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unit periutils;
interface
{$IFDEF FPC} {$H+} {$ENDIF}
uses metagraph, define_types, sysutils,nifti_hdr, classes;
function FSLMatName (lFeatDir: string): string;
function FSLFuncName (lFeatDir: string): string;//Given feat folder returns name of filtered data
function FSLReslicedVOIName (lFeatDir, lMNIVOIName: string): string;
procedure RegressTrace (var l4DTrace: T4DTrace);
function ConvertToTrace (var l4DHdr: TMRIcroHdr;var l4DTrace: T4DTrace; lX,lY,lZ: integer): boolean;
function ReadCond (l3ColTextFileName: string; var l4DTrace: T4DTrace; lCond: integer): boolean;
procedure FSLEVNames (lFeatDir: string; var lEVlist: TStringList);
implementation
uses nifti_img_view, text,dialogs,periplot;
function ReadCond (l3ColTextFileName: string; var l4DTrace: T4DTrace; lCond: integer): boolean;
var
lOnsetText: TextFile;
lnEvents: integer;
lFloat,lFloat2,lFloat3: single;
begin
result := false;
if (lCond < 1) or (lCond > kMaxCond) then
exit;
CloseCond(l4DTrace,lCond);
Filemode := 0;
assignfile(lOnsetText,l3ColTextFileName);
{I-}
reset(lOnsetText);
{$I+}
if ioresult <> 0 then begin
Showmessage('Unable to read file [may be in use by another program '+ l3ColTextFileName);
exit;
end;
lnEvents := 0;
while not EOF(lOnsetText) do begin
{$I-}
read(lOnsetText,lFloat,lFloat2,lFloat3); //read triplets instead of readln: this should load UNIX files
{$I+}
if (ioresult = 0) and (lFloat3 > 0) then
inc(lnEvents);
end;
if lnEvents < 1 then begin
closefile(lOnsetText);
showmessage('No events detected. Is this really a FSL-style 3 Column format file? '+l3ColTextFileName);
exit;
end;
InitCond (l4DTrace, lCond, lnEvents);
reset(lOnsetText);
lnEvents := 0;
while not EOF(lOnsetText) do begin
lFloat := 0;
{$I-}
read(lOnsetText,lFloat,lFloat2,lFloat3); //read triplets instead of readln: this should load UNIX files
{$I+}
if (ioresult = 0) and (lFloat3 > 0) then begin
inc(lnEvents);
l4DTrace.Conditions[lCond].EventRA^[lnEvents] := lFloat;
l4DTrace.Conditions[lCond].DurRA^[lnEvents] := lFloat2;
//l4DTrace.DurRA[lCond]^[lnEvents] := lFloat2;
end;
end;
closefile(lOnsetText);
l4DTrace.Conditions[lCond].ELabel := parsefilename(extractfilename(l3ColTextFileName));
result := true;
end;
function ConvertToTrace (var l4DHdr: TMRIcroHdr;var l4DTrace: T4DTrace; lX,lY,lZ: integer): boolean;
var
lVol,lVolSz,lPos,lSamples,lLine,lnLines,lROI: integer;
l16Buf : SmallIntP;
l32Buf : SingleP;
begin
result := false;
lSamples := l4DHdr.NIFTIhdr.dim[4];
lVolSz := l4DHdr.NIFTIhdr.dim[1]*l4DHdr.NIFTIhdr.dim[2]*l4DHdr.NIFTIhdr.dim[3];
if lSamples < 2 then
exit;
lnLines := 0;
for lVol := (kBGOverlayNum+1) to knMaxOverlay do
if gMRIcroOverlay[lVol].ScrnBufferItems > 0 then //for each ROI
inc(lnLines);
if lnLines = 0 then begin //no ROIs
lLine := 1;
lPos := lX + ((lY-1)*gBGImg.ScrnDim[1])+((lZ-1)*gBGImg.ScrnDim[1]*gBGImg.ScrnDim[2]);
if (lPos > l4DHdr.ImgBufferItems) or (lPos < 1) then exit;
Init4DTrace(lSamples, 1,l4DTrace,false);
l4DTrace.Lines[1].ELabel := inttostr(lX)+'x'+inttostr(lY)+'x'+inttostr(lZ);
if (l4DHdr.ImgBufferBPP = 4) then begin
l32Buf := SingleP(l4DHdr.ImgBuffer );
for lVol := 1 to lSamples do begin
l4DTrace.Lines[lLine].EventRA[lVol] := l32Buf[lPos];
lPos := lPos + lVolSz;
end;
end else if (l4DHdr.ImgBufferBPP = 2) then begin
l16Buf := SmallIntP(l4DHdr.ImgBuffer );
for lVol := 1 to lSamples do begin
l4DTrace.Lines[lLine].EventRA^[lVol] := l16Buf^[lPos];
lPos := lPos + lVolSz;
end;
end else if l4DHdr.ImgBufferBPP = 1 then begin
for lVol := 1 to lSamples do begin
l4DTrace.Lines[lLine].EventRA^[lVol] := l4DHdr.ImgBuffer^[lPos];
lPos := lPos + lVolSz;
end;
end else
showmessage('Serious error: unknown data size!');
end else begin //>0 ROIS
Init4DTrace(lSamples, lnLines,l4DTrace,false);
for lLine := 1 to lnLines do begin
lROI := ROIoverlayNum(lLine);
l4DTrace.Lines[lLine].ELabel := ParseFileName(extractfilename(gMRIcroOverlay[lROI].HdrFileName));
for lVol := 1 to lSamples do
l4DTrace.Lines[lLine].EventRA^[lVol] := ROImean(l4DHdr,lROI,lVol{,lVolSz});
end;
end;
MinMax4DTrace(l4DTrace);
result := true;
end;
function ComputeRegress (ldataRA: singlep; lndata: integer): string;
const
//kMax = 1000;
kCR = chr (13);
Var
gx : Array[1..4] of extended;
gy : Array[1..4] of extended;
Exy : Array[1..4] of extended;
Ex : Array[1..4] of extended;
Ey : Array[1..4] of extended;
Ex2 : Array[1..4] of extended;
Ey2 : Array[1..4] of extended;
a : Array[1..4] of extended;
b : Array[1..4] of extended;
r : Array[1..4] of extended;
chtX: Array[1..4] of extended;
chtY: Array[1..4] of extended;
no : Integer;
gInter, gSlope,gRSqr : extended;
function calcit: string;
Var
q : Integer;
Begin
For q := 1 To 4 Do Begin
b[q] := (no * Exy[q] - Ex[q] * Ey[q]) / (no * Ex2[q] - (Ex[q]*Ex[q]) );
a[q] := (Ey[q] - b[q] * Ex[q]) / no;
r[q] := (no * Exy[q] - Ex[q] * Ey[q]) / (Sqrt((no * Ex2[q] - (Ex[q]*Ex[q]) ) * (no * Ey2[q] - (Ey[q]*Ey[q]) ) ));
End; // for
a[2] := Exp(a[2]);
a[4] := Exp(a[4]);
result := (' Linear Y=' + RealToStr(a[1],8) + ' +' + RealToStr(b[1],8) + ' * X'+' R=' + RealToStr(r[1],8)+' R^2=' + RealToStr(r[1]*r[1],8));
gInter := a[1];
gSlope := b[1];
gRSqr := r[1];
result := result + (', Exp Y=' + RealToStr(a[2],8) + ' * e ^' + RealToStr(b[2],8) + ' * X'+' R=' + RealToStr(r[2],8)+' R^2=' + RealToStr(r[2]*r[2],8));
result := result + (', Log Y=' + RealToStr(a[3],8) + ' +' + RealToStr(b[3],8) + ' * LOG(X)'+' R=' + RealToStr(r[3],8)+' R^2=' + RealToStr(r[3]*r[3],8));
result := result +(', Power Y=' + RealToStr(a[4],8) + ' * X ^' + RealToStr(b[4],8)+' R=' + RealToStr(r[4],8)+' R^2=' + RealToStr(r[4]*r[4],8));
End; // nested calcit()
Procedure inpcalc (lX, lY: extended);
Var
q : Integer;
Begin
gx[1] := lX;
gy[1] := lY;
//inc(gnVal);
inc(no);
gx[2] := gx[1];
gy[2] := Ln(gy[1]); // exp
gx[3] := Ln(gx[1]);
gy[3] := gy[1]; // log
gx[4] := Ln(gx[1]);
gy[4] := Ln(gy[1]); // power
For q := 1 To 4 Do Begin
Exy[q] := Exy[q] + gx[q] * gy[q];
Ex[q] := Ex[q] + gx[q];
Ey[q] := Ey[q] + gy[q];
Ex2[q] := Ex2[q] + (gx[q]*gx[q]);
Ey2[q] := Ey2[q] + (gy[q]*gy[q]);
End; // For
End; //nested inpcalc
procedure initReg;
var lC: byte;
begin
for lC := 1 to 4 do begin
gx [lC]:= 0;
gy [lC]:= 0;
Exy [lC]:= 0;
Ex[lC]:= 0;
Ey[lC]:= 0;
Ex2[lC]:= 0;
Ey2[lC]:= 0;
a[lC]:= 0;
b[lC]:= 0;
r[lC]:= 0;
chtX[lC]:= 0;
chtY[lC]:= 0;
end; //for lC
end;//nested inp calc
const
kDeleteVols = 3;
var
i: integer;
begin //computeRegress
result := '';
no := 0;
if lndata < (kDeleteVols+5) then exit;
//gnVal := 0;
initReg;
for i := kDeleteVols to lndata do begin
//fx(i,ldatara[i]);
inpcalc (i, ldataRA^[i]);
end;
result := calcit;
end; //func ComputeRegress
procedure RegressTrace (var l4DTrace: T4DTrace);
var
lStr: string;
lE,lCond, lnCond,lnE: integer;
lMean : double;
ldataRA: singlep;
begin
lncond := 0;
for lCond := 1 to kMaxCond do
if l4DTrace.Lines[lCond].Events > 0 then
inc(lnCond);
if lncond = 0 then
exit;
for lCond := 1 to kMaxCond do begin
if l4DTrace.Lines[lCond].Events > 0 then begin
lnE := l4DTrace.Lines[lCond].Events;
getmem(ldataRA,lnE * sizeof(single));
lStr := gMRIcroOverlay[kBGOverlayNum].HdrFileName+','+l4DTrace.Lines[lCond].ELabel;
//load data
lMean := 0;
for lE := 1 to lnE do begin
ldataRA[lE] := l4DTrace.Lines[lCond].EventRA[lE];
lMean := ldataRA^[lE] + lMean; //sum
end;
lMean := lMean / lnE;
//fx(lMean);
//normalize data...
for lE := 1 to lnE do
ldataRA^[lE] := ldataRA^[lE]/lMean;
//compute functions
lStr := lStr +kTextSep+ (ComputeRegress (ldataRA, lnE) );
TextForm.MemoT.lines.add(lStr);
//TextForm.Memo1.lines.add(lStr);
freemem(ldataRA);
end;
end;
//TextForm.show;
end;
//NEXT SECTION - FSL UTILITIES
procedure FSLEVNames (lFeatDir: string; var lEVlist: TStringList);
//Given feat folder returns name of matrix to reorient MNI image to functional data
var
lEVdir : string;
lSearchRec: TSearchRec;
begin
lEVList.clear;
lEVdir := lFEATDir+pathdelim+'custom_timing_files';
//showmessage(lEVdir);
if not DirExists(lEVdir) then
exit;
//showmessage(lEVdir);
if FindFirst(lEVdir+pathdelim+'*'+'.txt', faAnyFile, lSearchRec) = 0 then begin
repeat
lEVlist.Add(lEVdir+pathdelim+lSearchRec.Name)
until (FindNext(lSearchRec) <> 0);
end;
FindClose(lSearchRec);
//fx(lEVlist.count);
//result := lFeatDir+PathDelim+'reg'+PathDelim+'example_func2standard.mat';
end; //MatName
function FSLMatName (lFeatDir: string): string;
//Given feat folder returns name of matrix to reorient MNI image to functional data
begin
result := lFeatDir+PathDelim+'reg'+PathDelim+'example_func2standard.mat';
end; //MatName
function FSLFuncName (lFeatDir: string): string;//Given feat folder returns name of filtered data
begin
result := lFeatDir+PathDelim+'filtered_func_data.nii.gz';
end; //FuncName
function FSLReslicedVOIName (lFeatDir, lMNIVOIName: string): string;
//Given FSL .feat folder name and source MNI volume name retuns resliced VOI name
begin
result := lFeatDir+PathDelim+extractfilename(lMNIVOIName);
(*result := extractfilename(lMNIVOIName);
result := lFeatDir+PathDelim+ChangeFileExtX(result,'.nii.gz'); //;
*)
end; //ReslicedVOIName
end.
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