1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
|
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.
|