
for i=1:numsubs
for j=1:size(QC(i).restruns,1)
LASTIMG{i,j,stage}=cell2mat(strcat(QC(i).subbolddir{j},'/',QC(i).vcnum,'_b',QC(i).restruns(j,:),'_faln_dbnd_xr3d_uwrp_atl'));
end
cd(QC(i).subdir);
% write a concfile
fid=fopen([LASTCONC{stage} '.conc'],'w');
fprintf(fid,'number_of_files: %d\n',size(QC(i).restruns,1));
for j=1:size(QC(i).restruns,1)
fprintf(fid,'\tfile:%s\n',[LASTIMG{i,j,stage} '.4dfp.img' ]);
end
fclose(fid);
end
%% COMPUTE DEFINED VOXELS FOR THE BOLD RUNS
for i=1:numsubs
cd(QC(i).subdir);
fprintf('COMPUTE DEFINED VOXELS\t%d\t%s\n',i,QC(i).vcnum);
commands=['compute_defined_4dfp ' QC(i).subdir '/' LASTCONC{stage} '.conc >/dev/null' ];
system(commands);
pause(5);
QC(i).DFNDVOXELS=read_4dfpimg_HCP([LASTCONC{stage} '_dfnd.4dfp.img']);
end
%% CHECK FOR NUISANCE SEEDS
%if switches.doregression
needtostop=0;
switch switches.regressiontype
% case 0 % classic WashU seeds in WM and V
%
% for i=1:numsubs
% QC(i).GLMmaskfile=['//data/hcp-zfs/home/laumannt/Poldrome/shared_for_washu/freesurfer_washu/FREESURFER_fs_LR/sub013/7112b_fs_LR/brainmask_fs_222.4dfp.img'];% ['/home/usr/fidl/lib/glm_atlas_mask_' voxdim '.4dfp.img'];
% QC(i).WMmaskfile=['/home/usr/fidl/lib/small_WM.4dfp.img'];
% QC(i).CSFmaskfile=['/home/usr/fidl/lib/711-2B_lat_vent_' voxdim '.4dfp.img'];
% end
%
% for i=1:numsubs
% fprintf('CHECKING NUISANCE SEEDS\t%d\t%s\n',i,QC(i).vcnum);
% needtostop=0;
%
% tmpmask=read_4dfpimg_HCP(QC(i).GLMmaskfile);
% tmpmask=tmpmask & QC(i).DFNDVOXELS;
% if nnz(tmpmask)==0
% fprintf('%s is empty!\n',QC(i).GLMmaskfile);
% needtostop=1;
% else
% QC(i).GLMMASK=~~tmpmask;
% end
%
% tmpmask=read_4dfpimg_HCP(QC(i).WMmaskfile);
% tmpmask=tmpmask & QC(i).DFNDVOXELS;
% if nnz(tmpmask)==0
% fprintf('%s is empty!\n',QC(i).WMmaskfile);
% needtostop=1;
% else
% QC(i).WMMASK=~~tmpmask;
% end
%
% tmpmask=read_4dfpimg_HCP(QC(i).CSFmaskfile);
% tmpmask=tmpmask & QC(i).DFNDVOXELS;
% if nnz(tmpmask)==0
% fprintf('%s is empty!\n',QC(i).CSFmaskfile);
% needtostop=1;
% else
% QC(i).CSFMASK=~~tmpmask;
% end
%
% if needtostop
% error('Fix empty masks.\n');
% end
% end
%
% % create a holding variable for seeds and labels
% for i=1:numsubs
% seedcount=0;
% QC(i).seedhold=[];
% if switches.GS
% seedcount=seedcount+1;
% QC(i).seedhold=[QC(i).seedhold QC(i).GLMMASK];
% QC(i).seedholdlabel{seedcount}='WB';
% end
% if switches.WM
% seedcount=seedcount+1;
% QC(i).seedhold=[QC(i).seedhold QC(i).WMMASK];
% QC(i).seedholdlabel{seedcount}='WM';
% end
% if switches.V
% seedcount=seedcount+1;
% QC(i).seedhold=[QC(i).seedhold QC(i).CSFMASK];
% QC(i).seedholdlabel{seedcount}='CSF';
% end
% end
case {0,1,9} % freesurfer masks of WM and V
disp('hello')
% set basic names
for i=1:numsubs
QC(i).GLMmaskfile=['/data/cn4/laumannt/Standard/glm_atlas_mask_' voxdim '.4dfp.img'];
QC(i).WMmaskfile=[ QC(i).fsdir '/nusmask/aparc+aseg_cerebralwm_ero' num2str(switches.WMero) '_mask_' voxdim '.4dfp.img'];
QC(i).CSFmaskfile=[ QC(i).fsdir '/nusmask/aparc+aseg_CSF_ero' num2str(switches.CSFero) '_mask_' voxdim '.4dfp.img'];
QC(i).WBmaskfile=[ QC(i).fsdir '/nusmask/aparc+aseg_brainmask_mask_' voxdim '.4dfp.img'];
QC(i).GREYmaskfile=[ QC(i).fsdir '/nusmask/aseg_GM_mask_' voxdim '.4dfp.img'];
end
% check for existence of mask files
for i=1:numsubs
fprintf('CHECKING NUISANCE SEEDS\t%d\t%s\n',i,QC(i).vcnum);
needtostop=0;
if ~exist([QC(i).GLMmaskfile])
fprintf('No GLMmask found: %s\n',QC(i).GLMmaskfile);
needtostop=1;
end
if ~exist([ QC(i).fsdir '/' ])
fprintf('No FREESURFER folder! Subject %s needs to have mpr2caret run\n',QC(i).vcnum);
needtostop=1;
end
if ~exist(QC(i).WBmaskfile)
fprintf('%s missing!\n',QC(i).WBmaskfile);
needtostop=1;
end
if ~exist(QC(i).GREYmaskfile)
fprintf('%s missing!\n',QC(i).GREYmaskfile);
needtostop=1;
end
if ~exist(QC(i).WMmaskfile)
fprintf('%s missing!\n',QC(i).WMmaskfile);
needtostop=1;
end
if ~exist(QC(i).CSFmaskfile)
fprintf('%s missing!\n',QC(i).CSFmaskfile);
needtostop=1;
end
if needtostop
error('Fix the FREESURFER masks.\n');
end
end
% ensure masks contain something, relax erosions if not
for i=1:numsubs
needtostop=0;
tmpmask=read_4dfpimg(QC(i).GLMmaskfile);
tmpmask=tmpmask & QC(i).DFNDVOXELS;
if nnz(tmpmask)==0
fprintf('%s is empty!\n',QC(i).GLMmaskfile);
needtostop=1;
else
QC(i).GLMMASK=~~tmpmask;
end
tmpmask=read_4dfpimg_HCP(QC(i).WBmaskfile);
tmpmask=tmpmask & QC(i).DFNDVOXELS;
if nnz(tmpmask)==0
fprintf('%s is empty!\n',QC(i).WBmaskfile);
needtostop=1;
else
QC(i).WBMASK=~~tmpmask;
end
tmpmask=read_4dfpimg_HCP(QC(i).GREYmaskfile);
tmpmask=tmpmask & QC(i).DFNDVOXELS;
if nnz(tmpmask)==0
fprintf('%s is empty!\n',QC(i).GREYmaskfile);
needtostop=1;
else
QC(i).GMMASK=~~tmpmask;
end
tmpmask=read_4dfpimg_HCP(QC(i).WMmaskfile);
tmpmask=tmpmask & QC(i).DFNDVOXELS;
tmpWMero=switches.WMero;
while nnz(tmpmask)==0
tmpWMero=tmpWMero-1;
if tmpWMero==-1
fprintf('Subject %s has no white matter voxels!\n',QC(i).vcnum)
needtostop=1;
break;
end
fprintf('Reducing WM erosion to %d; zero voxels in %s\n',tmpWMero,QC(i).WMmaskfile);
QC(i).WMmaskfile = [ QC(i).fsdir '/nusmask/aparc+aseg_cerebralwm_ero' num2str(tmpWMero) '_mask_' voxdim '.4dfp.img'];
tmpmask=read_4dfpimg_HCP(QC(i).WMmaskfile);
tmpmask=tmpmask & QC(i).DFNDVOXELS;
end
QC(i).WMMASK=~~tmpmask;
QC(i).WMero=tmpWMero;
tmpmask=read_4dfpimg_HCP(QC(i).CSFmaskfile);
tmpmask=tmpmask & QC(i).DFNDVOXELS;
tmpCSFero=switches.CSFero;
while nnz(tmpmask)==0
tmpCSFero=tmpCSFero-1;
if tmpCSFero==-1
fprintf('Subject %s has no CSF voxels!\n',QC(i).vcnum)
needtostop=1;
break;
end
fprintf('Reducing CSF erosion to %d; zero voxels in %s\n',tmpCSFero,QC(i).CSFmaskfile);
QC(i).CSFmaskfile = [ QC(i).fsdir '/nusmask/aparc+aseg_cerebralwm_ero' num2str(tmpCSFero) '_mask_' voxdim '.4dfp.img'];
tmpmask=read_4dfpimg_HCP(QC(i).CSFmaskfile);
end
QC(i).CSFMASK=~~tmpmask;
QC(i).CSFero=tmpCSFero;
if needtostop
error('Fix empty masks.\n');
end
end
% create a holding variable for seeds and labels
for i=1:numsubs
seedcount=0;
QC(i).seedhold=[];
if switches.GS
seedcount=seedcount+1;
QC(i).seedhold=[QC(i).seedhold QC(i).WBMASK];
QC(i).seedholdlabel{seedcount}='WB';
end
if switches.WM
seedcount=seedcount+1;
QC(i).seedhold=[QC(i).seedhold QC(i).WMMASK];
QC(i).seedholdlabel{seedcount}='WM';
end
if switches.V
seedcount=seedcount+1;
QC(i).seedhold=[QC(i).seedhold QC(i).CSFMASK];
QC(i).seedholdlabel{seedcount}='CSF';
end
end
case 2 % external 4dfp of regressor ROIs
case 3 % external txt file
otherwise
end
%end
%% LINK NUISANCE SEEDS
for i=1:numsubs
QC(i).subseeddir=[QC(i).subdir '/nusseeds/'];
if ~exist(QC(i).subseeddir)
mkdir(QC(i).subseeddir);
end
cd(QC(i).subdir);
system(['mv ' LASTCONC{stage} '_dfnd.* ' QC(i).subseeddir ]);
% if switches.doregression
switch switches.regressiontype
% case 0
% [pth tmpseedimg]=fileparts(QC(i).GLMmaskfile);
% system([ 'ln -s ' pth '/' tmpseedimg '.img ' QC(i).subseeddir '/' tmpseedimg '.img' ]);
% system([ 'ln -s ' pth '/' tmpseedimg '.ifh ' QC(i).subseeddir '/' tmpseedimg '.ifh' ]);
% [pth tmpseedimg]=fileparts(QC(i).WMmaskfile);
% system([ 'ln -s ' pth '/' tmpseedimg '.img ' QC(i).subseeddir '/' tmpseedimg '.img' ]);
% system([ 'ln -s ' pth '/' tmpseedimg '.ifh ' QC(i).subseeddir '/' tmpseedimg '.ifh' ]);
% [pth tmpseedimg]=fileparts(QC(i).CSFmaskfile);
% system([ 'ln -s ' pth '/' tmpseedimg '.img ' QC(i).subseeddir '/' tmpseedimg '.img' ]);
% system([ 'ln -s ' pth '/' tmpseedimg '.ifh ' QC(i).subseeddir '/' tmpseedimg '.ifh' ]);
% write_4dfpimg(QC(i).seedhold,[ QC(i).subseeddir '/usedseeds.4dfp.img'],'bigendian');
% write_4dfpifh_222([ QC(i).subseeddir '/usedseeds.4dfp.img'],size(QC(i).seedhold,2),'bigendian',128,128,75,2,2,2);
%
case {0,1,9}
[pth tmpseedimg]=fileparts(QC(i).GLMmaskfile);
system([ 'ln -s ' pth '/' tmpseedimg '.img ' QC(i).subseeddir '/' tmpseedimg '.img' ]);
system([ 'ln -s ' pth '/' tmpseedimg '.ifh ' QC(i).subseeddir '/' tmpseedimg '.ifh' ]);
[pth tmpseedimg]=fileparts(QC(i).WMmaskfile);
system([ 'ln -s ' pth '/' tmpseedimg '.img ' QC(i).subseeddir '/' tmpseedimg '.img' ]);
system([ 'ln -s ' pth '/' tmpseedimg '.ifh ' QC(i).subseeddir '/' tmpseedimg '.ifh' ]);
[pth tmpseedimg]=fileparts(QC(i).CSFmaskfile);
system([ 'ln -s ' pth '/' tmpseedimg '.img ' QC(i).subseeddir '/' tmpseedimg '.img' ]);
system([ 'ln -s ' pth '/' tmpseedimg '.ifh ' QC(i).subseeddir '/' tmpseedimg '.ifh' ]);
[pth tmpseedimg]=fileparts(QC(i).GREYmaskfile);
system([ 'ln -s ' pth '/' tmpseedimg '.img ' QC(i).subseeddir '/' tmpseedimg '.img' ]);
system([ 'ln -s ' pth '/' tmpseedimg '.ifh ' QC(i).subseeddir '/' tmpseedimg '.ifh' ]);
[pth tmpseedimg]=fileparts(QC(i).WBmaskfile);
system([ 'ln -s ' pth '/' tmpseedimg '.img ' QC(i).subseeddir '/' tmpseedimg '.img' ]);
system([ 'ln -s ' pth '/' tmpseedimg '.ifh ' QC(i).subseeddir '/' tmpseedimg '.ifh' ]);
write_4dfpimg(QC(i).seedhold,[ QC(i).subseeddir '/usedseeds.4dfp.img'],'bigendian');
write_4dfpifh([ QC(i).subseeddir '/usedseeds.4dfp.img'],size(QC(i).seedhold,2),'bigendian',128,128,75,2,2,2);
case 2
end
end
%end
%% CALCULATE SUBJECT MOVEMENT
for i=1:numsubs
for j=1:size(QC(i).restruns,1)
cd(QC(i).subbolddir{j});
fprintf('CALCULATING MOTION\t%d\t%s\trun%s\n',i,QC(i).vcnum,cell2mat(QC(i).restruns(j,:)));
% obtain realignment parameters
system([ 'mat2dat -R -D -L ' tboldmat{i,j} ' >/dev/null' ]);
pause(5);
rdatfile{i,j}= cell2mat(strcat(df.filepath{i,1},'/',QC(i).vcnum,'/movement/',QC(i).vcnum,'_b',QC(i).restruns(j,:),'_faln_dbnd_xr3d.rdat'));
ddatfile{i,j}= cell2mat(strcat(df.filepath{i,1},'/',QC(i).vcnum,'/movement/',QC(i).vcnum,'_b',QC(i).restruns(j,:),'_faln_dbnd_xr3d.ddat'));
% convert realignment parameters to FD, write them
[rmstotal{i,j} rmstrans rmsrot rmscol mvm{i,j}] = rdat_calculations(rdatfile{i,j},QC(i).TRskip,50);
[drmstotal{i,j} drmstrans drmsrot drmscol ddt_mvm{i,j}] = rdat_calculations(ddatfile{i,j},QC(i).TRskip,50);
FD{i,j}=(sum(abs(ddt_mvm{i,j}),2));
dlmwrite('FDvals.txt',FD{i,j},'\t');
% write the movement parameters
dlmwrite('movement.txt',mvm{i,j},'\t');
dlmwrite('ddt_movement.txt',ddt_mvm{i,j},'\t');
% detrend the movement
system(['cat movement.txt | gawk -f ' releasedir '/trendout.awk >! movement_detrended.txt']);
system(['cat ddt_movement.txt | gawk -f ' releasedir '/trendout.awk >! ddt_movement_detrended.txt']);
% load in the detrended regressors
mvm_detrend{i,j}=load('movement_detrended.txt');
ddt_mvm_detrend{i,j}=load('ddt_movement_detrended.txt');
end
% WRITE TOTAL DATA FOR EACH SUBJECT
cd(QC(i).subdir);
% write the total movement data
QC(i).MVM=[];
QC(i).ddtMVM=[];
QC(i).DTMVM=[];
QC(i).ddtDTMVM=[];
QC(i).FD=[];
for j=1:size(QC(i).restruns,1)
QC(i).MVM=[QC(i).MVM; mvm{i,j}];
QC(i).ddtMVM=[QC(i).ddtMVM; ddt_mvm{i,j}];
QC(i).DTMVM=[QC(i).DTMVM; mvm_detrend{i,j}];
QC(i).ddtDTMVM=[QC(i).ddtDTMVM; ddt_mvm_detrend{i,j}];
QC(i).FD=[QC(i).FD; FD{i,j}];
end
dlmwrite('total_movement.txt',QC(i).MVM,'\t');
dlmwrite('total_ddt_movement.txt',QC(i).ddtMVM,'\t');
dlmwrite('total_movement_detrended.txt',QC(i).DTMVM,'\t');
dlmwrite('total_ddt_movement_detrended.txt',QC(i).ddtDTMVM,'\t');
dlmwrite('total_FD.txt',QC(i).FD,'\t');
QC(i).MVMrms=array_calc_rms(QC(i).MVM);
QC(i).DTMVMrms=array_calc_rms(QC(i).DTMVM);
QC(i).FDbar=mean(QC(i).FD);
QC(i).switches=switches;
end
%% DEFINE RUN BORDERS
for i=1:numsubs
trpos=0;
tr(i).tot=numel(QC(i).FD);
for j=1:size(QC(i).restruns,1)
tr(i).runtrs(j)=numel(FD{i,j});
tr(i).start(j,1:2)=[trpos+1 trpos+tr(i).runtrs(j)];
trpos=trpos+tr(i).runtrs(j);
QC(i).runborders(j,:) = [j tr(i).start(j,1:2)];
end
% QC(i).runborders=[QC(i).restruns' tr(i).start];
cd(QC(i).subdir);
dlmwrite('runborders.txt',QC(i).runborders,'\t');
end
[sortTR sortsubs]=sort(cell2mat({tr.tot}));
%% ASSEMBLE TEMPORAL MASKS
switch tmasktype
case 'ones'
for i=1:numsubs
for j=1:size(QC(i).restruns,1)
QC(i).runtmask{j}=ones(size(FD{i,j},1),1);
QC(i).runtmask{j}(1:QC(i).TRskip)=0;
end
QC(i).tmask=[];
for j=1:size(QC(i).restruns,1)
QC(i).tmask=[QC(i).tmask; QC(i).runtmask{j}];
end
end
otherwise
for i=1:numel(tm.tmaskfiles)
fprintf('GETTING TMASK FILE\t%d\t%s\t%s\n',i,QC(i).vcnum,tm.tmaskfiles{i,1});
QC(i).tmask=load(tm.tmaskfiles{i,1});
if ~isequal(numel(QC(i).tmask),numel(QC(i).FD))
error('tmask length does not match the subject data');
end
for j=1:size(QC(i).restruns,1)
QC(i).runtmask{j}=QC(i).tmask(QC(i).runborders(j,2):QC(i).runborders(j,3));
end
end
end
for i=1:numsubs
cd(QC(i).subdir);
dlmwrite('total_tmask.txt',QC(i).tmask,'\t');
tmask2format(QC(i).tmask,'total_tmask_avi.txt');
QC(i).tmask=~~QC(i).tmask;
for j=1:size(QC(i).restruns,1)
cd(QC(i).subbolddir{j});
dlmwrite('tmask.txt',QC(i).runtmask{j},'\t');
tmask2format(QC(i).runtmask{j},'tmask_avi.txt');
QC(i).runtmask{j}=~~QC(i).runtmask{j};
end
end
%% FUNCTIONAL CONNECTIVITY PROCESSING
bigstuff=1; % this saves voxelwise timecourses over processing.
skipvox=15; % downsample grey matter voxels for visuals.
set(0, 'DefaultFigureVisible', 'off');
for f=1:numsubs
% orders subjects in decreasing order to minimize memory fragmentation
i=sortsubs(f);
fprintf('FCPROCESSING SUBJECT %d %s\n',f,QC(i).vcnum);
pause(2);
%Select voxels in glmmask
QC(i).CSFMASK_glmmask = QC(i).CSFMASK(logical(QC(i).GLMMASK));
QC(i).WMMASK_glmmask = QC(i).WMMASK(logical(QC(i).GLMMASK));
QC(i).GMMASK_glmmask = QC(i).GMMASK(logical(QC(i).GLMMASK));
QC(i).WBMASK_glmmask = QC(i).WBMASK(logical(QC(i).GLMMASK));
QC(i).GLMMASK_glmmask = QC(i).GLMMASK(logical(QC(i).GLMMASK));
roimasks =roimasks_orig(logical(QC(i).GLMMASK),:);
%%%
% THE PROCESSING BEGINS
%%%
stage=1;
LASTCONC{stage}= '333';
allends='333';
for j=1:size(QC(i).restruns,1)
LASTIMG{i,j,stage}=cell2mat(strcat(QC(i).subbolddir{j},'/',QC(i).vcnum,'_b',QC(i).restruns(j,:),'_xr3d_uwrp_atl'));
end
cd(QC(i).subdir);
% obtain the raw images
ending='333';
[bolds]=conc2bolds([LASTCONC{stage} '.conc']);
[tempimg]=bolds2img(bolds,tr(i).tot,tr(i).start,QC(i).GLMMASK);
[QC]=tempimgsignals(QC,i,tempimg,switches,stage);
QC(i).process{stage}=ending;
QC(i).tc(:,:,stage)=gettcs(roimasks,tempimg);
dlmwrite(['total_DV_' LASTCONC{stage} '.txt'],QC(i).DV_GLM(:,stage));
if bigstuff
tmptcs=single(tempimg(QC(i).GMMASK_glmmask,:));
QC(i).GMtcs(:,:,stage)=tmptcs(1:skipvox:end,:);
QC(i).WMtcs(:,:,stage)=single(tempimg(QC(i).WMMASK_glmmask,:));
QC(i).CSFtcs(:,:,stage)=single(tempimg(QC(i).CSFMASK_glmmask,:));
end
makepictures(QC(i),stage,switches,[700:200:1300],[0:50:100],50);
saveas(gcf,[ num2str(i) '_' QC(i).vcnum '_' num2str(stage) '_' allends '.tiff'],'tiff');
%%%%%%%%%%%%%%%%%%%%%%%%