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|
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.
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