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unit reslice_fsl;
{$H+}
interface
uses
nifti_hdr,define_types,metagraph,sysutils;
function ResliceImg (lTargetImgName,lSrcImgName,lSrc2TargetMatName,lOutputName: string): boolean;
procedure ResliceFSL;
implementation
uses nifti_img_view,dialogs,nifti_img,text,graphx,math,nifti_hdr_view,GraphicsMathLibrary,classes;
procedure ResliceFSL;
label
666;
var
lInc,lNumberofFiles: integer;
lSrc2TargetMatName,lSrcImgName,lTargetImgName,lOutputName:string;
lStrings : TStringList;
begin
ImgForm.CloseImagesClick(nil);
if not OpenDialogExecute(kImgFilter,'Select source image[s]',true) then exit;
lNumberofFiles:= HdrForm.OpenHdrDlg.Files.Count;
if lNumberofFiles < 1 then
exit;
lStrings := TStringList.Create;
lStrings.AddStrings(HdrForm.OpenHdrDlg.Files);
if not OpenDialogExecute('FSL (*.mat)|*.mat','Select FSL source-to-target matrix',false) then goto 666;
lSrc2TargetMatName := HdrForm.OpenHdrDlg.Filename;
if not OpenDialogExecute(kImgFilter,'Select target image (source image will be warped to this)',false) then goto 666;
lTargetImgName := HdrForm.OpenHdrDlg.Filename;
TextForm.MemoT.Lines.Clear;
for lInc:= 1 to lNumberofFiles do begin
lSrcImgName := lStrings[lInc-1];
lOutputName := ChangeFilePrefix (lSrcImgName,'w');
TextForm.MemoT.Lines.Add(' Source->Matrix->Target '+lSrcImgName+'->'+ lSrc2TargetMatName+'->'+lTargetImgName);
ResliceImg (lTargetImgName,lSrcImgName,lSrc2TargetMatName,lOutputName);
end;//lLoop
TextForm.Show;
666:
lStrings.free;
end;
function ReadFSLMat (var lMat: TMatrix; lSrc2TargetMatName: string):boolean;
var
lF: TextFile;
xx,xy,xz,xo
,yx,yy,yz,yo
,zx,zy,zz,zo: double;
begin
result := false;
if not fileexists(lSrc2TargetMatName) then exit;
Assign(lF,lSrc2TargetMatName);
Filemode := 0;
Reset(lF);
readln(lF,xx,xy,xz,xo,yx,yy,yz,yo,zx,zy,zz,zo);
//read all with one readln -
// separate readlns only work for native eoln
CloseFile(lF);
lMat:= Matrix3D (xx,xy,xz,xo
,yx,yy,yz,yo
,zx,zy,zz,zo
,0,0,0,1);
result := true;
Filemode := 2;
end;
function Rx (var lDestHdr,lSrcHdr: TMRIcroHdr; var lInMat: TMatrix; var lOutputName: string):boolean;
var
lPos,lXYs,lXYZs,lXs,lYs,lZs,lXi,lYi,lZi,lX,lY,lZ,
lXo,lYo,lZo,lMinY,lMinZ,lMaxY,lMaxZ: integer;
lXrM1,lYrM1,lZrM1,
lXreal,lYreal,lZreal: double;
lOutImg: bytep;
lScale,lMat: TMatrix;
begin
result := false;
lXs := lSrcHdr.NIFTIhdr.Dim[1];
lYs := lSrcHdr.NIFTIhdr.Dim[2];
lZs := lSrcHdr.NIFTIhdr.Dim[3];
if (gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems <> lXs*lYs*lZs) then begin
showmessage('Reslice error: background image not loaded.');
exit;
end;
lXYs:=lXs*lYs; //slicesz
lXYZs := lXYs*lZs;
lX := lDestHdr.NIFTIhdr.Dim[1];
lY := lDestHdr.NIFTIhdr.Dim[2];
lZ := lDestHdr.NIFTIhdr.Dim[3];
//TextForm.Memo1.Lines.Add(inttostr(lXs)+'x'+inttostr(lYs)+'x'+inttostr(lZs)+'->'+inttostr(lX)+'x'+inttostr(lY)+'x'+inttostr(lZ));
lDestHdr.NIFTIhdr.Dim[4] := 1;
getmem(lOutImg, lX*lY*lZ*sizeof(byte));
lPos := 0;
//http://eeg.sourceforge.net/MJenkinson_coordtransforms.pdf
//FLIRT transforms are in world coordinates [mm]
//to convert to a vxl-vxl transform, the matrix must be
//PRE-multiplied by inv(Dest) and POST-multiplied by Src
//where Dest and Src are the spatial dimensions in mm
lScale:= Matrix3D (abs(lSrcHdr.NIFTIhdr.pixdim[1]),0,0,0
,0,abs(lSrcHdr.NIFTIhdr.pixdim[2]),0,0
,0,0,abs(lSrcHdr.NIFTIhdr.pixdim[3]),0
,0,0,0,1);
lScale := InvertMatrix3D(lScale);
lMat := MultiplyMatrices(lScale,lInMat);
lScale:= Matrix3D (abs(lDestHdr.NIFTIhdr.pixdim[1]),0,0,0
,0,abs(lDestHdr.NIFTIhdr.pixdim[2]),0,0
,0,0,abs(lDestHdr.NIFTIhdr.pixdim[3]),0
,0,0,0,1);
lMat := MultiplyMatrices(lMat,lScale);
for lZi := 0 to (lZ-1) do begin
for lYi := 0 to (lY-1) do begin
for lXi := 0 to (lX-1) do begin
inc(lPos);
lOutImg^[lPos] := 0;
lXreal := (lXi*lMat.matrix[1][1]+lYi*lMat.matrix[1][2]+lZi*lMat.matrix[1][3]+lMat.matrix[1][4]);
lYreal := (lXi*lMat.matrix[2][1]+lYi*lMat.matrix[2][2]+lZi*lMat.matrix[2][3]+lMat.matrix[2][4]);
lZreal := (lXi*lMat.matrix[3][1]+lYi*lMat.matrix[3][2]+lZi*lMat.matrix[3][3]+lMat.matrix[3][4]);
//need to test Xreal as -0.01 truncates to zero
if (lXreal >= 0) and (lYreal >= 1) and (lZreal >= 1) and
(lXreal < (lXs -1)) and (lYreal < (lYs -1) ) and (lZreal < (lZs -1))
then begin
lXo := trunc(lXreal);
lYo := trunc(lYreal);
lZo := trunc(lZreal);
lXreal := lXreal-lXo;
lYreal := lYreal-lYo;
lZreal := lZreal-lZo;
lXrM1 := 1-lXreal;
lYrM1 := 1-lYreal;
lZrM1 := 1-lZreal;
lMinY := ((lYo)*lXs);
lMinZ := ((lZo)*lXYs);
lMaxY := ((lYo+1)*lXs);
lMaxZ := ((lZo+1)*lXYs);
inc(lXo);//images incremented from 1 not 0
{if lMax <(lXreal) then
lMax := lXreal;
if lMin >(lXreal) then
lMin := lXreal; }
lOutImg^[lPos] :=
round (
{all min} ( (lXrM1*lYrM1*lZrM1)*gMRIcroOverlay[kBGOverlayNum].ScrnBuffer^[lXo+lMinY+lMinZ])
{x+1}+((lXreal*lYrM1*lZrM1)*gMRIcroOverlay[kBGOverlayNum].ScrnBuffer^[lXo+1+lMinY+lMinZ])
{y+1}+((lXrM1*lYreal*lZrM1)*gMRIcroOverlay[kBGOverlayNum].ScrnBuffer^[lXo+lMaxY+lMinZ])
{z+1}+((lXrM1*lYrM1*lZreal)*gMRIcroOverlay[kBGOverlayNum].ScrnBuffer^[lXo+lMinY+lMaxZ])
{x+1,y+1}+((lXreal*lYreal*lZrM1)*gMRIcroOverlay[kBGOverlayNum].ScrnBuffer^[lXo+1+lMaxY+lMinZ])
{x+1,z+1}+((lXreal*lYrM1*lZreal)*gMRIcroOverlay[kBGOverlayNum].ScrnBuffer^[lXo+1+lMinY+lMaxZ])
{y+1,z+1}+((lXrM1*lYreal*lZreal)*gMRIcroOverlay[kBGOverlayNum].ScrnBuffer^[lXo+lMaxY+lMaxZ])
{x+1,y+1,z+1}+((lXreal*lYreal*lZreal)*gMRIcroOverlay[kBGOverlayNum].ScrnBuffer^[lXo+1+lMaxY+lMaxZ]) );
end;
end;//z
end;//y
end;//z
deletefile(lOutputName);
SaveAsVOIorNIFTIcore (lOutputName,lOutImg, lX*lY*lZ, 1,1,lDestHdr.NIFTIhdr);
lPos := 1;
while (lPos <= (lX*lY*lZ)) and (lOutImg^[lPos] = 0) do
inc(lPos);
if lPos > (lX*lY*lZ) then
result := false
else
result := true;
freemem(lOutImg);
end;
function ResliceImg (lTargetImgName,lSrcImgName,lSrc2TargetMatName,lOutputName: string): boolean;
label
666;
var
lReslice,lOrtho : boolean;
lDestHdr,lSrcHdr: TMRIcroHdr;
lMat: TMatrix;
begin
result := false;
if not fileexists(lTargetImgName) then exit;
if not fileexists(lSrcImgName) then exit;
if not fileexists(lSrc2TargetMatName) then exit;
if not ReadFSLMat(lMat,lSrc2TargetMatName) then exit;
ImgForm.CloseImagesClick(nil);
lReslice := gBGImg.ResliceOnLoad;
lOrtho := gBGImg.OrthoReslice;
gBGImg.OrthoReslice := false;
gBGImg.ResliceOnLoad := false;
//if not HdrForm.OpenAndDisplayHdr(lTargetImgName,lDestHdr) then goto 666;
if not NIFTIhdr_LoadHdr(lTargetImgName, lDestHdr) then goto 666;
if not NIFTIhdr_LoadHdr(lSrcImgName, lSrcHdr) then goto 666;
ImgForm.OpenAndDisplayImg(lSrcImgName,True);
if not Rx(lDestHdr,lSrcHdr,lMat,lOutputName) then goto 666;
result := true;
666:
if not result then
showmessage('Error applying transform '+lSrcImgName+'->'+lTargetImgName+' using '+lSrc2TargetMatName);
gBGImg.ResliceOnLoad := lReslice;
gBGImg.OrthoReslice := lOrtho;
end;
end.
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