File: periplot.pas

package info (click to toggle)
mricron 0.20140804.1~dfsg.1-3
  • links: PTS, VCS
  • area: main
  • in suites: buster, sid
  • size: 13,508 kB
  • sloc: pascal: 114,876; sh: 49; makefile: 35
file content (706 lines) | stat: -rwxr-xr-x 29,247 bytes parent folder | download | duplicates (4)
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
unit periplot;
//peristimulus plotting routines

interface
uses
    nifti_hdr,define_types,metagraph,sysutils;

function CreatePeristimulusPlot (var l4DHdr: TMRIcroHdr; var l4DTrace: T4DTrace;
var lPSPlot: TPSPlot): boolean;
function ROIoverlayNameShort(lROI: integer): string;
function numROI: integer;
function ROIoverlayNum(lROI: integer): integer;
function NCond ( var l4DTrace: T4DTrace): integer;
function ROImean (var l4DHdr: TMRIcroHdr; lROInum,lVol: integer): double;

implementation


{$IFNDEF FPC}
{$DEFINE REMOVEREGRESS}
{$ENDIF}
uses nifti_img_view,dialogs,nifti_img,text,graphx,math
{$IFDEF REMOVEREGRESS},fmath, hrf,
matrices,Regmult{$ENDIF}; //need to specify path, e.g. C:\pas\mricron\npm\math


//var   gOffsetError: array [1..kMaxCond] of double;

function numROI: integer;
var
   lR: integer;
begin
     result := 0;
     for lR := (kBGOverlayNum+1) to knMaxOverlay do
              if gMRIcroOverlay[lR].ScrnBufferItems > 0 then
                 inc(result);
end;

function ROIoverlayNum(lROI: integer): integer;
var
   lR,lN: integer;
begin
     result := 0;
     lN := 0;
     for lR := (kBGOverlayNum+1) to knMaxOverlay do begin
              //fx(lR,gMRIcroOverlay[lR].ScrnBufferItems);
              if gMRIcroOverlay[lR].ScrnBufferItems > 0 then begin
                 inc(lN);
                 if lROI = lN then begin
                     result := lR;
                     exit;
                 end;
              end; //if ROI has items
     end;
end;


function ROIoverlayNameShort(lROI: integer): string;
begin
     if ROIoverlayNum(lROI) = 0 then
{$IFDEF FPC}
        result := inttostr(ImgForm.XViewEdit.value)+'x'+inttostr(ImgForm.YViewEdit.value)+'x'+inttostr(ImgForm.ZViewEdit.value)
{$ELSE}
        result := inttostr(ImgForm.XViewEdit.asinteger)+'x'+inttostr(ImgForm.YViewEdit.asinteger)+'x'+inttostr(ImgForm.ZViewEdit.asinteger)
{$ENDIF}
     else
         result := parsefilename(extractfilename(gMRIcroOverlay[ROIoverlayNum(lROI)].HdrFileName));
end;

function StDev (lSum, lSumSqr: single; lN: integer): single;
begin
	result := 0;
	if lN < 2 then
		exit; //avoid divide by zero. We divide by N-1
	result:= (lSumSqr - ((Sqr(lSum))/lN));
	if  (result > 0) then
				result :=  Sqrt ( result/(lN-1))
end;


function ROIoverlayNameLong(lROI: integer): string;
begin
     if ROIoverlayNum(lROI) = 0 then
{$IFDEF FPC}
        result := inttostr(ImgForm.XViewEdit.value)+'x'+inttostr(ImgForm.YViewEdit.value)+'x'+inttostr(ImgForm.ZViewEdit.value)
{$ELSE}
        result := inttostr(ImgForm.XViewEdit.asinteger)+'x'+inttostr(ImgForm.YViewEdit.asinteger)+'x'+inttostr(ImgForm.ZViewEdit.asinteger)
{$ENDIF}
     else
         result := gMRIcroOverlay[ROIoverlayNum(lROI)].HdrFileName;
end;


function NCond ( var l4DTrace: T4DTrace): integer;
var
   lCond: integer;
begin
  result := 0;
  for lCond := 1 to kMaxCond do
      if l4DTrace.Conditions[lCond].Events > 0 then
         inc(result);
end;

function StError (lSum, lSumSqr: single; lN: integer): single;
//= STANDARD DEVIATION / SQUARE ROOT OF THE POPULATION SIZE
//= STDEV(range of values)/SQRT(lN)
begin
	 if lN > 1 then
		result := StDev (lSum, lSumSqr, lN)/ sqrt(lN)
	else
		result := 0;
end;

const
	 kMaxEvents = 2048;

procedure TimecourseVoxinten (var l4DHdr: TMRIcroHdr; lVoxel: integer; lTimeCourse: DoubleP);
//could also use periutil's VoxInten, but this is faster...
var
   lVol,lVolOffset,lImgVox,lMaxStatVol: integer;
   l32Buf: singleP;
   l16Buf: smallintp;
begin //if ROI else no ROI - single voxel
      lImgVox  :=  l4DHdr.NIFTIhdr.dim[1]*l4DHdr.NIFTIhdr.dim[2]*l4DHdr.NIFTIhdr.dim[3];
     lMaxStatVol := l4DHdr.NIFTIhdr.dim[4];
      if (l4DHdr.ImgBufferBPP  = 4) then begin
         l32Buf := SingleP(l4DHdr.ImgBuffer );
         for lVol := 1 to lMaxStatVol do begin
             lVolOffset := (lVol-1)*lImgVox;
             lTimeCourse^[lVol] :=  l32Buf^[lVoxel+lVolOffset]
         end;
      end else if l4DHdr.ImgBufferBPP  = 2 then begin
          l16Buf := SmallIntP(l4DHdr.ImgBuffer );
          for lVol := 1 to lMaxStatVol do begin
             lVolOffset := (lVol-1)*lImgVox;
             lTimeCourse^[lVol] :=  l16Buf^[lVoxel+lVolOffset]
          end;
      end else if l4DHdr.ImgBufferBPP  = 1 then begin
          for lVol := 1 to lMaxStatVol do begin
             lVolOffset := (lVol-1)*lImgVox;
             lTimeCourse^[lVol] :=  l4DHdr.ImgBuffer^[lVoxel+lVolOffset];
          end;
      end; //if 1 bpp
end; //GenerateVoxinten

function ROImean (var l4DHdr: TMRIcroHdr; lROInum,lVol: integer): double;
var
   l32Buf: singleP;
   l16Buf: smallintp;
   lSum: double;
   lMaskVox: int64;
   lInc,lVolOffset,lImgVox: integer;
begin
     result := 0;
     //compute number of voxels in mask
     lImgVox  :=  l4DHdr.NIFTIhdr.dim[1]*l4DHdr.NIFTIhdr.dim[2]*l4DHdr.NIFTIhdr.dim[3];

     lMaskVox := 0;
     for lInc := 1 to lImgVox do
         if gMRIcroOverlay[lROInum].ScrnBuffer^[lInc] > 0 then //in mask
            lMaskVox := lMaskVox + gMRIcroOverlay[lROInum].ScrnBuffer^[lInc];
     if lMaskVox < 1 then
        exit;
     lSum := 0;
     lVolOffset := (lVol-1)*lImgVox;
     if (l4DHdr.ImgBufferBPP  = 4) then begin
            l32Buf := SingleP(l4DHdr.ImgBuffer );
            for lInc := 1 to lImgVox do begin
                if gMRIcroOverlay[lROInum].ScrnBuffer^[lInc] > 0 then begin//in mask
                      lSum := lSum + (gMRIcroOverlay[lROInum].ScrnBuffer^[lInc]*l32Buf^[lInc+lVolOffset]);
                end; //in mask
            end; //for each vox
     end else if (l4DHdr.ImgBufferBPP  = 2) then begin
            l16Buf := SmallIntP(l4DHdr.ImgBuffer );
            for lInc := 1 to lImgVox do begin
                if gMRIcroOverlay[lROInum].ScrnBuffer^[lInc] > 0 then begin//in mask
                       lSum := lSum + (gMRIcroOverlay[lROInum].ScrnBuffer^[lInc]*l16Buf^[lInc+lVolOffset]);
                end; //in mask
            end; //for each vox
     end else if (l4DHdr.ImgBufferBPP  = 1) then begin
            for lInc := 1 to lImgVox do begin
                if gMRIcroOverlay[lROInum].ScrnBuffer^[lInc] > 0 then begin//in mask
                       lSum := lSum + (gMRIcroOverlay[lROInum].ScrnBuffer^[lInc]*l4DHdr.ImgBuffer^[lInc+lVolOffset]);
                end; //for each volume
            end; //for each vox
     end; //for image type
     result := lSum/lMaskVox;
end;

function TimecourseROIinten (var l4DHdr: TMRIcroHdr; lROInum: integer; lTimeCourse: DoubleP): boolean;
var
   lVol,lMaxStatVol: integer;
begin
     lMaxStatVol := l4DHdr.NIFTIhdr.dim[4];
     //result := false;
     for lVol := 1 to lMaxStatVol do
         lTimeCourse^[lVol] := ROImean (l4DHdr,lROInum,lVol);
     //compute mean for each volume
     result := true;
end;

function ComputeMeanSE (lCountBin: longintp; lMnBin,lSEBin,lSumBin,lSumSqrBin: doublep;
        lNegBins,lPosBins: integer): boolean;
var
   lBin: integer;
begin
     result := false;

        (*var
   lBins,lBin,lnBinsWithSamples: integer;
   lIntensitySum: double;
begin
     result := false;
     lIntensitySum := 0;
     lnBinsWithSamples := 0;
     lBins := lNegBins;
     if lBins < 1 then
        lBins := lNegBins+lPosBins;
     for lBin := lBins downto 1 do begin //new only base pct on baseline
         if lCountBin^[lBin] > 0 then begin
            lIntensitySum := lIntensitySum+lMnBin^[lBin];
            inc(lnBinsWithSamples);
         end; //samples in bin
     end; //for each bin
     if lnBinsWithSamples < 1 then
        exit;*)
     if (lNegBins + lPosBins) < 1 then
        exit;
     for lBin := (lNegBins + lPosBins) downto 1 do
             lSEBin^[lBin] := StError(lSumBin^[lBin],lSumSqrBin^[lBin],lCountBin^[lBin]);
     result := true;
end; //ifunc ComputeMeanSE

{$IFDEF REMOVEREGRESS}

{procedure OutCSV (lTimeCourseRaw,lTimeCourseRegress,lTimeCourseFilt: DoubleP; lnVol,lC: integer; lSlope,lInter: double);
var
   lVol: integer;
   lF: TextFile;
   lStr: string;
begin
     AssignFile(lF, 'C:\fatigue\td'+inttostr(lC)+'.csv');
     Rewrite(lF);
    lStr := '';
    for lVol := 1 to lnVol do
        lStr := lStr+floattostr(lTimeCourseRaw^[lVol])+',';
    lStr := lStr + '666';
    writeln(lF,lStr);

    lStr := '';
    for lVol := 1 to lnVol do
        lStr := lStr+floattostr(lTimeCourseRegress^[lVol])+',';
    lStr := lStr + '666';
    writeln(lF,lStr);
    lStr := '';
    for lVol := 1 to lnVol do
        lStr := lStr+floattostr(lTimeCourseFilt^[lVol])+',';
    lStr := lStr + '666';
    writeln(lF,lStr);
    writeln(lF,'');
    writeln(lF,'');
    writeln(lF,floattostr(lSlope)+','+floattostr(lInter));
    CloseFile(lF);
end; }

function RemoveRegressors(lTimeCourseRaw,lTimeCourseFilt: DoubleP; var l4DTrace: T4DTrace;lCond,lnVol: integer;var lPSPlot: TPSPlot): boolean;
var
   lOK: boolean;
   lKernelBins,lncond,lC,lVol,lnCondincludeTD: integer;
   lHRFra, lTDra: doublep;
   lInputSum,lOutputSum : double;
   X: PMatrix;
   Y: PVector;
   //lDummy,lEstTimeCoursePrecise: DoubleP;
   lOutT,lOutSlope: DoubleP0;
begin
     result := false;
     lncond := NCond (l4DTrace);
     lnCondincludeTD := lnCond;
     if lPSPlot.TemporalDeriv then
        lnCondincludeTD := lnCondincludeTD * 2;
     if (lnCondincludeTD < 2) or (lPSPlot.SPMDefaultsStatsFmriT < 1) then begin
        Showmessage('You need at least two variables to remove regressors (you could add the temporal derivative)');
	    exit;
     end; //cond = 0
     if not CreateHRF (lPSPlot.TRsec, lKernelBins,lPSPlot.SPMDefaultsStatsFmriT, lHRFra, lTDra) then exit;
     //getmem(lTimeCourseRegress,lnVol*sizeof(double));
     for lVol := 1 to lnVol do
         lTimeCourseFilt^[lVol] := lTimeCourseRaw^[lVol];
     //compute sum intensity so we can adjust for shifts in the mean...
     lInputSum := 0;
     for lVol := 1 to lnVol do
         lInputSum := lInputSum+lTimeCourseRaw^[lVol];
     //convolve each condition...
     DimMatrix(X, lnCondincludeTD, lnVol);
     //lDummy := nil;
     //Getmem(lEstTimeCoursePrecise, lnVol *lPSPlot.SPMDefaultsStatsFmriT * sizeof(double));
     for lC := 1 to lnCond do begin
         (*if lC = lCond then
             ConvolveTimeCourse(X, lHRFra, lEstTimeCoursePrecise,l4DTrace, lC,lC,lnVol,lKernelBins,lPSPlot.SPMDefaultsStatsFmriT,lPSPlot.SPMDefaultsStatsFmriT0,lPSPlot.TRSec, lPSPlot.SliceTime)
         else*)
             ConvolveTimeCourse(X, lHRFra, l4DTrace, lC,lC,lnVol,lKernelBins,lPSPlot.SPMDefaultsStatsFmriT,lPSPlot.SPMDefaultsStatsFmriT0,lPSPlot.TRSec, lPSPlot.SliceTime);
     end;
     //convolve temporal derivatives for each condition
     if lPSPlot.TemporalDeriv then
        for lC := 1 to lnCond do
            ConvolveTimeCourse(X, lTDra, l4DTrace, lC,lC+lnCond,lnVol,lKernelBins,lPSPlot.SPMDefaultsStatsFmriT,lPSPlot.SPMDefaultsStatsFmriT0,lPSPlot.TRSec, lPSPlot.SliceTime);
     freemem(lHRFra);
     freemem(lTDra);
     DimVector(Y, lnVol);
     for lVol := 1 to lnVol do
         Y^[lVol] := lTimeCourseRaw^[lVol];
     getmem(lOutT, (lnCondincludeTD+1)* sizeof(double));
     getmem(lOutSlope, (lnCondincludeTD+1)* sizeof(double));
     lOK := MultipleRegressionVec (lnVol,lnCondincludeTD, X, Y, lOutT,lOutSlope);
     freemem(lOutT);
     DelVector(Y, lnVol);
     //begin test - show responses...
if lPSPlot.PlotModel then begin
     lC := lCond; //response for condition
     //if lTemporalDeriv then lC := lCond + lnCond; //lCond + lnCond = TD
      //if lPSPlot.TemporalDeriv then  fx( lC,lOutSlope^[lC-1],lOutSlope^[lnCond+lC-1] );
     for lVol := 1 to lnVol do
         lTimeCourseFilt^[lVol] := (X^[lC]^[lVol] *lOutSlope[lC-1]);
end else begin //not test
     if lOK then begin
        for lC := 1 to lnCondincludeTD do begin
            if lC <> lCond then begin
               for lVol := 1 to lnVol do
                   lTimeCourseFilt^[lVol] := lTimeCourseFilt^[lVol]- (X^[lC]^[lVol] *lOutSlope[lC-1]);

            end; //for each regressor
        end; //for lC
        result := true;//SUCCESS!
        //next - search for optimal fit of model to data..
        //if (lPSPlot.TextOutput) and (lCond > 0) and (lCond <= kMaxCond) then
        //  gOffsetError[lCond] := (OptimalOffset(lOutSlope^[lCond-1],lOutSlope^[lnCondincludeTD], lPSPlot.SPMDefaultsStatsFmriT0,lPSPlot.SPMDefaultsStatsFmriT,lnVol, lTimeCourseFilt,lEstTimeCoursePrecise)/ lPSPlot.SPMDefaultsStatsFmriT ) * lPSPlot.TRsec;
     end;//lOK
end;
     //Freemem(lEstTimeCoursePrecise);
     DelMatrix(X, lnCondincludeTD, lnVol);

     //adjust for shifts in the mean...
     lOutputSum := 0;
     for lVol := 1 to lnVol do
         lOutputSum := lOutputSum+lTimeCourseFilt^[lVol];
     if lOutputSum <> lInputsum then begin
        lOutputSum := (lOutputSum - lInputSum)/lnVol;
        for lVol := 1 to lnVol do
            lTimeCourseFilt^[lVol] := lTimeCourseFilt^[lVol] - lOutputSum;
     end; //correct for changes...
     freemem(lOutSlope);
end;

{$ENDIF} //IFDEF REMOVEREGRESS
//old TimeCourseToPSPlot - each event can contribute to several samples e.g. both before and after stimulus
(*function TimeCourseToPSPlot(lTimeCourse: DoubleP; var l4DTrace: T4DTrace;
         lCountBin: longintp; lMnBin,lSumBin,lSumSqrBin: doublep;
         var lTRsec,lBinWidthSec: single; lCond,lnNegBins,lnPosBins,lMaxStatVol: integer; lSliceTime: boolean): boolean;
var
   lOnsetRAx: doublep;
   lEvent,lnEvent,lBin,lVol: integer;
   lNegMS,lPosMS,lVolTime,lTRms,lHalfTRms,lPeristimulusTime,lmsPerBin: double;
begin
     result := false;
     if l4DTrace.Conditions[lCond].Events < 1 then exit;
     lmsPerBin := lBinWidthSec * 1000;
     lTRms := lTRsec * 1000;
     if lTRms = 0 then begin
        Showmessage('Unable to compute plots: You need to specify the TR in seconds.');
	    exit;
     end;
     lHalfTRms := lTRms/2;
     lNegMS := -lnNegBins * lmsPerBin;
     lPosMS := lnPosBins * lmsPerBin;
     lnEvent := l4DTrace.Conditions[lCond].Events;
     getmem(lOnsetRAx,lnEvent*sizeof(double) );
     if  lSliceTime then begin
         for lEvent := 1 to lnEvent do begin
             lOnsetRAx^[lEvent] := (l4DTrace.Conditions[lCond].EventRA^[lEvent]*1000)-lHalfTRms;
         end;
     end else
         for lEvent := 1 to lnEvent do
             lOnsetRAx^[lEvent] := (l4DTrace.Conditions[lCond].EventRA^[lEvent]*1000);
     //initialize bins
     for lBin := 1 to (lnNegBins + lnPosBins)  do  begin
         lMnBin^[lBin] := 0;
	lSumBin^[lBin] := 0;
         lSumSqrBin^[lBin] := 0;
         lCountBin^[lBin] := 0; //no samples in each cell
     end;
     for lVol := 1 to lMaxStatVol do begin
         lVolTime := (lVol-1) * lTRms;
         for lEvent := 1 to l4DTrace.Conditions[lCond].Events do begin
             lPeristimulusTime := lVolTime-lOnsetRAx^[lEvent];
             if (lPeristimulusTime >= lNegMS) and (lPeristimulusTime < lPosMS) then begin
			              lBin := trunc((lPeristimulusTime - lNegMS) / lmsPerBin)+1;
			              inc(lCountBin^[lBin]);
                          lSumBin^[lBin] := lSumBin^[lBin] + lTimeCourse^[lVol];
                          lSumSqrBin^[lBin] := lSumSqrBin^[lBin] + sqr(lTimeCourse^[lVol]);
             end; //if lPeristimulusTime within mix/max temporal window
         end; //for each event
     end; //for each vol
     //next compute mean
     for lBin := 1 to (lnNegBins + lnPosBins)  do
         if lCountBin^[lBin] > 0 then
            lMnBin^[lBin] := lSumBin^[lBin]/lCountBin^[lBin];
     freemem(lOnsetRAx);
     result := true;
end;//func TimeCourseToPS
*)
function TimeCourseToPSPlot(lTimeCourse: DoubleP; var l4DTrace: T4DTrace;
         lCountBin: longintp; lMnBin,lSumBin,lSumSqrBin: doublep;
         var lPSPlot: TPSPlot; lCond,lMaxStatVol: integer): boolean;
var
   lOnsetRAx: doublep;
   lEvent,lnEvent,lBin,lVol: integer;
   lNextEvent,lPrevEvent,lNegMS,lPosMS,lVolTime,lTRms,lHalfTRms,lPeristimulusTime,lmsPerBin: double;
begin
     result := false;
     if (l4DTrace.Conditions[lCond].Events < 1) or ((lPSPlot.nNegBins + lPSPlot.nPosBins)<1) then exit;
     lmsPerBin := lPSPlot.BinWidthSec * 1000;
     lTRms := lPSPlot.TRsec * 1000;
     if lTRms = 0 then begin
        Showmessage('Unable to compute plots: You need to specify the TR in seconds.');
	    exit;
     end;
     lHalfTRms := lTRms/2;
     lNegMS := -lPSPlot.nNegBins * lmsPerBin;
     lPosMS := lPSPlot.nPosBins * lmsPerBin;
     lnEvent := l4DTrace.Conditions[lCond].Events;
     getmem(lOnsetRAx,lnEvent*sizeof(double) );
     if  lPSPlot.SliceTime then begin
         for lEvent := 1 to lnEvent do begin
             lOnsetRAx^[lEvent] := (l4DTrace.Conditions[lCond].EventRA^[lEvent]*1000)-lHalfTRms;
         end;
     end else
         for lEvent := 1 to lnEvent do
             lOnsetRAx^[lEvent] := (l4DTrace.Conditions[lCond].EventRA^[lEvent]*1000);
     //initialize bins
     for lBin := 1 to (lPSPlot.nNegBins + lPSPlot.nPosBins)  do  begin
         lMnBin^[lBin] := 0;
	     lSumBin^[lBin] := 0;
         lSumSqrBin^[lBin] := 0;
         lCountBin^[lBin] := 0; //no samples in each cell
     end;
     //find volume's peristimulus time
     //note: we assume periutil's ReadCond ensures that Cond.Events are sorted in ascending order
     lEvent := 1;
     lPrevEvent := -MaxInt;
     lNextEvent := lOnsetRAx^[lEvent];
     for lVol := 1 to lMaxStatVol do begin
         lVolTime := (lVol-1) * lTRms;
         while lVolTime > lNextEvent do begin
             inc(lEvent);
             lPrevEvent := lNextEvent;
             if lEvent > lnEvent then
                lNextEvent := MaxInt
             else
                 lNextEvent := lOnsetRAx^[lEvent];
         end;
         lPeristimulusTime := lVolTime-lPrevEvent;
         if (lPeristimulusTime >= 0) and (lPeristimulusTime < lPosMS) then begin
			              lBin := trunc((lPeristimulusTime - lNegMS) / lmsPerBin)+1;
			              inc(lCountBin^[lBin]);
                          lSumBin^[lBin] := lSumBin^[lBin] + lTimeCourse^[lVol];
                          lSumSqrBin^[lBin] := lSumSqrBin^[lBin] + sqr(lTimeCourse^[lVol]);
         end else begin //if not after - check if before
             lPeristimulusTime := lVolTime-lNextEvent;
             if (lPeristimulusTime >= lNegMS) and (lPeristimulusTime < 0) then begin
			              lBin := trunc((lPeristimulusTime - lNegMS) / lmsPerBin)+1;
			              inc(lCountBin^[lBin]);
                          lSumBin^[lBin] := lSumBin^[lBin] + lTimeCourse^[lVol];
                          lSumSqrBin^[lBin] := lSumSqrBin^[lBin] + sqr(lTimeCourse^[lVol]);
             end; //if lPeristimulusTime within mix/max temporal window
         end; //if else... not after stimuli

         (*for lEvent := 1 to l4DTrace.Conditions[lCond].Events do begin
             lPeristimulusTime := lVolTime-lOnsetRAx^[lEvent];
             if (lPeristimulusTime >= lNegMS) and (lPeristimulusTime < lPosMS) then begin
			              lBin := trunc((lPeristimulusTime - lNegMS) / lmsPerBin)+1;
			              inc(lCountBin^[lBin]);
                          lSumBin^[lBin] := lSumBin^[lBin] + lTimeCourse^[lVol];
                          lSumSqrBin^[lBin] := lSumSqrBin^[lBin] + sqr(lTimeCourse^[lVol]);
             end; //if lPeristimulusTime within mix/max temporal window
         end; //for each event*)
     end; //for each vol
     //next compute mean
     for lBin := 1 to (lPSPlot.nNegBins + lPSPlot.nPosBins)  do
         if lCountBin^[lBin] > 0 then
            lMnBin^[lBin] := lSumBin^[lBin]/lCountBin^[lBin];
     freemem(lOnsetRAx);
     result := true;
end;//func TimeCourseToPS

function TextOutput (lROI,lCond: integer; var lPSPlot : TPSPlot; var l4DTrace: T4DTrace; lCountBin: longintp; lMnROI,lSEROI: doublep): boolean;
var
   lOutMnStr,lOutSDStr,lCondStr, lOutStr,lModelStr: string;
   lNegMS,lmsPerBin: double;
   lnBins,lBin,lMinBinCount,lMaxBinCount: integer;
begin
     result := false;
     lnBins := lPSPlot.nNegBins + lPSPlot.nPosBins;
     if lnBins < 1 then
        exit;
     lmsPerBin := lPSPlot.BinWidthSec * 1000;
     lNegMS := -lPSPlot.nNegBins * lmsPerBin;
     lMinBinCount :=  lCountBin^[1];
     lMaxBinCount := lCountBin^[1];
     for lBin := 1 to lnBins do begin
         if lCountBin^[lBin] < lMinBinCount then
            lMinBinCount := lCountBin^[lBin];
         if lCountBin^[lBin] > lMaxBinCount then
            lMaxBinCount := lCountBin^[lBin];
     end;
     lModelStr := ', Processing=,';
     if lPSPlot.RemoveRegressorVariability then begin
        if lPSPlot.PlotModel then
           lModelStr := lModelStr+'MODEL[hrf'
        else
            lModelStr := lModelStr+'observed[hrf';
        if lPSPlot.TemporalDeriv then
           lModelStr := lModelStr+'+TD';
        lModelStr := lModelStr+']';
        //if (lCond > 0) and (lCond <= kMaxCond) then  lModelStr := lModelStr+ floattostr(gOffsetError[lCond]);

     end else
         lModelStr := lModelStr+'observed[raw]';
     lModelStr := lModelStr+kTextSep;
     lCondStr := 'Image=,'+gMRIcroOverlay[kBGOverlayNum].HdrFileName+', '+inttostr(lCond)+',Condition=,'+l4DTrace.Conditions[lCond].ELabel+lModelStr+'Events=, '+inttostr(l4DTrace.Conditions[lCond].Events)+', samples per bin= '+inttostr(lMinBinCount)+'..'+inttostr(lMaxBinCount);
     lOutStr := kTextSep;
     for lBin := 1 to 11 do
         lOutStr := lOutStr+kTextSep;

         lOutStr := lOutStr+'Bin Starts At->';
     for lBin := 1 to lnBins do
         lOutStr := lOutStr+kTextSep+ RealToStr((lNegMS+ ((lBin-1)*  lmsPerBin)),0 );
     TextForm.MemoT.lines.add(lOutStr);
     TextForm.MemoT.Lines.add('samples per bin '+inttostr(lMinBinCount)+'..'+inttostr(lMaxBinCount));
     //next report number of samples averaged
     lOutStr := lCondStr+kTextSep+kTextSep+kTextSep+'samples in bin=';
     for lBin := 1 to lnBins do
         lOutStr := lOutStr+kTextSep+ inttostr(lCountBin^[lBin]  );
     TextForm.MemoT.lines.add(lOutStr);
     //next report mean signal
     lOutMnStr := lCondStr+kTextSep+'roiMn'+kTextSep+'MaskROI['+ROIoverlayNameShort(lROI)+']='+kTextSep+ROIoverlayNameLong(lROI);
     lOutSDStr := lCondStr+kTextSep+'roiSE'+kTextSep+'MaskROI['+ROIoverlayNameShort(lROI)+']='+kTextSep+ROIoverlayNameLong(lROI);
     for lBin := 1 to (lnBins) do begin
         lOutMnStr := lOutMnStr+kTextSep+ floattostr(lMnROI^[lBin]);//floattostr(lSumROI[lROI,lBin]/lBinCountRA[lBin]);
         lOutSDStr := lOutSDStr+kTextSep+ floattostr(lSEROI^[lBin]);//StDev(lSumROI[lROI,lBin],lSumSqrROI[lROI,lBin],lBinCountRA[lBin])  );
     end; //for each bin
     TextForm.MemoT.lines.add(lOutMnStr);
     TextForm.MemoT.lines.add(lOutSDStr);
     result := true;
end; //proc TextOutput

function CalcMean (lTimeCourse: DoubleP;lnVol: integer): double;
var
   lSum: double;
   lVol: integer;
begin
     result := 0;
     if lnVol < 1 then
        exit;
     lSum := 0;
     for lVol := 1 to lnVol do
         lSum := lSum + lTimeCourse^[lVol]; //Sum
     result := lSum / lnVol;
end;

procedure  PctSignal (lTimeCourse: DoubleP;lnVol: integer);
var
   lMean,lScale: double;
   lVol: integer;
begin
     if lnVol < 1 then
        exit;
     lMean := CalcMean (lTimeCourse,lnVol);
     if lMean = 0 then
        exit; //can't compute % signal change...
     lScale := abs(1/lMean);
     for lVol := 1 to lnVol do
         lTimeCourse^[lVol] := (lTimeCourse^[lVol]-lMean)*lScale; //Sum

end;

function CreatePeristimulusPlot (var l4DHdr: TMRIcroHdr; var l4DTrace: T4DTrace; var lPSPlot: TPSplot): boolean;
var
   lBinData:  T4DTrace;
   lTimeCourse,lTimeCourseFilt:  doublep;
   lCountBin: longintp;
   lMnBin,lSEBin,lSumBin,lSumSqrBin: doublep;
   lCond,lncond,lnVol,lnROI,lROI,lnROImin1,lLine,lBin: integer;
   lTR: double;
begin
     result := false;
     lncond := NCond (l4DTrace);
     if lncond = 0 then begin
        Showmessage('You need to specify event onset times before creating a peristimulus plot.');
	    exit;
     end; //cond = 0
     lnVol := l4DHdr.NIFTIhdr.dim[4];
     if lnVol < 3 then begin
        Showmessage('Unable to compute plots: You need to analyze a 4D image.');
	    exit;
     end;
     if (l4DHdr.ImgBufferItems = 0) then exit;

     lTR := lPSPlot.TRsec * 1000;
     if lTR = 0 then begin
        Showmessage('Unable to compute plots: You need to specify the TR in seconds.');
	    exit;
     end;
     lnROI := 0;
     for lROI := (kBGOverlayNum+1) to knMaxOverlay do
         if   gMRIcroOverlay[lROI].ScrnBufferItems > 0 then //current implementation only one ROI
           inc(lnROI);
     if lnROI < 1 then begin
        lnROImin1 := 1;
     end else begin
         lnROImin1 := lnROI;
     end;
     //allocate memory
     getmem(lTimeCourse,lnVol*sizeof(double));
     getmem(lTimeCourseFilt,lnVol*sizeof(double));
     getmem(lCountBin,(lPSPlot.nNegBins+lPSPlot.nPosBins)*sizeof(integer));
     getmem(lMnBin,(lPSPlot.nNegBins+lPSPlot.nPosBins)*sizeof(double));
     getmem(lSEBin,(lPSPlot.nNegBins+lPSPlot.nPosBins)*sizeof(double));
     getmem(lSumSqrBin,(lPSPlot.nNegBins+lPSPlot.nPosBins)*sizeof(double));
     getmem(lSumBin,(lPSPlot.nNegBins+lPSPlot.nPosBins)*sizeof(double));
     if lPSPlot.GraphOutput then  begin
        Create4DTrace (lBinData);
        Init4DTrace(lPSPlot.nNegBins + lPSPlot.nPosBins,lnROImin1*lnCond,lBinData,true);
        for lROI := 1 to lnROImin1 do
            lBinData.Lines[lROI].ELabel := ROIoverlayNameShort(lROI);
     end; //if graphoutput
     //repeat for each Region of interest
     for lROI := 1 to lnROImin1 do begin
         //compute complete timecourse for all volumes...
         if lnROI = 0 then begin
                {$IFDEF FPC}
                TimecourseVoxinten (l4DHdr, ImgForm.XViewEdit.value
                                 + ((ImgForm.YViewEdit.value-1)*gBGImg.ScrnDim[1])
                                 +((ImgForm.ZViewEdit.value-1)*gBGImg.ScrnDim[1]
                                 *gBGImg.ScrnDim[2]),lTimeCourse)
                {$ELSE}
                TimecourseVoxinten (l4DHdr, ImgForm.XViewEdit.asinteger
                                 + ((ImgForm.YViewEdit.asinteger-1)*gBGImg.ScrnDim[1])
                                 +((ImgForm.ZViewEdit.asinteger-1)*gBGImg.ScrnDim[1]
                                 *gBGImg.ScrnDim[2]),lTimeCourse)
                {$ENDIF}
         end else
                 TimecourseROIinten (l4DHdr, ROIoverlayNum(lROI), lTimeCourse);
         //next normalize signal
         if lPSPlot.PctSignal then
            PctSignal(lTimeCourse,lnVol);
         //next compute PSPlots
         for lCond := 1 to lnCond do begin
             //here is where we can remove variability predicted by regressors....
             {$IFDEF REMOVEREGRESS}
             if  lPSPlot.RemoveRegressorVariability then begin
                RemoveRegressors(lTimeCourse,lTimeCourseFilt,l4DTrace,lCond,lnVol,lPSPlot);
                TimeCourseToPSPlot(lTimeCourseFilt, l4DTrace,lCountBin, lMnBin,lSumBin,lSumSqrBin
               ,lPSPlot, lCond,lnVol);
             end else
             {$ENDIF}
                 TimeCourseToPSPlot(lTimeCourse, l4DTrace,lCountBin, lMnBin,lSumBin,lSumSqrBin
               ,lPSPlot,lCond,lnVol);
             //percent signal change and std error
             ComputeMeanSE (lCountBin, lMnBin,lSEBin,lSumBin,lSumSqrBin
                ,lPSPlot.nNegBins,lPSPlot.nPosBins);
             //report results
             if lPSPlot.TextOutput then
                TextOutput (lROI,lCond,lPSPlot, l4DTrace,lCountBin,lMnBin,lSEBin);
             if (lPSPlot.GraphOutput)  then begin
                lLine := lROI + ((lCond-1)* lnROImin1);
                for lBin := 1 to (lPSPlot.nNegBins + lPSPlot.nPosBins) do begin
                    lBinData.Lines[lLine].EventRA^[lBin] := lMnBin^[lBin];
                    lBinData.Conditions[lLine].EventRA^[lBin] := lSEBin^[lBin];
                end;//for each bin
             end; //if graphoutput
         end; //for each cond
     end; //for each ROI
     freemem(lCountBin); //12/2007
     freemem(lTimeCourse);
     freemem(lTimeCourseFilt);
     freemem(lMnBin);
     freemem(lSEBin);
     freemem(lSumSqrBin);
     freemem(lSumBin);
     if lPSPlot.TextOutput then
        TextForm.show;
     if (lPSPlot.GraphOutput)  then begin
        MinMax4DTrace(lBinData);
        for lCond := 1 to lnCond do
            lBinData.Conditions[lCond].eLabel:= l4DTrace.Conditions[lCond].eLabel;
        lBinData.HorzMin := (-lPSPlot.nNegBins+0.5)*lPSPlot.BinWidthSec;
        lBinData.HorzWidPerBin := lPSPlot.BinWidthSec;
        CorePlot4DTrace(lBinData,Graph4DForm.Image1,1,0,lnCond,lPSPlot.TRsec,Graph4DForm.MinEdit.value,Graph4DForm.MaxEdit.value,true);
        Close4DTrace(lBinData,true);
     end;//if graph
     result := true;
end;


end.