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unit statclustertable;
//USED by stats to select only regions with a given number of connected/contiguous voxels
interface
{$H+}
uses define_types,dialogs,SysUtils,nifti_hdr,nifti_img, classes;
//procedure FindClustersText (var lHdr: TMRIcroHdr; lThreshClusterSz: integer; lThresh: double);
procedure BatchCluster;
implementation
uses text,nifti_img_view, nifti_hdr_view, readfloat, readint;
procedure FindClustersText (var lHdr: TMRIcroHdr; lThreshIn: single; lMinClusterSz: integer);
var
lClusterMaxPos,lXdim,lYdim,lZdim,lScaledThresh,lClusterSz,lClusterFillVal,lQTail,lQHead,lSliceSz,lQSz,lInc,lVolSz: integer;
lThresh,lClusterMax: single;
lClusterBuffS: SingleP;
lQra: LongIntP;
lXcom,lYcom,lZcom,lBuffIn32 : SingleP;
lBuffIn16 : SmallIntP;
lCh: char;
procedure InitCenterOfMass;
begin
getmem(lXcom, lXDim*sizeof(single));
getmem(lYcom, lYDim*sizeof(single));
getmem(lZcom, lZDim*sizeof(single));
end;
procedure FreeCenterOfMass;
begin
freemem(lXcom);
freemem(lYcom);
freemem(lZcom);
end;
procedure ClearCenterOfMass;
var
i: integer;
begin
for i := 1 to lXDim do
lXcom^[i] := 0;
for i := 1 to lYDim do
lYcom^[i] := 0;
for i := 1 to lZDim do
lZcom^[i] := 0;
end;
procedure AddCenterOfMass (lVox: integer; lInten: single);
var
lXi,lYi,lZi: integer;
begin
//lukas
ImgPosToSlices(lVox,lXi,lYi,lZi);
lXcom^[lXi] := lXcom^[lXi] + lInten;
lYcom^[lYi] := lYcom^[lYi] + lInten;
lZcom^[lZi] := lZcom^[lZi] + lInten;
end;
function CenterOfMassPosition: integer;
var
i : integer;
lSum,lXs,lYs,lZs: double;
begin
lSum := 0;
lXs := 0;
for i := 1 to lXDim do
lSum := lSum +lXcom^[i];
for i := 1 to lXDim do
lXs := lXs +(i*lXcom^[i]);
if lSum > 0 then
lXs := lXs/lSum;
//
lSum := 0;
lYs := 0;
for i := 1 to lYDim do
lSum := lSum +lYcom^[i];
for i := 1 to lYDim do
lYs := lYs +(i*lYcom^[i]);
if lSum > 0 then
lYs := lYs/lSum;
//Z
lSum := 0;
lZs := 0;
for i := 1 to lZDim do
lSum := lSum +lZcom^[i];
for i := 1 to lZDim do
lZs := lZs +(i*lZcom^[i]);
if lSum > 0 then
lZs := lzs/lSum;
result := SlicesToImgPos(round(lXs),round(lYs),round(lZs));
//fx(result, lXs,lYs,lZs);
end;
function XYZstr (lPos: integer): string;
var lXmm,lYmm,lZmm: single;
begin
ImgPosToMM(lPos, lXmm,lYmm,lZmm);
result := inttostr(round(lXmm))+kTextSep+inttostr(round(lYmm))+kTextSep+inttostr(round(lZmm));
end;
procedure Report (lClusterMax: single; lClusterSz, lClusterMaxPos: integer);
var
lAALstr,lBAstr : string;
begin
if lClusterSz < lMinClusterSz then
exit;
lBAstr := '';
if gMRIcroOverlay[2].ImgBufferItems = lVolSz then //BA map loaded
lBAstr := inttostr(gMRIcroOverlay[2].ImgBuffer^[lClusterMaxPos]);
if gMRIcroOverlay[3].ImgBufferItems = lVolSz then //AAL map loaded
lAALstr := gBGImg.LabelStr20[gMRIcroOverlay[3].ImgBuffer^[lClusterMaxPos]];
TextForm.MemoT.lines.add(XYZstr(lClusterMaxPos)+kTextSep+XYZstr(CenterOfMassPosition)+kTextSep+inttostr(lClusterSz)+kTextSep+lCh+floattostr(lClusterMax)+kTextSep+(lBAStr)+kTextSep+(lAALstr));
end;
procedure ReportLabel;
begin
TextForm.MemoT.lines.add('# Data='+kTextSep+lHdr.HdrFileName +kTextSep+'Threshold='+kTextSep+floattostr(lThreshIn) +kTextSep+'MinCluster='+kTextSep+inttostr(lMinClusterSz));
TextForm.MemoT.lines.add('#X'+kTextSep+'Y'+kTextSep+'Z'+kTextSep+'Xcom'+kTextSep+'Ycom'+kTextSep+'Zcom'+kTextSep+'ClusterSize[Vox]'+kTextSep+'Max'+kTextSep+'BA'+kTextSep+'AAL');
end;
Procedure IncQra(var lVal, lQSz: integer);
begin
inc(lVal);
if lVal >= lQSz then
lVal := 1;
end;
procedure Check(lPixel: integer);
var
lVal: single;
begin
lVal := lClusterBuffS^[lPixel];
if (lVal= 0) then
exit;
AddCenterOfMass(lPixel,lVal);
if lVal > lClusterMax then begin
lClusterMax := lVal;
lClusterMaxPos := lPixel;
end;
incQra(lQHead,lQSz);
inc(lClusterSz);
lClusterBuffS^[lPixel] := 0;
lQra^[lQHead] := lPixel;
end;
PROCEDURE RetirePixel; //FIFO cleanup , 1410: added 18-voxel check
VAR
lVal,lValX,lXPos,lYPos,lZPos: integer;
BEGIN
lVal := lQra^[lQTail];
if lVal = 0 then begin
incQra(lQTail,lQSz); //done with this pixel
exit;
end;
lXpos := lVal mod lXdim;
if lXpos = 0 then lXPos := lXdim;
lYpos := (1+((lVal-1) div lXdim)) mod lYDim;
if lYPos = 0 then lYPos := lYdim;
lZpos := ((lVal-1) div lSliceSz)+1;
if (lXPos <= 1) or (lXPos >= lXDim) or
(lYPos <= 1) or (lYPos >= lYDim) or
(lZPos <= 1) or (lZPos >= lZDim) then
// retire and exiT
else begin
//lXDimM := lXDim;
Check(lVal-1); //left
Check(lVal+1); //right
Check(lVal-lXDim); //up
Check(lVal+lXDim); //down
Check(lVal-lSliceSz); //up
Check(lVal+lSliceSz); //down
//check plane above
lValX := lVal + lSLiceSz;
Check(lValX-1); //left
Check(lValX+1); //right
Check(lValX-lXDim); //up
Check(lValX+lXDim); //down
//check plane below
lValX := lVal - lSLiceSz;
Check(lValX-1); //left
Check(lValX+1); //right
Check(lValX-lXDim); //up
Check(lValX+lXDim); //down
//check diagonals of current plane
Check(lVal-lXDim-1); //up, left
Check(lVal-lXDim+1); //up, right
Check(lVal+lXDim-1); //down, left
Check(lVal+lXDim+1); //down, right
end; //not edge
incQra(lQTail,lQSz); //done with this pixel
END;
procedure FillStart (lPt: integer); {FIFO algorithm: keep memory VERY low}
var lI: integer;
begin
if (lClusterBuffS^[lPt]=0) then exit;
for lI := 1 to lQsz do
lQra^[lI] := 0;
lQHead := 0;
lQTail := 1;
Check(lPt);
RetirePixel;
// check that there was anything in the cluster at all
//showmessage('head'+inttostr(lQHead)+'.'+inttostr(lQTail));
//if lQHead > 2 then begin
// and do the recursion to get rid of it
while ((lQHead+1) <> lQTail) do begin//complete until all voxels in buffer have been tested
RetirePixel;
if (lQHead = lQSz) and (lQTail = 1) then
exit; //break condition: avoids possible infinite loop where QTail is being incremented but QHead is stuck at maximum value
end;
end;
begin
lCh := ' '; //assume positive values
lXDim := lHdr.NIFTIhdr.dim[1];
lYDim := lHdr.NIFTIhdr.dim[2];
lZDim := lHdr.NIFTIhdr.dim[3];
InitCenterOfMass;
lVolSz := lXdim*lYdim*lZdim;
lSliceSz := lXdim * lYdim;
if (lXDim < 4) or (lYDim < 4) or (lZDim < 4) or (lVolSz < 1) or (lHdr.ImgBufferItems <> lVolSz) then exit;
GetMem(lClusterBuffS, lVolSz* sizeof(Single));
ReportLabel;
if lHdr.ImgBufferBPP = 4 then begin
lBuffIn32 := SingleP(lHdr.ImgBuffer);
for lInc := 1 to lVolSz do
lClusterBuffS^[lInc] := lBuffIn32^[lInc];
end else if lHdr.ImgBufferBPP = 2 then begin //not 32bit - if 16bit input
lBuffIn16 := SmallIntP(lHdr.ImgBuffer);
for lInc := 1 to lVolSz do
lClusterBuffS^[lInc] := lBuffIn16^[lInc];
end else begin //not 16 or 32 bit input
for lInc := 1 to lVolSz do
lClusterBuffS^[lInc] := lHdr.ImgBuffer^[lInc];
end; //8-bit input
//Next - apply scale and intercept
if (lHdr.NIFTIhdr.scl_slope <> 0) and (lHdr.NIFTIhdr.scl_slope <> 1) then //if one then no effect - zero is meaningless
for lInc := 1 to lVolSz do
lClusterBuffS^[lInc] := lClusterBuffS^[lInc]*lHdr.NIFTIhdr.scl_slope;
if (lHdr.NIFTIhdr.scl_inter <> 0) then //if zero then no effect
for lInc := 1 to lVolSz do
lClusterBuffS^[lInc] := lClusterBuffS^[lInc]+lHdr.NIFTIhdr.scl_inter;
lThresh := lThreshIn;
if lThreshIn < 0 then begin //invert all values...
for lInc := 1 to lVolSz do
lClusterBuffS^[lInc] := -lClusterBuffS^[lInc];
lThresh := -lThresh;
lCh := '-';
end;
//Next - zero all voxels less than threshold
for lInc := 1 to lVolSz do
if (lClusterBuffS^[lInc]) < lThresh then
lClusterBuffS^[lInc] := 0;
//Next - get memory
lQSz := (lVolSz div 4)+8;
GetMem(lQra,lQsz * sizeof(longint) );
//check positive clusters....
ClearCenterOfMass;
for lInc := 1 to lVolSz do begin
if lClusterBuffS^[lInc] <> 0 then begin
lClusterSz := 0;
lClusterMax := 0;
FillStart(lInc);
// now fill the cluster with its size (=1 if the voxel was isolated)
Report (lClusterMax,lClusterSz,lClusterMaxPos);
ClearCenterOfMass;
end;
end;
FreeCenterOfMass;
Freemem(lQra);
Freemem(lClusterBuffS);
end;
procedure BatchCluster;
var
lInc,lNumberofFiles,lMinClusterSz: integer;
lFilename,lBAname,lAALname:string;
lPref: boolean;
lThresh: single;
begin
for lInc := 1 to (knMaxOverlay-1) do
FreeImgMemory(gMRIcroOverlay[lInc]);
ImgForm.UpdateLayerMenu;
lMinClusterSz := ReadIntForm.GetInt('Minimum cluster size [in voxels]: ', 1,4,9999);
lThresh := ReadFloatForm.GetFloat('Please enter statistical threshold. ', -9999,2.3,9999);
if not OpenDialogExecute(kImgFilter,'Select statistical maps',true) then exit;
lNumberofFiles:= HdrForm.OpenHdrDlg.Files.Count;
if lNumberofFiles < 1 then
exit;
lAALname := gTemplateDir+pathdelim+'aal.nii.gz';
if not fileexists(lAALname) then
lAALName := '';
lBAname := gTemplateDir+pathdelim+'brodmann.nii.gz';
if not fileexists(lBAname) then
lBAName := '';
TextForm.MemoT.Lines.Clear;
lPref := gBGImg.ResliceOnLoad;
gBGImg.ResliceOnLoad := false;
for lInc:= 1 to lNumberofFiles do begin
lFilename := HdrForm.OpenHdrDlg.Files[lInc-1];
ImgForm.OpenAndDisplayImg(lFilename,false);
if lBAName <> '' then
ImgForm.OverlayOpenCore ( lBAname, 2);
if lAALName <> '' then
ImgForm.OverlayOpenCore ( lAALname, 3);
FindClustersText(gMRIcroOverlay[kBGOverlayNum], lThresh,lMinClusterSz);
end;//lLoop
gBGImg.ResliceOnLoad := lPref;
TextForm.Show;
end;
end.
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