-
Notifications
You must be signed in to change notification settings - Fork 0
/
possum.cc
1079 lines (1035 loc) · 43.6 KB
/
possum.cc
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
/* POSSUM
Ivana Drobnjak, Mark Jenkinson and Matthew Webster
Copyright (C) 2005-2010 University of Oxford */
/* Part of FSL - FMRIB's Software Library
http://www.fmrib.ox.ac.uk/fsl
Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
Imaging of the Brain), Department of Clinical Neurology, Oxford
University, Oxford, UK
LICENCE
FMRIB Software Library, Release 5.0 (c) 2012, The University of
Oxford (the "Software")
The Software remains the property of the University of Oxford ("the
University").
The Software is distributed "AS IS" under this Licence solely for
non-commercial use in the hope that it will be useful, but in order
that the University as a charitable foundation protects its assets for
the benefit of its educational and research purposes, the University
makes clear that no condition is made or to be implied, nor is any
warranty given or to be implied, as to the accuracy of the Software,
or that it will be suitable for any particular purpose or for use
under any specific conditions. Furthermore, the University disclaims
all responsibility for the use which is made of the Software. It
further disclaims any liability for the outcomes arising from using
the Software.
The Licensee agrees to indemnify the University and hold the
University harmless from and against any and all claims, damages and
liabilities asserted by third parties (including claims for
negligence) which arise directly or indirectly from the use of the
Software or the sale of any products based on the Software.
No part of the Software may be reproduced, modified, transmitted or
transferred in any form or by any means, electronic or mechanical,
without the express permission of the University. The permission of
the University is not required if the said reproduction, modification,
transmission or transference is done without financial return, the
conditions of this Licence are imposed upon the receiver of the
product, and all original and amended source code is included in any
transmitted product. You may be held legally responsible for any
copyright infringement that is caused or encouraged by your failure to
abide by these terms and conditions.
You are not permitted under this Licence to use this Software
commercially. Use for which any financial return is received shall be
defined as commercial use, and includes (1) integration of all or part
of the source code or the Software into a product for sale or license
by or on behalf of Licensee to third parties or (2) use of the
Software or any derivative of it for research with the final aim of
developing software products for sale or license to a third party or
(3) use of the Software or any derivative of it for research with the
final aim of developing non-software products for sale or license to a
third party, or (4) use of the Software to provide any service to an
external organisation for which payment is received. If you are
interested in using the Software commercially, please contact Oxford
University Innovation ("OUI"), the technology transfer company of the
University, to negotiate a licence. Contact details are:
[email protected] quoting reference DE/9564. */
// POSSUM
#include <iostream>
#include <string>
#include <fstream>
#include <unistd.h>
#include <time.h>
#ifdef USE_MPI
#include <mpi.h>
#include <unistd.h>
#endif //USE_MPI
#include "libprob.h"
#include "newmatap.h"
#include "newmatio.h"
#include "newimage/newimageall.h"
#include "possumfns.h"
#include "utils/options.h"
#include "newimage/costfns.h"
#include "miscmaths/miscmaths.h"
#define _GNU_SOURCE 1
#define POSIX_SOURCE 1
using namespace NEWIMAGE;
using namespace NEWMAT;
using namespace MISCMATHS;
using namespace Utilities;
//using namespace std;
string title="possum\nCopyright(c) 2007, University of Oxford (Ivana Drobnjak)";
string examples="possum -i <input phantom volume> -x <MR parameters matrix> -p <pulse> -f <RF slice profile> -m <motion file> -o <output signal matrix> [optional arguments]";
Option<bool> verbose(string("-v,--verbose"), false,
string("switch on diagnostic messages"),
false, no_argument);
Option<bool> help(string("-h,--help"), false,
string("display this message"),
false, no_argument);
//INPUT object and its characteristics (including susc effects on B0 and the RF inhomogeneities)
Option<string> opt_object(string("-i,--inp"), string(""),
string("<input4Dvol-filename> (Input object)"),
true, requires_argument);
Option<string> opt_tissue(string("-x,--mrpar"),string("") ,
string("<inputmatrix-filename> (MR parameters)"),
true,requires_argument);
Option<string> opt_b0(string("-b,--b0p"), string(""),
string("<input3Dvol-basename> (B0 inhomogeneities due to the susceptibility differences - base name, without extras z_dz, z_dx etc)"),
false, requires_argument);
Option<string> opt_b0extra(string("--b0extra"), string(""),
string("<input3Dvol-filename> (B0 inhomogeneities due to an extra field - see b0time)"),
false, requires_argument);
Option<string> opt_b0timecourse4D(string("--b0time"),string(""),
string("<inputmatrix-filename> (B0inhomogeneities_timecourse [time(s) multiply_factor(perc 0 to 1)] - see b0extra) "),
false,requires_argument);
Option<string> opt_RFrec(string("-r,--rfr"), string(""),
string("<input3Dvol-filename> ( RF inhomogeneity - receive. NOTE: not yet to be used ) "),
false, requires_argument);
Option<string> opt_RFtrans(string("-s,--rft"), string(""),
string("<input3Dvol-filename> ( RF inhomogeneity - transmit. NOTE: not yet to be used )"),
false, requires_argument);
//INPUT motion and activation
Option<string> opt_activation4D(string("-q,--activ4D"),string(""),
string("<input4Dvol-filename> (Activation volume) "),
false,requires_argument);
Option<string> opt_timecourse4D(string("-u,--activt4D"),string(""),
string("<inputmatrix-filename> (Activation4D_timecourse [time(s)])"),
false,requires_argument);
Option<string> opt_activation(string("-a,--activ"),string(""),
string("<input3Dvol-filename> (Activation volume)"),
false,requires_argument);
Option<string> opt_timecourse(string("-t,--activt"),string(""),
string("<inputmatrix-filename> (Activation_timecourse [time(s) multiply_factor(perc 0 to 1)])"),
false,requires_argument);
Option<string> opt_motion(string("-m,--motion"), string(""),
string("<inputmatrix-filename> (Motion matrix [time(s) Tx(m) Ty(m) Tz(m) Rx(rad) Ry(rad) Rz(rad)]) "),
true, requires_argument);
//INPUT for the pulse sequence
Option<string> opt_pulse(string("-p,--pulse"), string(""),
string("<inputmatrix-basename> (Pulse sequence - all additional files .posx,.posy, etc, expected to be in the same directory)"),
true, requires_argument);
Option<string> opt_slcprof(string("-f,--slcprof"), string(""),
string("<inputmatrix-filename> (RF slice profile)"),
true, requires_argument);
Option<bool> opt_rfavg(string("--rfavg"), false,
string("If this option is ON it will use RF angle averging"),
false, no_argument);
//INPUT for the computational efficiency
Option<int> opt_level(string("-l,--lev"), 1,
string("{1,2,3,4} (Levels: 1.no motion//basic B0 2.motion//basic B0, 3.motion//full B0, 4.no motion//time changing B0)"),
false,requires_argument);
Option<bool> opt_nospeedup(string("--nospeedup"), false,
string("If this option is ON it will NOT do the speedup but will do signal for all the slices for each voxel."),
false, no_argument);
//INPUT for the manual paralelisation -- used with sge_possum
Option<int> opt_nproc(string("--nproc"), 1,
string("<int> (INPUT for the paralelisation -- Number of processors we have available)"),
false,requires_argument);
Option<int> opt_procid(string("--procid"), 0,
string("<int> (INPUT for the paralelisation -- ID of the processor we are on)"),
false,requires_argument);
//OUTPUT signal
Option<string> opt_signal(string("-o,--out"), string(""),
string("<outputmatrix-filename> (Signal - [sreal, simag])"),
true, requires_argument);
//INPUT main event matrix
Option<string> opt_mainmatrix(string("-e,--mainmatx"), string(""),
string("<inputmatrix-filename> (Main event matrix [t(s),rf_ang(rad),rf_freq_band(Hz),(4)=rf_cent_freq(Hz),read(1/0),Gx,Gy,Gz(T/m),Tx,Ty,Tz(m),angle_of_rot B(rad),rot_axis Bx,By,Bz(m),angle_of_rot A(rad),rot_axis Ax,Ay,Az(m)]) "),
true, requires_argument);
//OUTPUT kcoord if needed
Option<bool> opt_kcoord(string("-k,--kcoord"), false,
string("If this option is ON it will save the kspace coordinates"),
false, no_argument);
int nonoptarg;
/////////////////////////////////////////////////////////////////////////////////////////////////////
int compute_volume(int argc, char *argv[])
{
cout<<"Starting POSSUM..."<<endl;
cout<<""<<endl;
//tejas-22.11.12
//start time
time_t theTime = time(NULL);
cout << "possum-start-time\t"<< opt_procid.value() << "\t" << theTime << endl;
//end
/////////////////////////////////////////////////////////////////////////////
// SET UP COORDINATE SYSTEM with the CENTER IN THE CENTER OF THE OBJECT
/////////////////////////////////////////////////////////////////////////////
cout<<"Setting up the coordinate system..."<<endl;
RowVector posx;
RowVector posy;
RowVector posz;
posx=read_ascii_matrix(opt_pulse.value()+".posx");//in SI already
posy=read_ascii_matrix(opt_pulse.value()+".posy");//in SI already
posz=read_ascii_matrix(opt_pulse.value()+".posz");//in SI already
int Nxx=posx.Ncols();
cout<<""<<endl;
//////////////////////////////////////////////////////////////////////////
//PARALELL STUFF
//////////////////////////////////////////////////////////////////////////
cout<<"Setting up the process ID..."<<endl;
//int lo=0;
//int hi=Nxx;
int myid=0;
int numprocs=1;
#ifdef USE_MPI
MPI_Init(&argc,&argv);//MPI::Init(argc,argv);
MPI_Comm_size(MPI_COMM_WORLD,&numprocs);//int numprocs=MPI::COMM_WORLD.Get_size();
MPI_Comm_rank(MPI_COMM_WORLD,&myid);//myid=MPI::COMM_WORLD.Get_rank();
//lo=myid*(hi/numprocs);
//if (myid<numprocs-1) hi=(myid+1)*(hi/numprocs);
//cout<<" Process "<<myid<<" does from "<<lo<<" to "<<hi<<".\n";
#else
myid=opt_procid.value();
numprocs=opt_nproc.value();
#endif //USE_MPI
cout<<"Number of processors is "<<numprocs<<".; My ID is "<<myid<<"."<<endl;
cout<<""<<endl;
//////////////////////////////////////////////////////////////////////////
// READ IN THE OBJECT (BRAIN) and TISSUE PROPERTIES
//////////////////////////////////////////////////////////////////////////
sleep(myid*10);
cout<<"Reading the object for ID "<<myid<<"..."<<endl;
volume4D<double> phantom;//consists of gry,wht,csf,fat,mus,con,gli,skn (in that order)
read_volume4DROI(phantom,opt_object.value(),myid,0,0,0,Nxx,-1,-1,-1,numprocs,1,1,1);
//read_volume4D(phantom,opt_object.value());
int Nx=phantom.xsize();double xdim=phantom.xdim()*0.001;
int Ny=phantom.ysize();double ydim=phantom.ydim()*0.001;
int Nz=phantom.zsize();double zdim=phantom.zdim()*0.001;
int Nt=phantom.tsize();
print_volume_info(phantom,"object");
cout<<""<<endl;
cout<<"Reading the tissue properties..."<<endl;
Matrix tissue; //tissue caracteristics T1,T2*,PD,ChemicalShift=value(ppm)*gammabar*B0,T2
tissue=read_ascii_matrix(opt_tissue.value());//in SI already
cout<<"T1,T2*,SD,CS,T2: "<<endl;
cout<<tissue<<endl;
///////////////////////////////////////////////////////
//PULSE & MOTION MATRIX SORT IN MAINMATRIX
///////////////////////////////////////////////////////
RowVector pulseinfo;
pulseinfo=read_ascii_matrix(opt_pulse.value()+".info");//[SeqType,TE,TR,TRslc,Nx,Ny,dx,dy,maxG,RiseT,BWrec, Nvol,Nslc,SlcThk,SlcDir,Gap,zstart,FlipAngle]
cout<<"[SeqType,TE,TR,TRslc,Nx,Ny,dx,dy,maxG,RiseT,BW,Nvol,Nslc,SlcThk,SlcDir,Gap,zstart,FA]"<<endl;
cout<<pulseinfo<<endl;
cout<<""<<endl;
cout<<"Reading the motion file..."<<endl;
Matrix motion;
motion=read_ascii_matrix(opt_motion.value());
//cout<<"Motion file is "<<motion<<endl;
/////////////////////////////////////////////////////////////////////////
//SLICE PROFILE
/////////////////////////////////////////////////////////////////////////
cout<<"Creating table for the slice profile..."<<endl;
double* table_slcprof;
//slcprof has two columns: first one is normalised frequency (f-fc)/df -user defined, second is the normalised strength (0 1)- amount of the flip angle
Matrix slcprof=read_ascii_matrix(opt_slcprof.value());
int Nslc=slcprof.Nrows();
table_slcprof = new double[Nslc];
for (int n=0;n<=Nslc-1;n++){
table_slcprof[n]=slcprof(n+1,2);
}
double slcpr_range=slcprof(Nslc,1)-slcprof(1,1);
double dslcp=slcpr_range/(Nslc-1);//step size for table for the slcprof
double dslcp_first=slcprof(1,1);
double slcthk=pulseinfo(14);//slcthk(m)
double slcpr_add=(slcpr_range-1)/2*slcthk;
cout<<"Stepsize for the table: dslcp= "<<dslcp<<endl;
cout<<""<<endl;
//////////////////////////////////////////////////////////////////
//CALCULATING ZSTART, ZEND AND LEVEL, useful just for the speed up
//////////////////////////////////////////////////////////////////
cout<<"Calculating zstart, zend and level..."<<endl;
int numvol=(int) (pulseinfo(12));
int numslc=(int) (pulseinfo(13));
double gap=pulseinfo(16);// gap (m)
int resX=(int) (pulseinfo(5));
int resY=(int) (pulseinfo(6));
int kspacestart=(int) (pulseinfo(22));
int nrf=numslc*numvol;//number of rf pulses
if (pulseinfo(1) == 3 || pulseinfo(1) == 4) {
nrf = nrf *2; //Adjust nrf for spin-echo case
}
if (pulseinfo(1) == 2 || pulseinfo(1) == 4) {
nrf = nrf *resY; //Adjust nrf for line-by-line readouts
}
int motionsize=motion.Nrows();
double tzmax, tzmin, txmax, txmin, tymax,tymin, rxmaxabs, rymaxabs, rzmaxabs;
tzmax=0;tzmin=0; txmax=0;txmin=0; tymax=0; tymin=0; rxmaxabs=0; rymaxabs=0; rzmaxabs=0;
int level;
for (int k=1;k<=motionsize;k++){
if (motion(k,2)>txmax) txmax=motion(k,2);
if (motion(k,2)<txmin) txmin=motion(k,2);
if (motion(k,3)>tymax) tymax=motion(k,3);
if (motion(k,3)<tymin) tymin=motion(k,3);
if (motion(k,4)>tzmax) tzmax=motion(k,4);
if (motion(k,4)<tzmin) tzmin=motion(k,4);
if (fabs(motion(k,5))>rxmaxabs) rxmaxabs=fabs(motion(k,5));
if (fabs(motion(k,6))>rymaxabs) rymaxabs=fabs(motion(k,6));
if (fabs(motion(k,7))>rzmaxabs) rzmaxabs=fabs(motion(k,7));
}
//slc selection direction stuff
int slcdir=(int) (pulseinfo(15));
cout<<"Slice selection direction is "<<slcdir<<". (-+1 is z, -+2 is y and -+3 is x.)"<<endl;
double ssrxmaxabs,ssrymaxabs, sszdim, sstzmax,sstzmin;
int ssNz;
if (fabs((float)slcdir)==1){
sszdim=zdim;
ssNz=Nz;
ssrxmaxabs=rxmaxabs;
ssrymaxabs=rymaxabs;
sstzmax=tzmax;
sstzmin=tzmin;
}
else if (fabs((float)slcdir)==2){
sszdim=ydim;
ssNz=Ny;
ssrxmaxabs=rxmaxabs;
ssrymaxabs=rzmaxabs;
sstzmax=tymax;
sstzmin=tymin;
}
else {
sszdim=xdim;
ssNz=Nx;
ssrxmaxabs=rymaxabs;
ssrymaxabs=rzmaxabs;
sstzmax=txmax;
sstzmin=txmin;
}
//level calculation
if (opt_level.set()) level=opt_level.value();
else {
if (tzmax==0 && tzmin==0 && txmax==0 && txmin==0 && tymax==0 && tymin==0 && rxmaxabs==0 && rymaxabs==0 && rzmaxabs==0) level=1;
else if ( ssrxmaxabs==0 && ssrymaxabs==0 ) level=2;
else level=3;
}
cout<<"Level is "<<level<<endl;
cout<<""<<endl;
cout<<"Extra slc calculation..."<<endl;
//Basic
double sszstart_in=pulseinfo(17);// starting point in the volume in the direction of the slice selection (used to be just z)
double sszend_in=sszstart_in+numslc*slcthk+(numslc-1)*gap;
double nvox=1/sszdim;//number of voxels per 1m in slice selection direction
int sszstart_p=(int) (sszstart_in*nvox+0.0001);//zstart in vox, 0.0001 is just a fix so that it rounds it properly
int sszend_p=(int)ceil(sszend_in*nvox);
cout<<"Specified starting point is zstart= "<<sszstart_in<<" (in m) = "<<sszstart_p<<" (in voxels)"<<endl;
cout<<"Specified end point is zend= "<<sszend_in<<" (in m) = "<<sszend_p<<" (in voxels)"<<endl;
//Slice profile add ons
int slcpr_add_vox=(int)ceil(slcpr_add*nvox);
cout<<"Slice profile add-on up and down is "<<slcpr_add<<" (in m) = "<<slcpr_add_vox<<" (in voxels)"<<endl;
//Motion add ons
double rotation_add=max(fabs(posx(1))*sin(rymaxabs),fabs(posy(1))*sin(rxmaxabs));
double motion_add_down=fabs(sstzmax)+rotation_add;
double motion_add_up=fabs(sstzmin)+rotation_add;
int motion_add_down_vox=(int)ceil(motion_add_down*nvox);
int motion_add_up_vox=(int)ceil(motion_add_up*nvox);
cout<<"Motion add-on up is "<<motion_add_up<<" (in m) = "<<motion_add_up_vox<<" (in voxels)"<<endl;
cout<<"Motion add-on down is "<<motion_add_down<<" (in m) = "<<motion_add_down_vox<<" (in voxels)"<<endl;
//int extra_down_slc=(int)(ceil((motion_add_down+slcpr_add)/slcthk));
int sszstart=sszstart_p-slcpr_add_vox-motion_add_down_vox;
if (sszstart<0) sszstart=0;
//int extra_up_slc=(int)(ceil((motion_add_up+slcpr_add)/slcthk));
int sszend=sszend_p+slcpr_add_vox+motion_add_up_vox;
if (sszend>(ssNz-1)) sszend=ssNz-1;
cout<<"FINAL: Begining of the object is "<<sszstart<<" and the end is "<<sszend<<" (in vox, in slice select direction)."<<endl;
int nospeedup=0;
if (opt_nospeedup.value())nospeedup=1;//when no speed up used for slices
//counter endings for the main loop
int xstart=0;
int xend=Nx;
int ystart=0;
int yend=Ny;
int zstart=0;
int zend=Nz;
int sszz;
int sszz_slc=1;
if (fabs((float)slcdir)==1){
zstart=sszstart;
zend=sszend+1;
}
else if (fabs((float)slcdir)==2){
ystart=sszstart;
yend=sszend+1;
}
else {
xstart=sszstart;
xend=sszend+1;
}
cout<<""<<endl;
/////////////////////////////////////////////////////////////////////
// ACTIVATION (T2*)
/////////////////////////////////////////////////////////////////////
cout<<"Creating activation4D volume and timecourse vector..."<<endl;
volume4D<double> activation4D;
volume<double> activation(Nx,Ny,Nz);
double* timecourse;
double* timecourse_2=0;
double* activation4D_voxel;
int Nact;
if (opt_activation.set()) {
cout<<"3D activation mode"<<endl;
read_volumeROI(activation,opt_activation.value(),myid,0,0,Nxx,-1,-1,numprocs,1,1);
//read_volume(activation,opt_activation.value());
Matrix timecourse_tmp;
timecourse_tmp=read_ascii_matrix(opt_timecourse.value());//multiply with the activation file.
//cout<<"Timecourse_matrix is "<<timecourse_tmp<<endl;
Nact=timecourse_tmp.Nrows();
timecourse=new double[Nact];
timecourse_2=new double[Nact];
activation4D_voxel=new double[Nact];
cout<<"Testing if the values in the activation volumes are smaller than the T2* values"<<endl;
for (int n=0;n<=Nact-1;n++){
cout<<"vol= "<<n<<endl;
timecourse[n]=timecourse_tmp(n+1,1);
timecourse_2[n]=timecourse_tmp(n+1,2);
for (int xx=0;xx<Nx;xx++){
for (int yy=0;yy<Ny;yy++){
for (int zz=0;zz<Nz;zz++){
for (int tt=0;tt<Nt;tt++){
double test=fabs(activation(xx,yy,zz)*timecourse_2[n]);
if (test>=tissue(tt+1,2)) {
cout<<"WARNING: Perturbation in the T2* values in the input activation file bigger than the input T2* values."<<endl;
exit(EXIT_FAILURE);
}
}
}
}
}
}
}
else if (opt_activation4D.set()) {
cout<<"4D activation mode"<<endl;
read_volume4DROI(activation4D,opt_activation4D.value(),myid,0,0,0,Nxx,-1,-1,-1,numprocs,1,1,1);
//read_volume4D(activation4D,opt_activation4D.value());
Matrix timecourse_tmp;
timecourse_tmp=read_ascii_matrix(opt_timecourse4D.value());
Nact=timecourse_tmp.Nrows();
timecourse=new double[Nact];
activation4D_voxel=new double[Nact];
cout<<"Testing if the values in the activation volumes are smaller than the T2* values"<<endl;
for (int n=0;n<=Nact-1;n++){
cout<<"vol= "<<n<<endl;
timecourse[n]=timecourse_tmp(n+1,1);
for (int xx=0;xx<Nx;xx++){
for (int yy=0;yy<Ny;yy++){
for (int zz=0;zz<Nz;zz++){
for (int tt=0;tt<Nt;tt++){
double test=activation4D(xx,yy,zz,n);
if (test>=tissue(tt+1,2)) {
cout<<"WARNING: Perturbation in the T2* values bigger than the T2* values."<<endl;
exit(EXIT_FAILURE);
}
}
}
}
}
}
}
else {
cout<<"No activation mode"<<endl;
Nact=1;
activation4D_voxel=new double[Nact];
timecourse=new double[Nact];
timecourse[0]=0.0;
activation4D_voxel[0]=0.0;
}
cout<<""<<endl;
/////////////////////////////////////////////////////////////////////////
//RF INHOMOGENEITY
/////////////////////////////////////////////////////////////////////////
cout<<"Reading the RF inhomogeneity volumes..."<<endl;
volume<double> RFrec(Nx,Ny,Nz);//signal=signal*RFrec
volume<double> RFtrans(Nx,Ny,Nz);//flip_ang=flip_ang*RFtrans
//if (opt_RFrec.set()) read_volume_new(RFrec,opt_RFrec.value(),myid,numprocs,Nxx);
if (opt_RFrec.set()) read_volumeROI(RFrec,opt_RFrec.value(),myid,0,0,Nxx,-1,-1,numprocs,1,1);
else {
for (int px=0;px<Nx;px++){
for (int py=0;py<Ny;py++){
for (int pz=0;pz<Nz;pz++){
RFrec(px,py,pz)=1;
}
}
}
}
//if (opt_RFtrans.set()) read_volume_new(RFtrans,opt_RFtrans.value(),myid,numprocs,Nxx);
if (opt_RFtrans.set()) read_volumeROI(RFtrans,opt_RFtrans.value(),myid,0,0,Nxx,-1,-1,numprocs,1,1);
else {
for (int px=0;px<Nx;px++){
for (int py=0;py<Ny;py++){
for (int pz=0;pz<Nz;pz++){
RFtrans(px,py,pz)=1;
}
}
}
}
print_volume_info(RFrec,"RFobject");
//cout<<Nx<<" "<<Ny<<" "<<Nz<<"; RFrec(2,2,20)= "<<RFrec(2,2,20)<<"; RFrec(2,2,520)= "<<RFrec(2,2,520)<<endl;
cout<<""<<endl;
///////////////////////////////////////////////////////////////////////
//TESTING
///////////////////////////////////////////////////////////////////////
int opt_test=0;
if (verbose.value()) {
opt_test=1;
cout<<"Verbose is ON"<<endl;
}
///////////////////////////////////////////////////////////////////////
//K-SPACE COORDINATES
///////////////////////////////////////////////////////////////////////
int save_kcoord=0;
if (opt_kcoord.value()){
save_kcoord=-1;
cout<<"k-space coordinates will be saved"<<endl;
}
cout<<""<<endl;
/////////////////////////////////////////////////////////////////////////
// SIGNAL
/////////////////////////////////////////////////////////////////////////
cout<<"Calculating the signal..."<<endl;
int nreadp=resX*(resY-kspacestart+1)*numslc*numvol;
cout<<"Number of read out points is "<<nreadp<<endl;
Matrix signal(2,nreadp);//two rows, one real and one complex for the signal in sum
signal=0;
double* sreal;
double* simag;
sreal= new double[nreadp];
simag= new double[nreadp];
for (int i=0;i<=nreadp-1;i++){
sreal[i]=0.0;
simag[i]=0.0;
}
int voxelcounter=0;
double cxyz=xdim*ydim*zdim;
string outputname=opt_signal.value();
cout<<""<<endl;
///////////////////////////////////////////////////////////
//NO MOTION/
///////////////////////////////////////////////////////////
if (level==1){
cout<<"Reading the pulse sequence..."<<endl;
PMatrix pulse;
read_binary_matrix(pulse, opt_pulse.value());
////////////////////////
// B0 PERTURBATION
////////////////////////
cout<<"LEVEL1"<<endl;
cout<<"Creating 1 B0file together with 3 gradient files..."<<endl;
volume<double> b0(Nxx,Ny,Nz);
volume<double> b0x(Nxx,Ny,Nz);
volume<double> b0y(Nxx,Ny,Nz);
volume<double> b0z(Nxx,Ny,Nz);
if (opt_b0.set()) {
read_volume(b0,opt_b0.value()+"z_dz");
calc_gradientsROI(b0,b0x,b0y,b0z,myid,Nxx,numprocs);
}
else {
b0=phantom[0]*0;
b0x=b0;
b0y=b0;
b0z=b0;
}
print_volume_info(b0,"b0");
cout<<""<<endl;
//save_volume(b0z,"b0ztest");
/////////////
//MAIN LOOP
/////////////
cout<<"Main loop..."<<endl;
for (register int tt=0;tt<Nt;tt++){
for (register int zz=zstart;zz<zend;zz++){
cout<<"Tissue type="<<tt<<"; zstart="<<zstart<<"; zz="<<zz<<"; zend="<<zend<<"; Voxelnumber="<<voxelcounter<<endl;
for (register int yy=ystart;yy<yend;yy++){
int xxx=myid+xstart;
for (register int xx=xstart;xx<xend;xx++){
//slice speed up stuff
if (fabs((float)slcdir)==1) sszz=zz;
else if (fabs((float)slcdir)==2) sszz=yy;
else sszz=xx;
float slctmp=(sszz-sszstart_p)/(slcthk*nvox);
if(ceil(slctmp) == slctmp) {
sszz_slc=(int)(ceil(slctmp)+1);
} else {
sszz_slc=(int) (ceil(slctmp));
}
if (phantom(xx,yy,zz,tt)!=0){
voxelcounter=voxelcounter+1;
double den=phantom(xx,yy,zz,tt)*RFrec(xx,yy,zz)*cxyz;
if (opt_activation.set()) {
for (int n=0;n<=Nact-1;n++){
double a=activation(xx,yy,zz)*timecourse_2[n];
double b=tissue(tt+1,2);
activation4D_voxel[n]=a*b/(a+b);// conversion of beta into beta1 because of the integral (see possum no 7 page 121)
}
}
else if (opt_activation4D.set()){
for (int n=0;n<=Nact-1;n++){
double a=activation4D(xx,yy,zz,n);//zz-zstart_p when having only a pieace of the activation volume so we start from where the phantom starts
double b=tissue(tt+1,2);
activation4D_voxel[n]=a*b/(a+b);
}
}
voxel1(posx(xxx+1),posy(yy+1),posz(zz+1),tissue.Row(tt+1),
pulse,nreadp,voxelcounter,xdim,ydim,zdim,
b0(xx,yy,zz),b0x(xx,yy,zz),b0y(xx,yy,zz),b0z(xx,yy,zz),
timecourse,activation4D_voxel,Nact,outputname,
table_slcprof,dslcp,dslcp_first,Nslc,den,RFtrans(xx,yy,zz),
opt_test,nospeedup,save_kcoord,sreal,simag);
//srealT+=sreal*coil(xx,yy,zz); //Ivana 01.11.12 -trial
}
xxx=xxx+numprocs;
}
}
}
}
}
////////////////////////////////////////////////////////////
//MOTION WHEN ONLY POSSIBLE ROTATION CAN BE IN PLANE
////////////////////////////////////////////////////////////
if (level==2){
cout<<"LEVEL2"<<endl;
///////////////////////
//MAIN MATRIX
///////////////////////
cout<<"Sorting pulse sequence and the motion matrix in one large matrix..."<<endl;
cout<<"Reading the pulse sequence..."<<endl;
PMatrix pulse;
read_binary_matrix(pulse,opt_mainmatrix.value());
////////////////////////
// B0 PERTURBATION
////////////////////////
cout<<"Creating 1 B0file together with 3 gradient files..."<<endl;
volume<double> b0(Nxx,Ny,Nz);
volume<double> b0x(Nxx,Ny,Nz);
volume<double> b0y(Nxx,Ny,Nz);
volume<double> b0z(Nxx,Ny,Nz);
if (opt_b0.set()) {
read_volume(b0,opt_b0.value()+"z_dz");
calc_gradientsROI(b0,b0x,b0y,b0z,myid,Nxx,numprocs);
}
else {
b0=phantom[0]*0;
b0x=b0;
b0y=b0;
b0z=b0;
}
print_volume_info(b0,"b0");
////////////////
//MAIN LOOP
////////////////
cout<<"Main loop..."<<endl;
for (register int tt=0;tt<Nt;tt++){
for (register int zz=zstart;zz<zend;zz++){
cout<<"Tissue type="<<tt<<"; zstart="<<zstart<<"; zz="<<zz<<"; zend="<<zend<<"; Voxelnumber="<<voxelcounter<<endl;
for (register int yy=ystart;yy<yend;yy++){
int xxx=myid+xstart;
for (register int xx=xstart;xx<xend;xx++){
//slice speed up stuff
if (fabs((float)slcdir)==1) sszz=zz;
else if (fabs((float)slcdir)==2) sszz=yy;
else sszz=xx;
float slctmp=(sszz-sszstart_p)/(slcthk*nvox);
if(ceil(slctmp) == slctmp) {
sszz_slc=(int)(ceil(slctmp)+1);
} else {
sszz_slc=(int) (ceil(slctmp));
}
if (phantom(xx,yy,zz,tt)!=0){
voxelcounter=voxelcounter+1;
//cout<<"xx= "<<xx<<"; yy= "<<yy<<"; zz= "<<zz<<"; RFrec(xx,yy,zz)= "<<RFrec(xx,yy,zz)<<"; RFtrans(xx,yy,zz)= "<<RFtrans(xx,yy,zz)<<endl;
double den=phantom(xx,yy,zz,tt)*RFrec(xx,yy,zz)*cxyz;
if (opt_activation.set()) {
for (int n=0;n<=Nact-1;n++){
double a=activation(xx,yy,zz)*timecourse_2[n];
double b=tissue(tt+1,2);
activation4D_voxel[n]=a*b/(a+b);// conversion of beta into beta1 because of the integral (see possum no 7 page 121)
}
}
else if (opt_activation4D.set()){
for (int n=0;n<=Nact-1;n++){
double a=activation4D(xx,yy,zz,n);//zz-zstart_p when having only a pieace of the activation volume so we start from where the phantom starts
double b=tissue(tt+1,2);
activation4D_voxel[n]=a*b/(a+b);
}
}
voxel2(posx(xxx+1),posy(yy+1),posz(zz+1),tissue.Row(tt+1),
pulse,nrf,nreadp,voxelcounter,xdim,ydim,zdim,
b0(xx,yy,zz),b0x(xx,yy,zz),b0y(xx,yy,zz),b0z(xx,yy,zz),
timecourse,activation4D_voxel,Nact,outputname,
table_slcprof,dslcp,dslcp_first,Nslc,den,RFtrans(xx,yy,zz),
opt_test,nospeedup,save_kcoord,sreal,simag);
}
xxx=xxx+numprocs;
}
}
}
}
}
////////////////////////////////////////////////////////////
//MOTION INVOLVING ROTATION Rx or Ry or both
////////////////////////////////////////////////////////////
if (level==3){
cout<<"LEVEL3"<<endl;
////////////////////////////////////////////
// B0 PERTURBATION
////////////////////////////////////////////
cout<<"Creating 9 B0file together with 27 gradient files..."<<endl;
volume<double> b0x_dx, b0x_dy, b0x_dz, b0y_dx, b0y_dy, b0y_dz, b0z_dx,
b0z_dy, b0z_dz;//read in
volume<double> b0x_dx_gx, b0x_dx_gy, b0x_dx_gz, b0x_dy_gx, b0x_dy_gy,
b0x_dy_gz, b0x_dz_gx, b0x_dz_gy, b0x_dz_gz;//calculate from, the calc gradients
volume<double> b0y_dx_gx, b0y_dx_gy, b0y_dx_gz, b0y_dy_gx, b0y_dy_gy,
b0y_dy_gz, b0y_dz_gx, b0y_dz_gy, b0y_dz_gz;
volume<double> b0z_dx_gx, b0z_dx_gy, b0z_dx_gz, b0z_dy_gx, b0z_dy_gy,
b0z_dy_gz, b0z_dz_gx, b0z_dz_gy, b0z_dz_gz;
if (opt_b0.set()) {
read_volume(b0x_dx,opt_b0.value()+"x_dx");
calc_gradientsROI(b0x_dx,b0x_dx_gx,b0x_dx_gy,b0x_dx_gz,myid,Nxx,numprocs);
read_volume(b0x_dy,opt_b0.value()+"x_dy");
calc_gradientsROI(b0x_dy,b0x_dy_gx,b0x_dy_gy,b0x_dy_gz,myid,Nxx,numprocs);
read_volume(b0x_dz,opt_b0.value()+"x_dz");
calc_gradientsROI(b0x_dz,b0x_dz_gx,b0x_dz_gy,b0x_dz_gz,myid,Nxx,numprocs);
read_volume(b0y_dx,opt_b0.value()+"y_dx");
calc_gradientsROI(b0y_dx,b0y_dx_gx,b0y_dx_gy,b0y_dx_gz,myid,Nxx,numprocs);
read_volume(b0y_dy,opt_b0.value()+"y_dy");
calc_gradientsROI(b0y_dy,b0y_dy_gx,b0y_dy_gy,b0y_dy_gz,myid,Nxx,numprocs);
read_volume(b0y_dz,opt_b0.value()+"y_dz");
calc_gradientsROI(b0y_dz,b0y_dz_gx,b0y_dz_gy,b0y_dz_gz,myid,Nxx,numprocs);
read_volume(b0z_dx,opt_b0.value()+"z_dx");
calc_gradientsROI(b0z_dx,b0z_dx_gx,b0z_dx_gy,b0z_dx_gz,myid,Nxx,numprocs);
read_volume(b0z_dy,opt_b0.value()+"z_dy");
calc_gradientsROI(b0z_dy,b0z_dy_gx,b0z_dy_gy,b0z_dy_gz,myid,Nxx,numprocs);
read_volume(b0z_dz,opt_b0.value()+"z_dz");
calc_gradientsROI(b0z_dz,b0z_dz_gx,b0z_dz_gy,b0z_dz_gz,myid,Nxx,numprocs);
}
else {
b0x_dx=phantom[0]*0;
b0x_dx_gx=b0x_dx; b0x_dx_gy=b0x_dx; b0x_dx_gz=b0x_dx;
b0x_dy=b0x_dx; b0x_dy_gx=b0x_dx; b0x_dy_gy=b0x_dx; b0x_dy_gz=b0x_dx;
b0x_dz=b0x_dx; b0x_dz_gx=b0x_dx; b0x_dz_gy=b0x_dx; b0x_dz_gz=b0x_dx;
b0y_dx=b0x_dx; b0y_dx_gx=b0x_dx; b0y_dx_gy=b0x_dx; b0y_dx_gz=b0x_dx;
b0y_dy=b0x_dx; b0y_dy_gx=b0x_dx; b0y_dy_gy=b0x_dx; b0y_dy_gz=b0x_dx;
b0y_dz=b0x_dx; b0y_dz_gx=b0x_dx; b0y_dz_gy=b0x_dx; b0y_dz_gz=b0x_dx;
b0z_dx=b0x_dx; b0z_dx_gx=b0x_dx; b0z_dx_gy=b0x_dx; b0z_dx_gz=b0x_dx;
b0z_dy=b0x_dx; b0z_dy_gx=b0x_dx; b0z_dy_gy=b0x_dx; b0z_dy_gz=b0x_dx;
b0z_dz=b0x_dx; b0z_dz_gx=b0x_dx; b0z_dz_gy=b0x_dx; b0z_dz_gz=b0x_dx;
}
print_volume_info(b0z_dz,"b0z_dz");
///////////////////
//MAIN LOOP
///////////////////
cout<<"Main loop..."<<endl;
int nonzero=0;
for (register int tt=0;tt<Nt;tt++){
for (register int zz=zstart;zz<zend;zz++){
for (register int yy=ystart;yy<yend;yy++){
for (register int xx=xstart;xx<xend;xx++){
if (phantom(xx,yy,zz,tt)>1e-05) nonzero++;
}
}
}
}
cout<<"The number of non-zero voxels is "<<nonzero<<endl;
RowVector numpointstmp;
numpointstmp=read_ascii_matrix(opt_mainmatrix.value()+".numpoints");
int numpoints=(int)numpointstmp(1);
int seg=(int)numpointstmp(2);
if (seg==0 || seg>numpoints || save_kcoord==-1) seg=numpoints;
PMatrix pulse(seg,19);
pulse=0.0;
int segA=1;int segB=segA+seg-1;
while (segA<numpoints){
voxelcounter=0;
cout<<"Reading the main matrix.Portion SegA="<<segA<<" SegB="<<segB<<endl;
if ((segB-segA+1)!=pulse.Nrows()) pulse.ReSize(segB-segA+1,19);
read_binary_matrix(pulse,opt_mainmatrix.value(),segA,segB,1,19);//add boundaries
cout<<"MatrixFile="<<opt_mainmatrix.value()<<endl;
nrf=0;
for (int tmp=1;tmp<=(segB-segA+1);tmp++){
if (fabs(pulse(tmp,2))>1e-06) nrf++;
//cerr<<" Nrf="<<nrf<<"Pulse("<<tmp<<",2)="<<pulse(tmp,2)<<endl;
}
for (register int tt=0;tt<Nt;tt++){
for (register int zz=zstart;zz<zend;zz++){
cout<<"Tissue type="<<tt<<"; zstart="<<zstart<<"; zz="<<zz<<"; zend=";
cout<<zend<<"; Voxelnumber="<<voxelcounter<<endl;
for (register int yy=ystart;yy<yend;yy++){
int xxx=myid+xstart;
for (register int xx=0;xx<xend;xx++){
//slice speed up stuff
if (fabs((float)slcdir)==1) sszz=zz;
else if (fabs((float)slcdir)==2) sszz=yy;
else sszz=xx;
float slctmp=(sszz-sszstart_p)/(slcthk*nvox);
if(ceil(slctmp) == slctmp) {
sszz_slc=(int)(ceil(slctmp)+1);
} else {
sszz_slc=(int) (ceil(slctmp));
}
if (phantom(xx,yy,zz,tt)>1e-05){
voxelcounter=voxelcounter+1;
double den=phantom(xx,yy,zz,tt)*RFrec(xx,yy,zz)*cxyz;
if (opt_activation.set()) {
for (int n=0;n<=Nact-1;n++){
double a=activation(xx,yy,zz)*timecourse_2[n];
double b=tissue(tt+1,2);
activation4D_voxel[n]=a*b/(a+b);// conversion of beta
//into beta1 because of the integral (see possum no 7 page 121)
}
}
else if (opt_activation4D.set()){
for (int n=0;n<=Nact-1;n++){
double a=activation4D(xx,yy,zz,n);//zz-zstart_p
//when having only a pieace of the activation volume so we start
//from where the phantom starts
double b=tissue(tt+1,2);
activation4D_voxel[n]=a*b/(a+b);
}
}
voxel3(posx(xxx+1),posy(yy+1),posz(zz+1),tissue.Row(tt+1),
pulse ,segA, nrf,nreadp,nonzero,voxelcounter,xdim,ydim,zdim,
b0x_dx(xx,yy,zz),b0y_dx(xx,yy,zz),b0z_dx(xx,yy,zz),
b0x_dy(xx,yy,zz),b0y_dy(xx,yy,zz),b0z_dy(xx,yy,zz),
b0x_dz(xx,yy,zz),b0y_dz(xx,yy,zz),b0z_dz(xx,yy,zz),
b0x_dx_gx(xx,yy,zz),b0y_dx_gx(xx,yy,zz),b0z_dx_gx(xx,yy,zz),
b0x_dy_gx(xx,yy,zz),b0y_dy_gx(xx,yy,zz),b0z_dy_gx(xx,yy,zz),
b0x_dz_gx(xx,yy,zz),b0y_dz_gx(xx,yy,zz),b0z_dz_gx(xx,yy,zz),
b0x_dx_gy(xx,yy,zz),b0y_dx_gy(xx,yy,zz),b0z_dx_gy(xx,yy,zz),
b0x_dy_gy(xx,yy,zz),b0y_dy_gy(xx,yy,zz),b0z_dy_gy(xx,yy,zz),
b0x_dz_gy(xx,yy,zz),b0y_dz_gy(xx,yy,zz),b0z_dz_gy(xx,yy,zz),
b0x_dx_gz(xx,yy,zz),b0y_dx_gz(xx,yy,zz),b0z_dx_gz(xx,yy,zz),
b0x_dy_gz(xx,yy,zz),b0y_dy_gz(xx,yy,zz),b0z_dy_gz(xx,yy,zz),
b0x_dz_gz(xx,yy,zz),b0y_dz_gz(xx,yy,zz),b0z_dz_gz(xx,yy,zz),
timecourse,activation4D_voxel,Nact,outputname,table_slcprof,
dslcp,dslcp_first,Nslc,den,RFtrans(xx,yy,zz),opt_test,
nospeedup,save_kcoord,opt_rfavg.value(),
sreal,simag);
}
xxx=xxx+numprocs;
}
}
}
}
segA=segB;
segB=segA+seg-1;
if (segB>numpoints) segB=numpoints;
}
}
///////////////////////////////////////////////////////////
//NO MOTION BUT B0 PERTURBATION CHANGES WITH TIME
///////////////////////////////////////////////////////////
if (level==4){
cout<<"LEVEL4"<<endl;
cout<<"Reading the pulse sequence..."<<endl;
PMatrix pulse;
read_binary_matrix(pulse, opt_pulse.value());
////////////////////////
// B0 PERTURBATION
////////////////////////
cout<<"Creating 1 B0extra file together with 3 gradient files all changing in time..."<<endl;
Matrix b0timecourse_tmp;
double* b0timecourse;
double* b0timecourse_2;
double* b0time;
double* b0xtime;
double* b0ytime;
double* b0ztime;
b0timecourse_tmp=read_ascii_matrix(opt_b0timecourse4D.value());
int Nb0=b0timecourse_tmp.Nrows();
b0timecourse=new double[Nb0];
b0timecourse_2=new double[Nb0];
b0time=new double[Nb0];
b0xtime=new double[Nb0];
b0ytime=new double[Nb0];
b0ztime=new double[Nb0];
for (int n=0;n<=Nb0-1;n++){
b0timecourse[n]=b0timecourse_tmp(n+1,1);
b0timecourse_2[n]=b0timecourse_tmp(n+1,2);
}
volume<double> b0extra;
volume<double> b0xextra;
volume<double> b0yextra;
volume<double> b0zextra;
read_volume(b0extra,opt_b0extra.value());
calc_gradientsROI(b0extra,b0xextra,b0yextra,b0zextra,myid,Nxx,numprocs);
print_volume_info(b0extra,"b0extra");
cout<<"Creating 1 B0file together with 3 gradient files..."<<endl;
volume<double> b0(Nxx,Ny,Nz);
volume<double> b0x(Nxx,Ny,Nz);
volume<double> b0y(Nxx,Ny,Nz);
volume<double> b0z(Nxx,Ny,Nz);
if (opt_b0.set()) {
read_volume(b0,opt_b0.value()+"z_dz");
calc_gradientsROI(b0,b0x,b0y,b0z,myid,Nxx,numprocs);
}
else {
b0=phantom[0]*0;
b0x=b0;
b0y=b0;
b0z=b0;
}
print_volume_info(b0,"b0");
cout<<""<<endl;
/////////////
//MAIN LOOP
/////////////
cout<<"Main loop..."<<endl;
for (register int tt=0;tt<Nt;tt++){
for (register int zz=zstart;zz<zend;zz++){
cout<<"Tissue type="<<tt<<"; zstart="<<zstart<<"; zz="<<zz<<"; zend="<<zend<<"; Voxelnumber="<<voxelcounter<<endl;
for (register int yy=ystart;yy<yend;yy++){
int xxx=myid+xstart;
for (register int xx=xstart;xx<xend;xx++){
//slice speed up stuff
if (fabs((float)slcdir)==1) sszz=zz;
else if (fabs((float)slcdir)==2) sszz=yy;
else sszz=xx;
float slctmp=(sszz-sszstart_p)/(slcthk*nvox);
if(ceil(slctmp) == slctmp) {
sszz_slc=(int)(ceil(slctmp)+1);
} else {
sszz_slc=(int) (ceil(slctmp));
}
if (phantom(xx,yy,zz,tt)!=0){
voxelcounter=voxelcounter+1;
double den=phantom(xx,yy,zz,tt)*RFrec(xx,yy,zz)*cxyz;
if (opt_activation.set()) {
for (int n=0;n<=Nact-1;n++){
double a=activation(xx,yy,zz)*timecourse_2[n];
double b=tissue(tt+1,2);
activation4D_voxel[n]=a*b/(a+b);// conversion of beta into beta1 because of the integral (see possum no 7 page 121)
}
}
else if (opt_activation4D.set()){
for (int n=0;n<=Nact-1;n++){
double a=activation4D(xx,yy,zz,n);//zz-zstart_p when having only a pieace of the activation volume so we start from where the phantom starts
double b=tissue(tt+1,2);
activation4D_voxel[n]=a*b/(a+b);
}
}
for (int n=0;n<=Nb0-1;n++){
b0time[n]=b0extra(xx,yy,zz)*b0timecourse_2[n];
b0xtime[n]=b0xextra(xx,yy,zz)*b0timecourse_2[n];
b0ytime[n]=b0yextra(xx,yy,zz)*b0timecourse_2[n];
b0ztime[n]=b0zextra(xx,yy,zz)*b0timecourse_2[n];
if (voxelcounter==1){
cout<<"b0time[n]="<<b0time[n]<<"b0xtime[n]="<<b0xtime[n]<<"b0ytime[n]="<<b0ytime[n]<<"b0ztime[n]="<<b0ztime[n]<<endl;
}
}
voxel4(posx(xxx+1),posy(yy+1),posz(zz+1),tissue.Row(tt+1),
pulse,nreadp,voxelcounter,xdim,ydim,zdim,
b0time,b0xtime,b0ytime,b0ztime, b0timecourse, Nb0,
b0(xx,yy,zz),b0x(xx,yy,zz),b0y(xx,yy,zz),b0z(xx,yy,zz),
timecourse,activation4D_voxel,Nact,outputname,table_slcprof,
dslcp,dslcp_first,Nslc,den,RFtrans(xx,yy,zz),opt_test,
nospeedup,save_kcoord,sreal,simag);
}
xxx=xxx+numprocs;
}
}
}
}
}
/////////////////
//PARALEL STUFF
#ifdef USE_MPI
double* sreal_total;
sreal_total= new double[nreadp];
double* simag_total;
simag_total= new double[nreadp];
MPI_Reduce(sreal, sreal_total, nreadp, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD);//MPI::COMM_WORLD.Reduce(sreal,sreal_total,nreadp,MPI::DOUBLE,MPI::SUM,0);
MPI_Reduce(simag, simag_total, nreadp, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD);//MPI::COMM_WORLD.Reduce(simag,simag_total,nreadp,MPI::DOUBLE,MPI::SUM,0);
cout<<"Element nmb 1091 on "<<myid<<" is <"<<sreal[1091]<<", "<<simag[1091]<<">.\n";
if (myid==0){
cout<<"Element nmb 1091 on "<<myid<<" is <"<<sreal_total[1091]<<", "<<simag_total[1091]<<">.\n";
for (int i=1;i<=nreadp;i++) {
signal(1,i)=sreal_total[i-1]*1e06; //1e06 we need to make signal have larger values so that it more resembles the scanner
signal(2,i)=simag_total[i-1]*1e06; //1e06 we need to make signal have larger values so that it more resembles the scanner