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unit bet;
{$H+}
interface
uses
Classes, SysUtils, LResources, Forms, Controls, Graphics, Dialogs, StdCtrls,
ExtCtrls, Buttons, Spin,Process,nifti_img,define_types,CropEdges, userdir;
type
{ TBETForm }
TBETForm = class(TForm)
Memo1: TMemo;
SmoothnessEdit: TFloatSpinEdit;
Panel1: TPanel;
GoBtn: TSpeedButton;
AboutBtn: TSpeedButton;
CropBtn: TSpeedButton;
procedure CropBtnClick(Sender: TObject);
procedure GoBtnClick(Sender: TObject);
procedure SpeedButton2Click(Sender: TObject);
private
{ private declarations }
public
{ public declarations }
end;
var
BETForm: TBETForm;
implementation
uses
nifti_img_view;
{ TBETForm }
procedure TBETForm.SpeedButton2Click(Sender: TObject);
begin
Showmessage('You can skull strip scans to allow you to render the surface of the brain.'+chr (13)
+ 'This uses Steve Smith''s Brain Extraction Tool [BET].'+chr (13)+
'Default smoothness is 0.50, smaller values generate larger estimates of brain size.'+chr (13)
+'http://www.fmrib.ox.ac.uk/fsl');
end;
//lCmd := extractfilepath(paramstr(0))+'bet "'+lSourceFilename+'" "'+SaveDialog1.Filename
// +'" -f '+floattostr(SmoothnessEdit.value{/100});
function PathExists (lCmd: string): boolean;
begin
result := false;
if FSize(lCmd) < 1 then begin
BETForm.Memo1.Lines.Add('Unable to find executable named '+lCmd);
exit;
end;
result := true;
end;
procedure RunCmd (lCmd: string);
var
AProcess: TProcess;
AStringList: TStringList;
begin
AProcess := TProcess.Create(nil);
AStringList := TStringList.Create;
AProcess.CommandLine := lCmd;
{$IFDEF UNIX}
AProcess.Environment.Add(gBGImg.FSLDIR);
AProcess.Environment.Add(gBGImg.FSLOUTPUTTYPE);
//AProcess.Environment.Add('FSLDIR=/usr/local/fsl');
//AProcess.Environment.Add('FSLOUTPUTTYPE=NIFTI_GZ');
{$ENDIF}
AProcess.Options := AProcess.Options + [poWaitOnExit, poStderrToOutPut, poUsePipes];
AProcess.Execute;
AStringList.LoadFromStream(AProcess.Output);
BetForm.Memo1.Lines.AddStrings(AStringList);
AStringList.Free;
AProcess.Free;
end;
function DoBET(lInFile,lOutFile: string; lFrac: single):boolean;
var
//AProcess: TProcess;
lCmd: string;
begin
result := false;
lCmd := extractfilepath(paramstr(0))+'bet';
{$IFNDEF Unix}
lCmd := lCmd+'.exe';
{$ENDIF}
if not PathExists (lCmd) then begin
lCmd := '/usr/local/fsl/bin/bet_8UI';
if not PathExists (lCmd) then begin
lCmd := '/usr/local/fsl/bin/bet';
if not PathExists (lCmd) then
exit;
end;
end; //no bet in home folder...
lCmd := lCmd+' "'+lInFile+'" "'+lOutFile +'" -f '+floattostr(lFrac);
BETForm.Memo1.Lines.Add(lCmd);
RunCmd(lCmd);
(*AProcess := TProcess.Create(nil);
{$IFDEF UNIX}
AProcess.Environment.Add('FSLDIR=/usr/local/fsl');
AProcess.Environment.Add('FSLOUTPUTTYPE=NIFTI_GZ');
{$ENDIF}
AProcess.CommandLine := lCmd;
//AProcess.CommandLine := 'C:\bet "C:\txx.hdr" "C:\btxx.hdr" -f 0.5';
AProcess.Options := AProcess.Options + [poWaitOnExit];
AProcess.Execute;
AProcess.Free; *)
result := true;
end;
function Bright95Pct: byte;//returns intensity of 95th percentile
var
lPos,l5Pct,lCumulative: integer;
lHisto: array [0..255] of integer;
begin
result := 0;
if (gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems<1) or (gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems<>gMRIcroOverlay[kVOIOverlayNum].ScrnBufferItems) then exit;
//next - create histogram of intensity
for lPos := 0 to 255 do
lHisto[lPos] := 0;
for lPos := 1 to gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems do
inc(lHisto[gMRIcroOverlay[kBGOverlayNum].ScrnBuffer^[lPos]]);
//next find 95th percentile
l5Pct := (gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems div 20);
lCumulative := 0;
lPos := 256;
while (lPos > 0) and (lCumulative < l5Pct) do begin
dec(lPos);
lCumulative := lCumulative + lHisto[lPos];
end;
result := lPos;
end;
procedure CropVOI (lVOIIntensity: byte);
var
lPos: integer;
begin
if (gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems<1) or (gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems<>gMRIcroOverlay[kVOIOverlayNum].ScrnBufferItems) then exit;
for lPos := 1 to gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems do
if gMRIcroOverlay[kVOIOverlayNum].ScrnBuffer^[lPos] = kVOI8bit then
gMRIcroOverlay[kBGOverlayNum].ScrnBuffer^[lPos] := lVOIIntensity;
end;
procedure DeleteHdrImg(lFilename: string);
begin
//exit;
if lFilename = '' then
exit;
DeleteFile(lFilename);
if (UpCaseExt(lFileName)='.IMG') then
DeleteFile(changefileext(lFilename,'.hdr'));
if (UpCaseExt(lFileName)='.HDR') then
DeleteFile(changefileext(lFilename,'.img'));
end;
function Mask8BitImg(lImgName,lMaskName: string): boolean;
//should be two 8-bit image files of identical dimensions
//all non-zero voxels in the mask are written with value of img
//Warning - only works with .img files with zero voxoffset - can corrupt .nii files - would need to read header....
var
lPos2,lPos,lC,lSz,lMaskSz,lBPP: integer;
lImg,lMask: bytep;
lInF: File;
begin
result := false;
lSz := FSize(lImgName);
lMaskSz := FSize(lMaskName);
if lSz = lMaskSz then
lBPP := 1
else if lSz = (2*lMaskSz) then
lBPP := 2
else if lSz = (2*lMaskSz) then
lBPP := 4
else
lBPP := 0;
if (lSz < 1) or (lBPP = 0 ) then
exit;
//next read mask
GetMem(lMask,lSz);
AssignFile(lInF, lMaskName);
Reset(lInF,1);
BlockRead(lInF, lMask^, lMaskSz);
CloseFile(lInF);
//next: read image
GetMem(lImg,lSz);
AssignFile(lInF, lImgName);
Reset(lInF,1);
BlockRead(lInF, lImg^, lSz);
CloseFile(lInF);
//next mask image
for lPos := 1 to lMaskSz do
if lMask^[lPos] = 0 then begin
lPos2 := ((lPos-1)*lBPP);
for lC := 1 to lBPP do
lImg^[lC+lPos2] := 0;
end;
Freemem(lMask);
//next save masked image
AssignFile(lInF, lImgName); //1/2008....
//AssignFile(lInF, lMaskName);
Rewrite(lInF,1);
BlockWrite(lInF, lImg^, lSz);
CloseFile(lInF);
Freemem(lImg);
result := true;
end;
(*function Mask8BitImg(lImgName,lMaskName: string): boolean;//should be two 8-bit image files of identical dimensions
//all non-zero voxels in the mask are written with value of img
//Note: the mask file is changed - not the image
var
lPos,lSz: integer;
lImg,lMask: bytep;
lInF: File;
begin
//showmessage( lMaskName+'xx'+lImgName);
result := false;
lSz := FSize(lImgName);
if (lSz < 1) or (lSz <> FSize(lMaskName)) then
exit;
//fx(lSz,778899);
//next read mask
GetMem(lMask,lSz);
AssignFile(lInF, lMaskName);
Reset(lInF,1);
BlockRead(lInF, lMask^, lSz);
CloseFile(lInF);
//next: read image
GetMem(lImg,lSz);
AssignFile(lInF, lImgName);
Reset(lInF,1);
BlockRead(lInF, lImg^, lSz);
CloseFile(lInF);
//next mask image
for lPos := 1 to lSz do
if lMask^[lPos] = 0 then
lImg^[lPos] := 0;
Freemem(lMask);
//next save masked image
AssignFile(lInF, lMaskName);
Rewrite(lInF,1);
BlockWrite(lInF, lImg^, lSz);
CloseFile(lInF);
Freemem(lImg);
result := true;
end;*)
function DefaultsDirCmd: string;
//Lazarus for Unix does not seem to execute TProcess commands to ~/.. we need to write them to /Home/chris/..
var
lLen,lP: integer;
lStr: string;
begin
{$IFDEF UNIX}
lStr := extractfiledir(GetAppConfigFile(false));
lLen := length(lStr);
if lLen < 1 then exit;
lP := lLen;
while (lP > 0) and (lStr[lP] <> '.') do
dec(lP);
if lP > 1 then begin
for lLen := 1 to (lP-1) do
result := result + lStr[lLen];
end;
{$ELSE} //else ... assume windows
result := DefaultsDir('')
{$ENDIF}
//showmessage('x'+result+'x');
end;
procedure TBETForm.GoBtnClick(Sender: TObject);
label
666;
var
lTempNameOrig,lTempName8bitMask,lTempBetName,lTempGZName: string;
begin
Memo1.Clear;
Memo1.lines.add('Startup Timestamp: '+DateTimeToStr(Now));
if (gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems < 1) then begin
showmessage('BET error: please use File/Open to display the image you want to brain extract.');
end;
//showmessage(DefaultsDirCmd);
lTempNameOrig :=DefaultsDirCmd+'orig.hdr';//lTempNameOrig := extractfilepath(paramstr(0))+'orig.hdr';
SaveAsVOIorNIFTIcore (lTempNameOrig, gMRIcroOverlay[kBGOverlayNum].ImgBuffer,gMRIcroOverlay[kBGOverlayNum].ImgBufferItems, gMRIcroOverlay[kBGOverlayNum].ImgBufferBPP,1,gMRIcroOverlay[kBGOverlayNum].NiftiHdr);
//SaveAsVOIorNIFTIcore (lTempNameOrig, gMRIcroOverlay[kBGOverlayNum].ImgBuffer,gMRIcroOverlay[kBGOverlayNum].ImgBufferItems, gMRIcroOverlay[kBGOverlayNum].ImgBufferBPP,gMRIcroOverlay[kBGOverlayNum].NiftiHdr);
if gMRIcroOverlay[kVOIOverlayNum].ScrnBufferItems > 0 then begin
case MessageDlg('Do you wish to protect tissue shown by the VOI drawing?', mtConfirmation, [mbYes, mbNo], 0) of
mrYes: CropVOI(Bright95Pct);
end; //case for protecting VOI
ImgForm.CloseVOIClick(nil);
end;
if gMRIcroOverlay[kBGOverlayNum].ImgBufferBPP <> 1 then
Memo1.lines.add('Warning: converted image downsampled to 8-bit precision.');
lTempName8bitMask := DefaultsDirCmd+'temp8.hdr';//lTempName8bitMask := extractfilepath(paramstr(0))+'temp8.hdr';
SaveAsVOIorNIFTIcore (lTempName8bitMask, gMRIcroOverlay[kBGOverlayNum].ScrnBuffer,gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems, 1,1,gMRIcroOverlay[kBGOverlayNum].NiftiHdr);
lTempName8bitMask := changefileext(lTempName8bitMask,'.hdr'); //SaveAs renames the .hdr to .img
lTempBetName := DefaultsDirCmd+'btemp8.hdr';//lTempBetName := extractfilepath(paramstr(0))+'btemp8.hdr';
// showmessage(lTempBetName);
if not DoBET(lTempName8bitMask,lTempBetName,SmoothnessEdit.value) then goto 666;
Memo1.lines.add('Shutdown Timestamp: '+DateTimeToStr(Now));
if Fileexists(lTempBetName) then begin
CopyFileEXoverwrite(lTempName8bitMask,lTempBetName); //the old version of BET corrupts some NIfTI information
end else begin
//assume new version of bet_8UI has saved as .nii.gz
lTempGZName := ChangeFileExt(lTempBetName,'.nii.gz');
if not Fileexists(lTempGZName) then begin
Memo1.lines.add('BET Error: unable to find BET image '+lTempBetName+ ' or '+lTempGZName);
{$IFDEF Darwin}
Memo1.lines.add(' Try relaunching MRIcron from the Terminal command line, e.g. /Applications/mricron.app/mricron &');
{$ENDIF}
//Memo1.Lines.SaveToFile('/Users/crlab/junk.txt');
goto 666;
end;
//convert .nii.gz to hdr/.img so we can mask it...
ImgForm.CloseImagesClick(nil);
ImgForm.OpenAndDisplayImg(lTempGZName,True);
SaveAsVOIorNIFTIcore (lTempBetName,gMRIcroOverlay[kBGOverlayNum].ScrnBuffer, gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems, 1,1,gMRIcroOverlay[kBGOverlayNum].NiftiHdr);
//SaveAsVOIorNIFTIcore (lTempBetName, gMRIcroOverlay[kBGOverlayNum].ScrnBuffer,gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems, 1,1,gMRIcroOverlay[kBGOverlayNum].NiftiHdr);
DeleteHdrImg(lTempGZName);
ImgForm.CloseImagesClick(nil);
end;
Mask8BitImg(changefileext(lTempNameOrig,'.img'),changefileext(lTempBetName,'.img'));
//ImgForm.OpenAndDisplayImg(lTempBetName,True); // 1/2008
ImgForm.OpenAndDisplayImg(lTempNameOrig,True);
Memo1.lines.add('Use File/SaveAsNIfTI to save the stripped 8-bit image.');
666:
DeleteHdrImg(lTempBetName);
DeleteHdrImg(lTempNameOrig);
DeleteHdrImg(lTempName8bitMask);
end;
procedure TBETForm.CropBtnClick(Sender: TObject);
begin
CropEdgeForm.Show;
end;
(*var
lTempNameOrig,lTempName8bitMask,lTempBetName: string;
begin
Memo1.Clear;
Memo1.lines.add('Startup Timestamp: '+DateTimeToStr(Now));
if (gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems < 1) then begin
showmessage('BET error: please use File/Open to display the image you want to brain extract.');
end;
lTempNameOrig := '';
if gMRIcroOverlay[kVOIOverlayNum].ScrnBufferItems > 0 then begin
case MessageDlg('Do you wish to remove tissue shown by the VOI drawing?', mtConfirmation,
[mbYes, mbNo], 0) of
mrYes: CropVOI(0);
else case MessageDlg('Do you wish to protect tissue shown by the VOI drawing?', mtConfirmation,
[mbYes, mbNo], 0) of
mrYes: begin
lTempNameOrig := DefaultsDir('')+'orig8.hdr';
SaveAsVOIorNIFTIcore (lTempNameOrig, gMRIcroOverlay[kBGOverlayNum].ScrnBuffer,gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems, 1,gMRIcroOverlay[kBGOverlayNum].NiftiHdr);
CropVOI(Bright95Pct);
end;
end; //case for protecting VOI
end; //case for deleting VOI
ImgForm.CloseVOIClick(nil);
end;
if gMRIcroOverlay[kBGOverlayNum].ImgBufferBPP <> 1 then
Memo1.lines.add('Warning: converted image downsampled to 8-bit precision.');
lTempName8bitMask := DefaultsDir('')+'temp8.hdr';
SaveAsVOIorNIFTIcore (lTempName8bitMask, gMRIcroOverlay[kBGOverlayNum].ScrnBuffer,gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems, 1,gMRIcroOverlay[kBGOverlayNum].NiftiHdr);
lTempName8bitMask := changefileext(lTempName8bitMask,'.hdr'); //SaveAs renames the .hdr to .img
lTempBetName := DefaultsDir('')+'btemp8.hdr';
DoBET(lTempName8bitMask,lTempBetName,SmoothnessEdit.value);
Memo1.lines.add('Shutdown Timestamp: '+DateTimeToStr(Now));
CopyFileEXoverwrite(lTempName8bitMask,lTempBetName); //the old version of BET corrupts some NIfTI information
DeleteHdrImg(lTempName8bitMask);
if lTempNameOrig <> '' then begin
Mask8BitImg(changefileext(lTempNameOrig,'.img'),changefileext(lTempBetName,'.img'));
DeleteHdrImg(lTempNameOrig);
end;
ImgForm.OpenAndDisplayImg(lTempBetName,True);
Memo1.lines.add('Use File/SaveAsNIfTI to save the stripped 8-bit image.');
DeleteHdrImg(lTempBetName);
end;*)
(*procedure TBETForm.GoBtnClick(Sender: TObject);
begin
Memo1.Clear;
Memo1.lines.add('Startup Timestamp: '+DateTimeToStr(Now));
DoBET('C:\txx.hdr','C:\btxx.hdr',SmoothnessEdit.value);
Memo1.lines.add('Shutdown Timestamp: '+DateTimeToStr(Now));
end; *)
initialization
{$I bet.lrs}
end.
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