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|
unit nifti_hdr;
interface
{$H+}
{$Include isgui.inc}
uses
{$IFNDEF FPC}
DiskSpaceKludge,gziod,
{$ELSE}
gzio2,
{$ENDIF}
{$IFNDEF Unix} Windows, {$ENDIF}
define_types,SysUtils,GraphicsMathLibrary,
{$IFDEF GUI}dialogs;{$ELSE} dialogsx;{$ENDIF}
type
int64_t= int64;
TNIFTIhdr2 = packed record //Next: analyze Format Header structure
HdrSz : longint; //MUST BE 348
Data_Type: array [1..10] of char; //unused
db_name: array [1..18] of char; //unused
extents: longint; //unused
session_error: smallint; //unused `
regular: char; ////unused: in Analyze 7.5 this must be 114
dim_info: byte; //MRI slice order
dim: array[0..7] of int64_t; //Data array dimensions
intent_p1, intent_p2, intent_p3: single;
intent_code: smallint;
datatype: smallint;
bitpix: smallint;
slice_start: smallint;
pixdim: array[0..7]of single;
vox_offset: int64_t;
scl_slope: single;//scaling slope
scl_inter: single;//scaling intercept
slice_end: smallint;
slice_code: byte; //e.g. ascending
xyzt_units: byte; //e.g. mm and sec
cal_max,cal_min: single; //unused
slice_duration: single; //time for one slice
toffset: single; //time axis to shift
glmax, glmin: longint; //UNUSED
descrip: array[1..80] of char;
aux_file: array[1..24] of char;
qform_code, sform_code: smallint;
quatern_b,quatern_c,quatern_d,
qoffset_x,qoffset_y,qoffset_z: double;
srow_x, srow_y,srow_z: array[0..3]of double;
intent_name: array[1..16] of char;
magic: longint;
unused_str: array[1..4] of char;
end; //TNIFTIhdr Header Structure
TNIFTIhdr1 = packed record //Next: analyze Format Header structure
HdrSz : longint; //MUST BE 348
Data_Type: array [1..10] of char; //unused
db_name: array [1..18] of char; //unused
extents: longint; //unused
session_error: smallint; //unused `
regular: char; ////unused: in Analyze 7.5 this must be 114
dim_info: byte; //MRI slice order
dim: array[0..7] of smallint; //Data array dimensions
intent_p1, intent_p2, intent_p3: single;
intent_code: smallint;
datatype: smallint;
bitpix: smallint;
slice_start: smallint;
pixdim: array[0..7]of single;
vox_offset: single;
scl_slope: single;//scaling slope
scl_inter: single;//scaling intercept
slice_end: smallint;
slice_code: byte; //e.g. ascending
xyzt_units: byte; //e.g. mm and sec
cal_max,cal_min: single; //unused
slice_duration: single; //time for one slice
toffset: single; //time axis to shift
glmax, glmin: longint; //UNUSED
descrip: array[1..80] of char;
aux_file: array[1..24] of char;
qform_code, sform_code: smallint;
quatern_b,quatern_c,quatern_d,
qoffset_x,qoffset_y,qoffset_z: single;
srow_x: array[0..3]of single;
srow_y: array[0..3]of single;
srow_z: array[0..3]of single;
intent_name: array[1..16] of char;
magic: longint;
end; //TNIFTIhdr Header Structure
TNIFTIhdr = TNIFTIhdr1; //Next: analyze Format Header structure
TAnalyzeHdrSection = packed record //Next: analyze Format Header structure
Pad: array [1..253] of byte;
originator: array [1..5] of smallint;
end;//TAnalyzeHdrSection Structure
TMRIcroHdr = record //Next: analyze Format Header structure
NIFTIhdr : TNIFTIhdr;
AutoBalMinUnscaled,AutoBalMaxUnscaled
,WindowScaledMin,WindowScaledMax
,GlMinUnscaledS,GlMaxUnscaledS,Zero8Bit,Slope8bit: single; //brightness and contrast
NIfTItransform,DiskDataNativeEndian,UsesCustomPalette,LutFromZero: boolean;
HdrFileName,ImgFileName: string;
NIFTIVersion,LUTindex,ScrnBufferItems,ImgBufferItems,RenderBufferItems,ImgBufferBPP,RenderDim,Index: longint;
ImgBufferUnaligned: Pointer; //raw address of Image Buffer: address may not be aligned
ScrnBuffer,ImgBuffer,RenderBuffer: Bytep;
LUTinvisible: TRGBQuad;//DWord;
LUT: array[0..255] of TRGBQuad;
Mat: TMatrix;
end; //TNIFTIhdr Header Structure
const
//DataTypes
kDT_BINARY =1; // binary (1 bit/voxel)
kDT_UNSIGNED_CHAR =2; // unsigned char (8 bits/voxel)
kDT_SIGNED_SHORT =4; // signed short (16 bits/voxel)
kDT_SIGNED_INT =8; // signed int (32 bits/voxel)
kDT_FLOAT =16; // float (32 bits/voxel)
kDT_COMPLEX =32; // complex (64 bits/voxel)
kDT_DOUBLE =64; // double (64 bits/voxel)
kDT_RGB =128; // RGB triple (24 bits/voxel)
kDT_INT8 =256; // signed char (8 bits)
kDT_UINT16 =512; // unsigned short (16 bits)
kDT_UINT32 =768; // unsigned int (32 bits)
kDT_INT64 =1024; // long long (64 bits)
kDT_UINT64 =1280; // unsigned long long (64 bits)
kDT_FLOAT128 =1536; // long double (128 bits)
kDT_COMPLEX128 =1792; // double pair (128 bits)
kDT_COMPLEX256 =2048; // long double pair (256 bits)
// slice_code values
kNIFTI_SLICE_SEQ_UNKNOWN = 0;
kNIFTI_SLICE_SEQ_INC = 1;
kNIFTI_SLICE_SEQ_DEC = 2;
kNIFTI_SLICE_ALT_INC = 3;
kNIFTI_SLICE_ALT_DEC = 4;
//xyzt_units values: note 3bit space and 3bit time packed into single byte
kNIFTI_UNITS_UNKNOWN = 0;
kNIFTI_UNITS_METER = 1;
kNIFTI_UNITS_MM = 2;
kNIFTI_UNITS_MICRON = 3;
kNIFTI_UNITS_SEC = 8;
kNIFTI_UNITS_MSEC = 16;
kNIFTI_UNITS_USEC = 24;
kNIFTI_UNITS_HZ = 32;
kNIFTI_UNITS_PPM = 40;
//qform_code, sform_code values
kNIFTI_XFORM_UNKNOWN = 0;
kNIFTI_XFORM_SCANNER_ANAT = 1;//Scanner-based anatomical coordinates
kNIFTI_XFORM_ALIGNED_ANAT = 2; //Coordinates aligned to another file e.g. EPI coregistered to T1
kNIFTI_XFORM_TALAIRACH = 3; //Talairach-Tournoux Atlas; (0,0,0)=AC, etc.
kNIFTI_XFORM_MNI_152 = 4; //MNI 152 normalized coordinates
//Magic values
kNIFTI_MAGIC_SEPARATE_HDR = $0031696E;//$6E693100;
kNIFTI_MAGIC_EMBEDDED_HDR = $00312B6E;//$6E2B3100;
kNIFTI2_MAGIC_SEPARATE_HDR = $0032696E;//$6E693100;
kNIFTI2_MAGIC_EMBEDDED_HDR = $00322B6E;//$6E2B3100;
kNIFTI_MAGIC_DCM = $0044434D;
//byte-swapped magic values
kswapNIFTI_MAGIC_SEPARATE_HDR = $6E693100;
kswapNIFTI_MAGIC_EMBEDDED_HDR = $6E2B3100;
kswapNIFTI2_MAGIC_SEPARATE_HDR = $6E693200;
kswapNIFTI2_MAGIC_EMBEDDED_HDR = $6E2B3200;
//Statistics Intention
kNIFTI_INTENT_NONE =0;
kNIFTI_INTENT_CORREL =2;
kNIFTI_INTENT_TTEST =3;
kNIFTI_INTENT_FTEST =4;
kNIFTI_INTENT_ZSCORE =5;
kNIFTI_INTENT_CHISQ =6;
kNIFTI_INTENT_BETA =7;
kNIFTI_INTENT_BINOM =8;
kNIFTI_INTENT_GAMMA =9;
kNIFTI_INTENT_POISSON =10;
kNIFTI_INTENT_NORMAL =11;
kNIFTI_INTENT_FTEST_NONC =12;
kNIFTI_INTENT_CHISQ_NONC =13;
kNIFTI_INTENT_LOGISTIC =14;
kNIFTI_INTENT_LAPLACE =15;
kNIFTI_INTENT_UNIFORM =16;
kNIFTI_INTENT_TTEST_NONC =17;
kNIFTI_INTENT_WEIBULL =18;
kNIFTI_INTENT_CHI =19;
kNIFTI_INTENT_INVGAUSS =20;
kNIFTI_INTENT_EXTVAL =21;
kNIFTI_INTENT_PVAL =22;
NIFTI_INTENT_LOGPVAL =23;
NIFTI_INTENT_LOG10PVAL =24;
kNIFTI_LAST_STATCODE = 24;//kNIFTI_INTENT_PVAL;
kNIFTI_INTENT_ESTIMATE =1001;
kNIFTI_FIRST_NONSTATCODE = kNIFTI_INTENT_ESTIMATE;
kNIFTI_INTENT_LABEL =1002;
kNIFTI_INTENT_NEURONAME =1003;
kNIFTI_INTENT_GENMATRIX =1004;
kNIFTI_INTENT_SYMMATRIX =1005;
kNIFTI_INTENT_DISPVECT =1006;
kNIFTI_INTENT_VECTOR =1007;
kNIFTI_INTENT_POINTSET =1008;
kNIFTI_INTENT_TRIANGLE =1009;
kNIFTI_INTENT_QUATERNION =1010;
function NII1_2_NII2 ( lS: TNIfTIHdr1; var lD: TNIfTIHdr2): boolean;
function IsVOIROIExt (var lFName: string):boolean;
function ComputeImageDataBytes (var lHdr: TMRIcroHdr): longint; //size of image data in bytes
function ComputeImageDataBytes8bpp (var lHdr: TMRIcroHdr): longint; //size of image as 32-bit per voxel data in bytes
function ComputeImageDataBytes32bpp (var lHdr: TMRIcroHdr): longint; //size of image as 32-bit per voxel data in bytes
procedure NIFTIhdr_SwapBytes (var lAHdr: TNIFTIhdr); //Swap Byte order for the Analyze type
procedure NIFTIhdr_ClearHdr (var lHdr: TMRIcroHdr); //set all values of header to something reasonable
function NIFTIhdr_LoadHdr (var lFilename: string; var lHdr: TMRIcroHdr): boolean;
function NIFTIhdr_SaveHdr (var lFilename: string; var lHdr: TMRIcroHdr; lAllowOverwrite: boolean): boolean; overload;
function NIFTIhdr_SaveHdr (var lFilename: string; var lHdr: TNIFTIHdr; lAllowOverwrite,lSPM2: boolean): boolean; overload;
procedure NIFTIhdr_SetIdentityMatrix (var lHdr: TMRIcroHdr); //create neutral rotation matrix
function IsNIfTIHdrExt (var lFName: string):boolean; //1494
function IsNifTiMagic (var lHdr: TNIFTIhdr): boolean;
//procedure NearestOrtho(var lHdr: TMRIcroHdr);
//function nifti_mat44_orthog( lR :TMatrix; lImm,lJmm,lKmm: double): TMatrix;
function CopyNiftiHdr (var lInHdr,lOutHdr: TNIFTIhdr): boolean;
procedure WriteNiftiMatrix (var lHdr: TNIFTIhdr;
m11,m12,m13,m14,
m21,m22,m23,m24,
m31,m32,m33,m34: Single);
procedure nifti_mat44_to_quatern( lR :TMatrix;
var qb, qc, qd,
qx, qy, qz,
dx, dy, dz, qfac : single);
implementation
uses dicomhdr;//2/2208
function CopyNiftiHdr (var lInHdr,lOutHdr: TNIFTIhdr): boolean;
begin
move(lInHdr,lOutHdr,sizeof(TNIFTIhdr));
result := true;
end;
procedure WriteNiftiMatrix (var lHdr: TNIFTIhdr;
m11,m12,m13,m14,
m21,m22,m23,m24,
m31,m32,m33,m34: Single);
begin
with lHdr do begin
srow_x[0] := m11;
srow_x[1] := m12;
srow_x[2] := m13;
srow_x[3] := m14;
srow_y[0] := m21;
srow_y[1] := m22;
srow_y[2] := m23;
srow_y[3] := m24;
srow_z[0] := m31;
srow_z[1] := m32;
srow_z[2] := m33;
srow_z[3] := m34;
end; //with lHdr
end;
function IsNifTi2Magic (var lHdr: TNIFTIhdr): boolean;
begin
if (lHdr.magic =kNIFTI2_MAGIC_SEPARATE_HDR) or (lHdr.Magic = kNIFTI2_MAGIC_EMBEDDED_HDR ) then
result := true
else
result :=false; //analyze
end;
function IsNifTi1Magic (var lHdr: TNIFTIhdr): boolean;
begin
if (lHdr.magic =kNIFTI_MAGIC_SEPARATE_HDR) or (lHdr.Magic = kNIFTI_MAGIC_EMBEDDED_HDR ) then
result := true
else
result :=false; //analyze
end;
function IsNifTiMagic (var lHdr: TNIFTIhdr): boolean;
begin
if (IsNifTi1Magic(lHdr)) or (IsNifTi2Magic(lHdr)) then
result := true
else
result :=false; //analyze
end;
function IsNIfTIHdrExt (var lFName: string):boolean;
var
lExt: string;
begin
lExt := UpCaseExt(lFName);
if (lExt='.NII') or (lExt = '.HDR') or (lExt = '.NII.GZ') or (lExt = '.VOI') then
result := true
else
result := false;
end;
function IsVOIROIExt (var lFName: string):boolean;
var
lExt: string;
begin
lExt := UpCaseExt(lFName);
if (lExt = '.VOI') or (lExt = '.ROI') then
result := true
else
result := false;
end;
function ComputeImageDataBytes32bpp (var lHdr: TMRIcroHdr): integer;
var
lDim, lSzInBits : integer;
begin
result := 0;
with lHdr.NIFTIhdr do begin
if Dim[0] < 1 then begin
ShowMessage('NIFTI format error: datasets must have at least one dimension (dim[0] < 1).');
exit;
end;
lSzInBits := 32; //bits per voxel
for lDim := 1 to 3 {Dim[0]} do
lSzInBits := lSzInBits * Dim[lDim];
end; //with niftihdr
result := (lSzInBits + 7) div 8; //+7 to ensure binary data not clipped
end; //func ComputeImageDataBytes32bpp
function ComputeImageDataBytes8bpp (var lHdr: TMRIcroHdr): integer;
var
lDim, lSzInBits : integer;
begin
result := 0;
with lHdr.NIFTIhdr do begin
if Dim[0] < 1 then begin
ShowMessage('NIFTI format error: datasets must have at least one dimension (dim[0] < 1).');
exit;
end;
lSzInBits := 8; //bits per voxel
for lDim := 1 to 3 {Dim[0]} do
lSzInBits := lSzInBits * Dim[lDim];
end; //with niftihdr
result := (lSzInBits + 7) div 8; //+7 to ensure binary data not clipped
end; //func ComputeImageDataBytes8bpp
function ComputeImageDataBytes (var lHdr: TMRIcroHdr): integer;
var
lDim, lSzInBits : integer;
begin
result := 0;
with lHdr.NIFTIhdr do begin
if Dim[0] < 1 then begin
ShowMessage('NIFTI format error: datasets must have at least one dimension (dim[0] < 1).');
exit;
end;
lSzInBits := bitpix; //bits per voxel
//showmessage(inttostr(Dim[0]));
for lDim := 1 to 3 {Dim[0]} do
lSzInBits := lSzInBits * Dim[lDim];
end; //with niftihdr
result := (lSzInBits + 7) div 8; //+7 to ensure binary data not clipped
end; //func ComputeImageDataBytes
function orthogonalMatrix(var lHdr: TMRIcroHdr): boolean;
var
lM: TMatrix;
lRow,lCol,lN0: integer;
begin
result := false;
lM := Matrix3D (
lHdr.NIFTIhdr.srow_x[0],lHdr.NIFTIhdr.srow_x[1],lHdr.NIFTIhdr.srow_x[2],lHdr.NIFTIhdr.srow_x[3], // 3D "graphics" matrix
lHdr.NIFTIhdr.srow_y[0],lHdr.NIFTIhdr.srow_y[1],lHdr.NIFTIhdr.srow_y[2],lHdr.NIFTIhdr.srow_y[3], // 3D "graphics" matrix
lHdr.NIFTIhdr.srow_z[0],lHdr.NIFTIhdr.srow_z[1],lHdr.NIFTIhdr.srow_z[2],lHdr.NIFTIhdr.srow_z[3], // 3D "graphics" matrix
0,0,0,1);
for lRow := 1 to 3 do begin
lN0 := 0;
for lCol := 1 to 3 do
if lM.matrix[lRow,lCol] = 0 then
inc(lN0);
if lN0 <> 2 then exit; //exactly two values are zero
end;
for lCol := 1 to 3 do begin
lN0 := 0;
for lRow := 1 to 3 do
if lM.matrix[lRow,lCol] = 0 then
inc(lN0);
if lN0 <> 2 then exit; //exactly two values are zero
end;
result := true;
end;
function EmptyRow (lRow: integer; var lM: TMatrix): boolean;
begin
//fx(lM.matrix[lRow,1],lM.matrix[lRow,2],lM.matrix[lRow,3]);
if (abs(lM.matrix[lRow,1]) < 0.00000001) and (abs(lM.matrix[lRow,2]) < 0.00000001) and (abs(lM.matrix[lRow,3]) < 0.00000001) then
result := true
else
result := false;
end;
procedure ReportMatrix (lStr: string;lM:TMatrix);
begin
ShowMessage(lStr+kCR+
RealToStr(lM.matrix[1,1],6)+','+RealToStr(lM.matrix[1,2],6)+','+RealToStr(lM.matrix[1,3],6)+','+RealToStr(lM.matrix[1,4],6)+
kCR+RealToStr(lM.matrix[2,1],6)+','+RealToStr(lM.matrix[2,2],6)+','+RealToStr(lM.matrix[2,3],6)+','+RealToStr(lM.matrix[2,4],6)+
kCR+RealToStr(lM.matrix[3,1],6)+','+RealToStr(lM.matrix[3,2],6)+','+RealToStr(lM.matrix[3,3],6)+','+RealToStr(lM.matrix[3,4],6)+
kCR+RealToStr(lM.matrix[4,1],6)+','+RealToStr(lM.matrix[4,2],6)+','+RealToStr(lM.matrix[4,3],6)+','+RealToStr(lM.matrix[4,4],6));
end;
function EmptyMatrix(var lHdr: TMRIcroHdr): boolean;
var
lM: TMatrix;
lRow,lCol: integer;
begin
result := false;
lM := Matrix3D (
lHdr.NIFTIhdr.srow_x[0],lHdr.NIFTIhdr.srow_x[1],lHdr.NIFTIhdr.srow_x[2],lHdr.NIFTIhdr.srow_x[3], // 3D "graphics" matrix
lHdr.NIFTIhdr.srow_y[0],lHdr.NIFTIhdr.srow_y[1],lHdr.NIFTIhdr.srow_y[2],lHdr.NIFTIhdr.srow_y[3], // 3D "graphics" matrix
lHdr.NIFTIhdr.srow_z[0],lHdr.NIFTIhdr.srow_z[1],lHdr.NIFTIhdr.srow_z[2],lHdr.NIFTIhdr.srow_z[3], // 3D "graphics" matrix
0,0,0,1);
if EmptyRow(1,lM) or EmptyRow(2,lM) or EmptyRow(3,lM) then begin
ReportMatrix('Matrix appears bogus',lm);
end else begin
for lRow := 1 to 3 do begin {3/2008}
for lCol := 1 to 4 do begin
if (lRow = lCol) then begin
if lM.matrix[lRow,lCol] <> 1 then
exit;
end else begin
if lM.matrix[lRow,lCol] <> 0 then
exit;
end// unity matrix does not count - mriconvert creates bogus [1 0 0 0; 0 1 0 0; 0 0 1 0; 0 0 0 0]
end; //each col
end;//each row
end;//not bogus
result := true;
end;
procedure FromMatrix (M: TMatrix; var m11,m12,m13, m21,m22,m23,
m31,m32,m33: DOUBLE) ;
BEGIN
m11 := M.Matrix[1,1];
m12 := M.Matrix[1,2];
m13 := M.Matrix[1,3];
m21 := M.Matrix[2,1];
m22 := M.Matrix[2,2];
m23 := M.Matrix[2,3];
m31 := M.Matrix[3,1];
m32 := M.Matrix[3,2];
m33 := M.Matrix[3,3];
END {FromMatrix3D};
function nifti_mat33_determ( R: TMatrix ):double;
begin
result := r.matrix[1,1]*r.matrix[2,2]*r.matrix[3,3]
-r.matrix[1,1]*r.matrix[3,2]*r.matrix[2,3]
-r.matrix[2,1]*r.matrix[1,2]*r.matrix[3,3]
+r.matrix[2,1]*r.matrix[3,2]*r.matrix[1,3]
+r.matrix[3,1]*r.matrix[1,2]*r.matrix[2,3]
-r.matrix[3,1]*r.matrix[2,2]*r.matrix[1,3] ;
end;
procedure FixCrapMat(var lMat: TMatrix);
var
lVec000,lVec100,lVec010,lVec001: TVector;
begin
lVec000 := Vector3D (0, 0, 0);
lVec100 := Vector3D (1, 0, 0);
lVec010 := Vector3D (0, 1, 0);
lVec001 := Vector3D (0, 0, 1);
lVec000 := Transform (lVec000, lMat);
lVec100 := Transform (lVec100, lMat);
lVec010 := Transform (lVec010, lMat);
lVec001 := Transform (lVec001, lMat);
if SameVec(lVec000,lVec100) or
SameVec(lVec000,lVec010) or
SameVec(lVec000,lVec001) then begin
lMat := eye3D;
ShowMessage('Warning: the transformation matrix is corrupt [some dimensions have zero size]');
end;
end;
function nifti_mat33_rownorm( A: TMatrix ): single; //* max row norm of 3x3 matrix */
var
r1,r2,r3: single ;
begin
r1 := abs(A.matrix[1,1])+abs(A.matrix[1,2])+abs(A.matrix[1,3]) ;
r2 := abs(A.matrix[2,1])+abs(A.matrix[2,2])+abs(A.matrix[2,3]) ;
r3 := abs(A.matrix[3,1])+abs(A.matrix[3,2])+abs(A.matrix[3,3]) ;
if( r1 < r2 ) then r1 := r2 ;
if( r1 < r3 ) then r1 := r3 ;
result := r1 ;
end;
function nifti_mat33_colnorm( A: TMatrix ): single; //* max column norm of 3x3 matrix */
var
r1,r2,r3: single ;
begin
r1 := abs(A.matrix[1,1])+abs(A.matrix[2,1])+abs(A.matrix[3,1]) ;
r2 := abs(A.matrix[1,2])+abs(A.matrix[2,2])+abs(A.matrix[3,2]) ;
r3 := abs(A.matrix[1,3])+abs(A.matrix[2,3])+abs(A.matrix[3,3]) ;
if( r1 < r2 ) then r1 := r2 ;
if( r1 < r3 ) then r1 := r3 ;
result := r1 ;
end;
function nifti_mat33_inverse( R: TMatrix ): TMatrix; //* inverse of 3x3 matrix */
var
r11,r12,r13,r21,r22,r23,r31,r32,r33 , deti: double ;
Q: TMatrix ;
begin
FromMatrix(R,r11,r12,r13,r21,r22,r23,r31,r32,r33);
deti := r11*r22*r33-r11*r32*r23-r21*r12*r33
+r21*r32*r13+r31*r12*r23-r31*r22*r13 ;
if( deti <> 0.0 ) then deti := 1.0 / deti ;
Q.matrix[1,1] := deti*( r22*r33-r32*r23) ;
Q.matrix[1,2] := deti*(-r12*r33+r32*r13) ;
Q.matrix[1,3] := deti*( r12*r23-r22*r13) ;
Q.matrix[2,1] := deti*(-r21*r33+r31*r23) ;
Q.matrix[2,2] := deti*( r11*r33-r31*r13) ;
Q.matrix[2,3] := deti*(-r11*r23+r21*r13) ;
Q.matrix[3,1] := deti*( r21*r32-r31*r22) ;
Q.matrix[3,2] := deti*(-r11*r32+r31*r12) ;
Q.matrix[3,3] := deti*( r11*r22-r21*r12) ;
result := Q;
end;
function nifti_mat33_polar( A: TMatrix ): TMatrix;
var
k:integer;
X , Y , Z: TMatrix ;
dif,alp,bet,gam,gmi : single;
begin
dif := 1;
k := 0;
X := A ;
// force matrix to be nonsingular
//reportmatrix('x',X);
gam := nifti_mat33_determ(X) ;
while( gam = 0.0 )do begin //perturb matrix
gam := 0.00001 * ( 0.001 + nifti_mat33_rownorm(X) ) ;
X.matrix[1,1] := X.matrix[1,1]+gam ;
X.matrix[2,2] := X.matrix[2,2]+gam ;
X.matrix[3,3] := X.matrix[3,3] +gam ;
gam := nifti_mat33_determ(X) ;
end;
while true do begin
Y := nifti_mat33_inverse(X) ;
if( dif > 0.3 )then begin // far from convergence
alp := sqrt( nifti_mat33_rownorm(X) * nifti_mat33_colnorm(X) ) ;
bet := sqrt( nifti_mat33_rownorm(Y) * nifti_mat33_colnorm(Y) ) ;
gam := sqrt( bet / alp ) ;
gmi := 1.0 / gam ;
end else begin
gam := 1.0;
gmi := 1.0 ; //close to convergence
end;
Z.matrix[1,1] := 0.5 * ( gam*X.matrix[1,1] + gmi*Y.matrix[1,1] ) ;
Z.matrix[1,2] := 0.5 * ( gam*X.matrix[1,2] + gmi*Y.matrix[2,1] ) ;
Z.matrix[1,3] := 0.5 * ( gam*X.matrix[1,3] + gmi*Y.matrix[3,1] ) ;
Z.matrix[2,1] := 0.5 * ( gam*X.matrix[2,1] + gmi*Y.matrix[1,2] ) ;
Z.matrix[2,2] := 0.5 * ( gam*X.matrix[2,2] + gmi*Y.matrix[2,2] ) ;
Z.matrix[2,3] := 0.5 * ( gam*X.matrix[2,3] + gmi*Y.matrix[3,2] ) ;
Z.matrix[3,1] := 0.5 * ( gam*X.matrix[3,1] + gmi*Y.matrix[1,3] ) ;
Z.matrix[3,2] := 0.5 * ( gam*X.matrix[3,2] + gmi*Y.matrix[2,3] ) ;
Z.matrix[3,3] := 0.5 * ( gam*X.matrix[3,3] + gmi*Y.matrix[3,3] ) ;
dif := abs(Z.matrix[1,1]-X.matrix[1,1])+abs(Z.matrix[1,2]-X.matrix[1,2])
+abs(Z.matrix[1,3]-X.matrix[1,3])+abs(Z.matrix[2,1]-X.matrix[2,1])
+abs(Z.matrix[2,2]-X.matrix[2,2])+abs(Z.matrix[2,3]-X.matrix[2,3])
+abs(Z.matrix[3,1]-X.matrix[3,1])+abs(Z.matrix[3,2]-X.matrix[3,2])
+abs(Z.matrix[3,3]-X.matrix[3,3]) ;
k := k+1 ;
if( k > 100) or (dif < 3.e-6 ) then begin
result := Z;
break ; //convergence or exhaustion
end;
X := Z ;
end;
result := Z ;
end;
procedure nifti_mat44_to_quatern( lR :TMatrix;
var qb, qc, qd,
qx, qy, qz,
dx, dy, dz, qfac : single);
var
r11,r12,r13 , r21,r22,r23 , r31,r32,r33, xd,yd,zd , a,b,c,d : double;
P,Q: TMatrix; //3x3
begin
(* offset outputs are read write out of input matrix *)
qx := lR.matrix[1,4];
qy := lR.matrix[2,4];
qz := lR.matrix[3,4];
(* load 3x3 matrix into local variables *)
FromMatrix(lR,r11,r12,r13,r21,r22,r23,r31,r32,r33);
(* compute lengths of each column; these determine grid spacings *)
xd := sqrt( r11*r11 + r21*r21 + r31*r31 ) ;
yd := sqrt( r12*r12 + r22*r22 + r32*r32 ) ;
zd := sqrt( r13*r13 + r23*r23 + r33*r33 ) ;
(* if a column length is zero, patch the trouble *)
if( xd = 0.0 )then begin r11 := 1.0 ; r21 := 0; r31 := 0.0 ; xd := 1.0 ; end;
if( yd = 0.0 )then begin r22 := 1.0 ; r12 := 0; r32 := 0.0 ; yd := 1.0 ; end;
if( zd = 0.0 )then begin r33 := 1.0 ; r13 := 0; r23 := 0.0 ; zd := 1.0 ; end;
(* assign the output lengths *)
dx := xd;
dy := yd;
dz := zd;
(* normalize the columns *)
r11 := r11/xd ; r21 := r21/xd ; r31 := r31/xd ;
r12 := r12/yd ; r22 := r22/yd ; r32 := r32/yd ;
r13 := r13/zd ; r23 := r23/zd ; r33 := r33/zd ;
(* At this point, the matrix has normal columns, but we have to allow
for the fact that the hideous user may not have given us a matrix
with orthogonal columns.
So, now find the orthogonal matrix closest to the current matrix.
One reason for using the polar decomposition to get this
orthogonal matrix, rather than just directly orthogonalizing
the columns, is so that inputting the inverse matrix to R
will result in the inverse orthogonal matrix at this point.
If we just orthogonalized the columns, this wouldn't necessarily hold. *)
Q := Matrix2D (r11,r12,r13, // 2D "graphics" matrix
r21,r22,r23,
r31,r32,r33);
P := nifti_mat33_polar(Q) ; (* P is orthog matrix closest to Q *)
FromMatrix(P,r11,r12,r13,r21,r22,r23,r31,r32,r33);
//ReportMatrix('xxx',Q);
//ReportMatrix('svd',P);
(* [ r11 r12 r13 ] *)
(* at this point, the matrix [ r21 r22 r23 ] is orthogonal *)
(* [ r31 r32 r33 ] *)
(* compute the determinant to determine if it is proper *)
zd := r11*r22*r33-r11*r32*r23-r21*r12*r33
+r21*r32*r13+r31*r12*r23-r31*r22*r13 ; (* should be -1 or 1 *)
if( zd > 0 )then begin (* proper *)
qfac := 1.0 ;
end else begin (* improper ==> flip 3rd column *)
qfac := -1.0 ;
r13 := -r13 ; r23 := -r23 ; r33 := -r33 ;
end;
(* now, compute quaternion parameters *)
a := r11 + r22 + r33 + 1.0;
if( a > 0.5 ) then begin (* simplest case *)
a := 0.5 * sqrt(a) ;
b := 0.25 * (r32-r23) / a ;
c := 0.25 * (r13-r31) / a ;
d := 0.25 * (r21-r12) / a ;
end else begin (* trickier case *)
xd := 1.0 + r11 - (r22+r33) ; (* 4*b*b *)
yd := 1.0 + r22 - (r11+r33) ; (* 4*c*c *)
zd := 1.0 + r33 - (r11+r22) ; (* 4*d*d *)
if( xd > 1.0 ) then begin
b := 0.5 * sqrt(xd) ;
c := 0.25* (r12+r21) / b ;
d := 0.25* (r13+r31) / b ;
a := 0.25* (r32-r23) / b ;
end else if( yd > 1.0 ) then begin
c := 0.5 * sqrt(yd) ;
b := 0.25* (r12+r21) / c ;
d := 0.25* (r23+r32) / c ;
a := 0.25* (r13-r31) / c ;
end else begin
d := 0.5 * sqrt(zd) ;
b := 0.25* (r13+r31) / d ;
c := 0.25* (r23+r32) / d ;
a := 0.25* (r21-r12) / d ;
end;
if( a < 0.0 )then begin b:=-b ; c:=-c ; d:=-d; {a:=-a; this is not used} end;
end;
qb := b ;
qc := c ;
qd := d ;
//fx(qb,qc,qd);
end;
procedure nifti_quatern_to_mat44( var lR :TMatrix;
var qb, qc, qd,
qx, qy, qz,
dx, dy, dz, qfac : single);
var
a,b,c,d,xd,yd,zd: double;
begin
//a := qb;
b := qb;
c := qc;
d := qd;
//* last row is always [ 0 0 0 1 ] */
lR.matrix[4,1] := 0;
lR.matrix[4,2] := 0;
lR.matrix[4,3] := 0;
lR.matrix[4,4] := 1;
//* compute a parameter from b,c,d */
a := 1.0 - (b*b + c*c + d*d) ;
if( a < 1.e-7 ) then begin//* special case */
a := 1.0 / sqrt(b*b+c*c+d*d) ;
b := b*a ; c := c*a ; d := d*a ;//* normalize (b,c,d) vector */
a := 0.0 ;//* a = 0 ==> 180 degree rotation */
end else begin
a := sqrt(a) ; //* angle = 2*arccos(a) */
end;
//* load rotation matrix, including scaling factors for voxel sizes */
if dx > 0 then
xd := dx
else
xd := 1;
if dy > 0 then
yd := dy
else
yd := 1;
if dz > 0 then
zd := dz
else
zd := 1;
if( qfac < 0.0 ) then zd := -zd ;//* left handedness? */
lR.matrix[1,1]:= (a*a+b*b-c*c-d*d) * xd ;
lR.matrix[1,2]:= 2.0 * (b*c-a*d ) * yd ;
lR.matrix[1,3]:= 2.0 * (b*d+a*c ) * zd ;
lR.matrix[2,1]:= 2.0 * (b*c+a*d ) * xd ;
lR.matrix[2,2]:= (a*a+c*c-b*b-d*d) * yd ;
lR.matrix[2,3]:= 2.0 * (c*d-a*b ) * zd ;
lR.matrix[3,1]:= 2.0 * (b*d-a*c ) * xd ;
lR.matrix[3,2]:= 2.0 * (c*d+a*b ) * yd ;
lR.matrix[3,3]:= (a*a+d*d-c*c-b*b) * zd ;
//* load offsets */
lR.matrix[1,4]:= qx ;
lR.matrix[2,4]:= qy ;
lR.matrix[3,4]:= qz ;
end;
function TryQuat2Matrix( var lHdr: TNIfTIHdr ): boolean;
var lR :TMatrix;
begin
result := false;
if (lHdr.qform_code <= kNIFTI_XFORM_UNKNOWN) or (lHdr.qform_code > kNIFTI_XFORM_MNI_152) then
exit;
result := true;
nifti_quatern_to_mat44(lR,lHdr.quatern_b,lHdr.quatern_c,lHdr.quatern_d,
lHdr.qoffset_x,lHdr.qoffset_y,lHdr.qoffset_z,
lHdr.pixdim[1],lHdr.pixdim[2],lHdr.pixdim[3],
lHdr.pixdim[0]);
lHdr.srow_x[0] := lR.matrix[1,1];
lHdr.srow_x[1] := lR.matrix[1,2];
lHdr.srow_x[2] := lR.matrix[1,3];
lHdr.srow_x[3] := lR.matrix[1,4];
lHdr.srow_y[0] := lR.matrix[2,1];
lHdr.srow_y[1] := lR.matrix[2,2];
lHdr.srow_y[2] := lR.matrix[2,3];
lHdr.srow_y[3] := lR.matrix[2,4];
lHdr.srow_z[0] := lR.matrix[3,1];
lHdr.srow_z[1] := lR.matrix[3,2];
lHdr.srow_z[2] := lR.matrix[3,3];
lHdr.srow_z[3] := lR.matrix[3,4];
lHdr.sform_code := 1;
end;
{procedure ReportMatrix (lM:TMatrix);
var lStr: string;
begin
lStr := ( RealToStr(lM.matrix[1,1],6)+','+RealToStr(lM.matrix[1,2],6)+','+RealToStr(lM.matrix[1,3],6)+','+RealToStr(lM.matrix[1,4],6))
+kCR+( RealToStr(lM.matrix[2,1],6)+','+RealToStr(lM.matrix[2,2],6)+','+RealToStr(lM.matrix[2,3],6)+','+RealToStr(lM.matrix[2,4],6))
+kCR+( RealToStr(lM.matrix[3,1],6)+','+RealToStr(lM.matrix[3,2],6)+','+RealToStr(lM.matrix[3,3],6)+','+RealToStr(lM.matrix[3,4],6))
+kCR+( RealToStr(lM.matrix[4,1],6)+','+RealToStr(lM.matrix[4,2],6)+','+RealToStr(lM.matrix[4,3],6)+','+RealToStr(lM.matrix[4,4],6));
showmessage(lStr);
end; }
function FixDataType (var lHdr: TMRIcroHdr {; lCompress: boolean}): boolean;
//correct mistakes of datatype and bitpix - especially for software which only sets one
label
191;
var
ldatatypebpp,lbitpix: integer;
begin
result := true;
lbitpix := lHdr.NIFTIhdr.bitpix;
case lHdr.NIFTIhdr.datatype of
kDT_BINARY : ldatatypebpp := 1;
kDT_UNSIGNED_CHAR : ldatatypebpp := 8; // unsigned char (8 bits/voxel)
kDT_SIGNED_SHORT : ldatatypebpp := 8; // signed short (16 bits/voxel)
kDT_SIGNED_INT : ldatatypebpp := 32; // signed int (32 bits/voxel)
kDT_FLOAT : ldatatypebpp := 32; // float (32 bits/voxel)
kDT_COMPLEX : ldatatypebpp := 64; // complex (64 bits/voxel)
kDT_DOUBLE : ldatatypebpp := 64; // double (64 bits/voxel)
kDT_RGB : ldatatypebpp := 24; // RGB triple (24 bits/voxel)
kDT_INT8 : ldatatypebpp := 8; // signed char (8 bits)
kDT_UINT16 : ldatatypebpp := 16; // unsigned short (16 bits)
kDT_UINT32 : ldatatypebpp := 32; // unsigned int (32 bits)
kDT_INT64 : ldatatypebpp := 64; // long long (64 bits)
kDT_UINT64 : ldatatypebpp := 64; // unsigned long long (64 bits)
kDT_FLOAT128 : ldatatypebpp := 128; // long double (128 bits)
kDT_COMPLEX128 : ldatatypebpp := 128; // double pair (128 bits)
kDT_COMPLEX256 : ldatatypebpp := 256; // long double pair (256 bits)
else
ldatatypebpp := 0;
end;
if (ldatatypebpp = lHdr.NIFTIhdr.bitpix) and (ldatatypebpp <> 0) then
exit;
if (lbitpix = 0) and (ldatatypebpp <> 0) then begin
//use bitpix from datatype...
lHdr.NIFTIhdr.bitpix := ldatatypebpp;
exit;
end;
if (lbitpix <> 0) and (ldatatypebpp = 0) then begin
//assume bitpix is correct....
//note that several datatypes correspond to each bitpix, so assume most popular...
case lbitpix of
1: lHdr.NIFTIhdr.datatype := kDT_BINARY;
8: lHdr.NIFTIhdr.datatype := kDT_UNSIGNED_CHAR;
16: lHdr.NIFTIhdr.datatype := kDT_SIGNED_SHORT;
24: lHdr.NIFTIhdr.datatype := kDT_RGB;
32: lHdr.NIFTIhdr.datatype := kDT_FLOAT;
64: lHdr.NIFTIhdr.datatype := kDT_DOUBLE;
else goto 191; //impossible bitpix
end;
exit;
end;
191:
//Both bitpix and datatype are wrong... assume most popular format
lHdr.NIFTIhdr.bitpix := 16;
lHdr.NIFTIhdr.datatype := kDT_SIGNED_SHORT;
//fx(lHdr.NIFTIhdr.bitpix, lHdr.NIFTIhdr.datatype);
end;
function NII1_2_NII2 ( lS: TNIfTIHdr1; var lD: TNIfTIHdr2): boolean;
var i: integer;
begin
with lD do begin
HdrSz := sizeof(TNIfTIHdr2);//B.HdrSz;
for i := 1 to 10 do
Data_Type[i]:= lS.Data_Type[i]; //unused
for i := 1 to 18 do
db_name[i]:= lS.db_name[i]; //unused
extents:= lS.extents;
session_error:= lS.session_error;
regular:= lS.regular; ////unused: in Analyze 7.5 this must be 114
dim_info:= lS.dim_info; //MRI slice order
for i := 0 to 7 do
dim[i]:= lS.dim[i];
intent_p1:= lS.intent_p1;
intent_p2:= lS.intent_p2;
intent_p3:= lS.intent_p3;
intent_code:= lS.intent_code;
datatype:= lS.datatype;
bitpix:= lS.bitpix;
slice_start:= lS.slice_start;
for i := 0 to 7 do
pixdim[i] := lS.pixdim[i];
vox_offset:= round(lS.vox_offset);
scl_slope:= lS.scl_slope;
scl_inter:= lS.scl_inter;
slice_end:= lS.slice_end;
slice_code:= lS.slice_code;
xyzt_units:= lS.xyzt_units;
cal_max:=lS.cal_max;
cal_min:=lS.cal_min;
slice_duration:=lS.slice_duration;
toffset:=lS.toffset;
glmax:=lS.glmax;
glmin:=lS.glmin;
for i := 1 to 80 do
descrip[i]:= lS.descrip[i];
for i := 1 to 24 do
aux_file[i]:= lS.aux_file[i];
qform_code:=lS.qform_code;
sform_code:=lS.sform_code;
quatern_b:=lS.quatern_b;
quatern_c:=lS.quatern_c;
quatern_d:=lS.quatern_d;
qoffset_x:=lS.qoffset_x;
qoffset_y:=lS.qoffset_y;
qoffset_z:=lS.qoffset_z;
for i := 0 to 3 do begin
srow_x[i]:= lS.srow_x[i];
srow_y[i]:= lS.srow_y[i];
srow_z[i]:= lS.srow_z[i];
end;
for i := 1 to 16 do
intent_name[i]:=lS.intent_name[i];
magic:=lS.magic;
result := true;
//unused_str:='NA ';
end; //with A
end;
function NII2_2_NII1 ( lS: TNIfTIHdr2; var lD: TNIfTIHdr1): boolean;
var i: integer;
begin
result := true;
with lD do begin
HdrSz := 348;//B.HdrSz;
for i := 1 to 10 do
Data_Type[i]:= lS.Data_Type[i]; //unused
for i := 1 to 18 do
db_name[i]:= lS.db_name[i]; //unused
extents:= lS.extents;
session_error:= lS.session_error;
regular:= lS.regular; ////unused: in Analyze 7.5 this must be 114
dim_info:= lS.dim_info; //MRI slice order
for i := 0 to 7 do begin
if lS.dim[i] > 32767 then begin
Showmessage('Error, NIfTI2 format image dimensions too large to be stored as a NIfTI1 image.');
result := false;
end;
dim[i]:= lS.dim[i];
end;
intent_p1:= lS.intent_p1;
intent_p2:= lS.intent_p2;
intent_p3:= lS.intent_p3;
intent_code:= lS.intent_code;
datatype:= lS.datatype;
bitpix:= lS.bitpix;
slice_start:= lS.slice_start;
for i := 0 to 7 do
pixdim[i] := lS.pixdim[i];
vox_offset:= lS.vox_offset;
scl_slope:= lS.scl_slope;
scl_inter:= lS.scl_inter;
slice_end:= lS.slice_end;
slice_code:= lS.slice_code;
xyzt_units:= lS.xyzt_units;
cal_max:=lS.cal_max;
cal_min:=lS.cal_min;
slice_duration:=lS.slice_duration;
toffset:=lS.toffset;
glmax:=lS.glmax;
glmin:=lS.glmin;
for i := 1 to 80 do
descrip[i]:= lS.descrip[i];
for i := 1 to 24 do
aux_file[i]:= lS.aux_file[i];
qform_code:=lS.qform_code;
sform_code:=lS.sform_code;
quatern_b:=lS.quatern_b;
quatern_c:=lS.quatern_c;
quatern_d:=lS.quatern_d;
qoffset_x:=lS.qoffset_x;
qoffset_y:=lS.qoffset_y;
qoffset_z:=lS.qoffset_z;
for i := 0 to 3 do begin
srow_x[i]:= lS.srow_x[i];
srow_y[i]:= lS.srow_y[i];
srow_z[i]:= lS.srow_z[i];
end;
for i := 1 to 16 do
intent_name[i]:=lS.intent_name[i];
magic:=lS.magic;
//unused_str:='NA ';
end; //with A
end;
function NIFTIhdr_LoadHdr (var lFilename: string; var lHdr: TMRIcroHdr): boolean;
var
lHdrFile: file;
lOri: array [1..3] of single;
lBuff: Bytep;
lAHdr: TAnalyzeHdrSection;
lHdr2: TNIfTIHdr2;
lCompress: boolean;
lReportedSz, lSwappedReportedSz,lHdrSz2,lHdrSz1,lFileSz: Longint;
lExt: string; //1494
begin
Result := false; //assume error
if lFilename = '' then exit;
lExt := UpCaseExt(lFilename);
if lExt = '.IMG' then
lFilename := changeFileExt(lFilename,'.hdr');
if (lExt = '.NII.GZ') or (lExt = '.VOI') then
lCompress := true
else
lCompress := false;
lHdrSz1 := sizeof(TniftiHdr1);
lHdrSz2 := sizeof(TniftiHdr2);
lFileSz := FSize (lFilename);
if lFileSz = 0 then begin
ShowMessage('Unable to find NIFTI header named '+lFilename);
exit;
end;
if (lFileSz < lHdrSz1) and (not lCompress) then begin
ShowMessage('Error in reading NIFTI header: NIfTI headers need to be at least '+inttostr(lHdrSz1)+ ' bytes: '+lFilename);
exit;
end;
FileMode := 0; { Set file access to read only }
if lCompress then begin//1388
lBuff := @lHdr;
UnGZip(lFileName,lBuff,0,lHdrSz1); //1388
end else begin //if gzip
{$I-}
AssignFile(lHdrFile, lFileName);
FileMode := 0; { Set file access to read only }
Reset(lHdrFile, 1);
{$I+}
if ioresult <> 0 then begin
ShowMessage('Error in reading NIFTI header.'+inttostr(IOResult));
FileMode := 2;
exit;
end;
BlockRead(lHdrFile, lHdr, lHdrSz1);
CloseFile(lHdrFile);
end;
FileMode := 2;
if (IOResult <> 0) then exit;
lReportedSz := lHdr.niftiHdr.HdrSz;
lSwappedReportedSz := lReportedSz;
swap4(lSwappedReportedSz);
lHdr.NIFTIVersion := 1;
if lReportedSz = lHdrSz1 then begin
lHdr.DiskDataNativeEndian := true;
end else if lSwappedReportedSz = lHdrSz1 then begin
lHdr.DiskDataNativeEndian := false;
NIFTIhdr_SwapBytes (lHdr.niftiHdr);
end else if (lSwappedReportedSz = lHdrSz2) or (lReportedSz = lHdrSz2) then begin
//reload header...nifti version 2
FileMode := 0; { Set file access to read only }
if lCompress then begin//1388
lBuff := @lHdr2;
UnGZip(lFileName,lBuff,0,lHdrSz2); //1388
end else begin //if gzip
{$I-}
AssignFile(lHdrFile, lFileName);
FileMode := 0; { Set file access to read only }
Reset(lHdrFile, 1);
{$I+}
if ioresult <> 0 then begin
ShowMessage('Error in reading NIFTI header.'+inttostr(IOResult));
FileMode := 2;
exit;
end;
BlockRead(lHdrFile, lHdr2, lHdrSz2);
CloseFile(lHdrFile);
end;
FileMode := 2;
lHdr.NIFTIVersion := 2;
if not NII2_2_NII1(lHdr2,lHdr.NiftiHdr) then begin
ShowMessage('Warning: compatibility with this version of NIfTI has not been tested.');
end;
end else begin
result := NIFTIhdr_LoadDCM (lFilename,lHdr); //2/2008
if not result then
ShowMessage('Warning: the header file is not in NIfTi format [the first 4 bytes do not have the value 348]. Assuming big-endian data.');
exit;
end;
if (lHdr.NIFTIhdr.dim[0] > 7) or (lHdr.NIFTIhdr.dim[0] < 1) then begin //only 1..7 dims, so this
ShowMessage('Illegal NIfTI Format Header: this header does not specify 1..7 dimensions.');
exit;
end;
FixDataType(lHdr);
result := true;
//tx('nHdr',lHdr.NIFTIhdr.srow_x[3]);
lHdr.HdrFileName:= lFilename;
if ((lHdr.niftiHdr.magic = kNIFTI_MAGIC_EMBEDDED_HDR) and (lFileSz > lHdrSz1)) or ((lHdr.niftiHdr.magic = kNIFTI2_MAGIC_EMBEDDED_HDR) and (lFileSz > lHdrSz2)) or (lExt = '.NII.GZ') or (lExt = '.VOI') or (lExt = '.NII'){1494} then
lHdr.ImgFileName:= lFilename
else
lHdr.ImgFileName:= changefileext(lFilename,'.img');
if IsNifTiMagic(lHdr.niftiHdr) then begin //must match MAGMA in nifti_img
lOri[1] := (lHdr.NIFTIhdr.dim[1]+1) div 2;
lOri[2] := (lHdr.NIFTIhdr.dim[2]+1) div 2;
lOri[3] := (lHdr.NIFTIhdr.dim[3]+1) div 2;
//TryQuat2Matrix(lHdr.NiftiHdr);
if (lHdr.NIFTIhdr.sform_code <= kNIFTI_XFORM_UNKNOWN) or (lHdr.NIFTIhdr.sform_code > kNIFTI_XFORM_MNI_152) then
TryQuat2Matrix(lHdr.NiftiHdr);
if emptymatrix(lHdr) then begin
(*if HasQuat(lHdr.NiftiHdr) then
//HasQuat will specify
else*) begin
lHdr.NIFTIhdr.srow_x[0] := lHdr.NIFTIhdr.pixdim[1];
lHdr.NIFTIhdr.srow_x[1] := 0;
lHdr.NIFTIhdr.srow_x[2] := 0;
lHdr.NIFTIhdr.srow_y[0] := 0;
lHdr.NIFTIhdr.srow_y[1] := lHdr.NIFTIhdr.pixdim[2];
lHdr.NIFTIhdr.srow_y[2] := 0;
lHdr.NIFTIhdr.srow_z[0] := 0;
lHdr.NIFTIhdr.srow_z[1] := 0;
lHdr.NIFTIhdr.srow_z[2] := lHdr.NIFTIhdr.pixdim[3];
lHdr.NIFTIhdr.srow_x[3] := -round(lHdr.NIFTIhdr.dim[1]*lHdr.NIFTIhdr.pixdim[1]*0.5);
lHdr.NIFTIhdr.srow_y[3] := -round(lHdr.NIFTIhdr.dim[2]*lHdr.NIFTIhdr.pixdim[2]*0.5);
lHdr.NIFTIhdr.srow_z[3] := -round(lHdr.NIFTIhdr.dim[3]*lHdr.NIFTIhdr.pixdim[3]*0.5);
lHdr.NIFTIhdr.sform_code := 1;
end;
end;
if (lHdr.NIFTIhdr.srow_x[0] > 0) and (lHdr.NIFTIhdr.srow_y[1] > 0) and (lHdr.NIFTIhdr.srow_z[2] > 0) and
(lHdr.NIFTIhdr.srow_x[3] > 0) and (lHdr.NIFTIhdr.srow_y[3] > 0) and (lHdr.NIFTIhdr.srow_z[3] > 0) then begin
lHdr.NIFTIhdr.srow_x[3] := -lHdr.NIFTIhdr.srow_x[3];
lHdr.NIFTIhdr.srow_y[3] := -lHdr.NIFTIhdr.srow_y[3];
lHdr.NIFTIhdr.srow_z[3] := -lHdr.NIFTIhdr.srow_z[3];
lHdr.NIFTIhdr.sform_code := 1;
end; //added 4Mar2006 -> corrects for improperly signed offset values...
lHdr.NIfTItransform := true;//NIfTI 12/2010
end else begin //not NIFT: Analyze
lHdr.NIfTItransform := false;//Analyze
if not lHdr.DiskDataNativeEndian then begin
NIFTIhdr_SwapBytes (lHdr.niftiHdr);
move(lHdr.niftiHdr,lAHdr,sizeof(lAHdr));
NIFTIhdr_SwapBytes (lHdr.niftiHdr);
lAHdr.Originator[1] := swap(lAHdr.Originator[1]);
lAHdr.Originator[2] := swap(lAHdr.Originator[2]);
lAHdr.Originator[3] := swap(lAHdr.Originator[3]);
end else
move(lHdr.niftiHdr,lAHdr,sizeof(lAHdr));
lOri[1] :=lAHdr.Originator[1];
lOri[2] := lAHdr.Originator[2];
lOri[3] := lAHdr.Originator[3];
if (lOri[1]=76) and (lOri[2]=116) and (lOri[3]=64)
and (lHdr.NIFTIhdr.dim[1]=151) and (lHdr.NIFTIhdr.dim[2]=188) and (lHdr.NIFTIhdr.dim[3]=154) then begin
lOri[2] := 111;
lOri[3] := 68;
end; //2/2008 Juelich fudge factor
if ((lOri[1]<1) or (lOri[1]> lHdr.NIFTIhdr.dim[1])) and
((lOri[2]<1) or (lOri[2]> lHdr.NIFTIhdr.dim[2])) and
((lOri[3]<1) or (lOri[3]> lHdr.NIFTIhdr.dim[3])) then begin
lOri[1] := (lHdr.NIFTIhdr.dim[1]+1) / 2; //May07 use / not div
lOri[2] := (lHdr.NIFTIhdr.dim[2]+1) / 2; //May07 use / not div
lOri[3] := (lHdr.NIFTIhdr.dim[3]+1) / 2; //May07 use / not div : if 20 slices, then origin is between 10 and 11
end;
//showmessage(inttostr(sizeof(lAHdr))+' '+realtostr(lHdr.Ori[1],1)+' '+ realtostr(lHdr.Ori[2],1)+' '+realtostr(lHdr.Ori[3],1) );
//DANGER: This header was from ANALYZE format, not NIFTI: make sure the rotation matrix is switched off
NIFTIhdr_SetIdentityMatrix(lHdr);
lHdr.NIFTIhdr.qform_code := kNIFTI_XFORM_UNKNOWN;
lHdr.NIFTIhdr.sform_code := kNIFTI_XFORM_UNKNOWN;
//test - input estimated orientation matrix
lHdr.NIFTIhdr.sform_code := kNIFTI_XFORM_SCANNER_ANAT ;
lHdr.NIFTIhdr.srow_x[0] := lHdr.NIFTIhdr.pixdim[1];
lHdr.NIFTIhdr.srow_y[1] := lHdr.NIFTIhdr.pixdim[2];
lHdr.NIFTIhdr.srow_z[2] := lHdr.NIFTIhdr.pixdim[3];
lHdr.NIFTIhdr.srow_x[3] := (lOri[1]-1)*-lHdr.NIFTIhdr.pixdim[1];
lHdr.NIFTIhdr.srow_y[3] := (lOri[2]-1)*-lHdr.NIFTIhdr.pixdim[2];
lHdr.NIFTIhdr.srow_z[3] := (lOri[3]-1)*-lHdr.NIFTIhdr.pixdim[3];
//fx(lHdr.NIFTIhdr.srow_z[3],lOri[3]);
//end test
//Warning: some of the NIFTI float values that do exist as integer values in Analyze may have bizarre values like +INF, -INF, NaN
lHdr.NIFTIhdr.toffset := 0;
lHdr.NIFTIhdr.intent_code := kNIFTI_INTENT_NONE;
lHdr.NIFTIhdr.dim_info := kNIFTI_SLICE_SEQ_UNKNOWN + (kNIFTI_SLICE_SEQ_UNKNOWN shl 2) + (kNIFTI_SLICE_SEQ_UNKNOWN shl 4); //Freq, Phase and Slie all unknown
lHdr.NIFTIhdr.xyzt_units := kNIFTI_UNITS_UNKNOWN;
lHdr.NIFTIhdr.slice_duration := 0; //avoid +inf/-inf, NaN
lHdr.NIFTIhdr.intent_p1 := 0; //avoid +inf/-inf, NaN
lHdr.NIFTIhdr.intent_p2 := 0; //avoid +inf/-inf, NaN
lHdr.NIFTIhdr.intent_p3 := 0; //avoid +inf/-inf, NaN
lHdr.NIFTIhdr.pixdim[0] := 1; //QFactor should be 1 or -1
end;
if (lHdr.NIFTIhdr.sform_code > kNIFTI_XFORM_UNKNOWN) and (lHdr.NIFTIhdr.sform_code <= kNIFTI_XFORM_MNI_152) then begin //DEC06
lHdr.Mat:= Matrix3D(
lHdr.NIFTIhdr.srow_x[0],lHdr.NIFTIhdr.srow_x[1],lHdr.NIFTIhdr.srow_x[2],lHdr.NIFTIhdr.srow_x[3], // 3D "graphics" matrix
lHdr.NIFTIhdr.srow_y[0],lHdr.NIFTIhdr.srow_y[1],lHdr.NIFTIhdr.srow_y[2],lHdr.NIFTIhdr.srow_y[3], // 3D "graphics" matrix
lHdr.NIFTIhdr.srow_z[0],lHdr.NIFTIhdr.srow_z[1],lHdr.NIFTIhdr.srow_z[2],lHdr.NIFTIhdr.srow_z[3], // 3D "graphics" matrix
0,0,0,1);
end else begin
lHdr.Mat:= Matrix3D(
lHdr.NIFTIhdr.pixdim[1],0,0,(lOri[1]-1)*-lHdr.NIFTIhdr.pixdim[1], // 3D "graphics" matrix
0,lHdr.NIFTIhdr.pixdim[2],0,(lOri[2]-1)*-lHdr.NIFTIhdr.pixdim[2], // 3D "graphics" matrix
0,0,lHdr.NIFTIhdr.pixdim[3],(lOri[3]-1)*-lHdr.NIFTIhdr.pixdim[3], // 3D "graphics" matrix
0,0,0,1);
end;
FixCrapMat(lHdr.Mat);
//ReportMatrix(lHdr.mat);
end; //func NIFTIhdr_LoadHdr
procedure NIFTIhdr_SetIdentityMatrix (var lHdr: TMRIcroHdr); //create neutral rotation matrix
var lInc: integer;
begin
with lHdr.NIFTIhdr do begin
for lInc := 0 to 3 do
srow_x[lInc] := 0;
for lInc := 0 to 3 do
srow_y[lInc] := 0;
for lInc := 0 to 3 do
srow_z[lInc] := 0;
for lInc := 1 to 16 do
intent_name[lInc] := chr(0);
//next: create identity matrix: if code is switched on there will not be a problem
srow_x[0] := 1;
srow_y[1] := 1;
srow_z[2] := 1;
end;
end; //proc NIFTIhdr_IdentityMatrix
procedure NIFTIhdr_ClearHdr (var lHdr: TMRIcroHdr); //put sensible default values into header
var lInc: byte;
begin
lHdr.NIFTIVersion := 1;
lHdr.UsesCustomPalette := false;
lHdr.DiskDataNativeEndian := true;
lHdr.LutFromZero := false;
lHdr.NIfTItransform := true;//assume genuine NIfTI, not Analyze
with lHdr.NIFTIhdr do begin
{set to 0}
HdrSz := sizeof(TNIFTIhdr);
for lInc := 1 to 10 do
Data_Type[lInc] := chr(0);
for lInc := 1 to 18 do
db_name[lInc] := chr(0);
extents:=0;
session_error:= 0;
regular:='r'{chr(0)};
dim_info:=(0);
dim[0] := 4;
for lInc := 1 to 7 do
dim[lInc] := 0;
intent_p1 := 0;
intent_p2 := 0;
intent_p3 := 0;
intent_code:=0;
datatype:=0 ;
bitpix:=0;
slice_start:=0;
for lInc := 1 to 7 do
pixdim[linc]:= 1.0;
vox_offset:= 0.0;
scl_slope := 1.0;
scl_inter:= 0.0;
slice_end:= 0;
slice_code := 0;
xyzt_units := 10;
cal_max:= 0.0;
cal_min:= 0.0;
slice_duration:=0;
toffset:= 0;
glmax:= 0;
glmin:= 0;
for lInc := 1 to 80 do
descrip[lInc] := chr(0);{80 spaces}
for lInc := 1 to 24 do
aux_file[lInc] := chr(0);{80 spaces}
{below are standard settings which are not 0}
bitpix := 16;//vc16; {8bits per pixel, e.g. unsigned char 136}
DataType := 4;//vc4;{2=unsigned char, 4=16bit int 136}
Dim[0] := 3;
Dim[1] := 256;
Dim[2] := 256;
Dim[3] := 128;
Dim[4] := 1; {n vols}
Dim[5] := 1;
Dim[6] := 1;
Dim[7] := 1;
glMin := 0;
glMax := 255;
qform_code := kNIFTI_XFORM_UNKNOWN;
sform_code:= kNIFTI_XFORM_UNKNOWN;
quatern_b := 0;
quatern_c := 0;
quatern_d := 0;
qoffset_x := 0;
qoffset_y := 0;
qoffset_z := 0;
NIFTIhdr_SetIdentityMatrix(lHdr);
magic := kNIFTI_MAGIC_SEPARATE_HDR;
end; //with the NIfTI header...
with lHdr do begin
ScrnBufferItems := 0;
ImgBufferItems := 0;
ImgBufferBPP := 0;
RenderBufferItems := 0;
ScrnBuffer:= nil;
ImgBuffer := nil;
end;
end; //proc NIFTIhdr_ClearHdr
function NIFTIhdr_SaveHdr2 (var lFilename: string; var lHdr1: TNIFTIHdr; lAllowOverwrite,lSPM2: boolean): boolean; overload;
var
lExt: string;
lF: File;
lOverwrite: boolean;
lOutHdr,lHdr: TNIFTIHdr2;
begin
result := false;
if not NII1_2_NII2(lHdr1,lHdr) then
exit;
if lHdr.magic = kNIFTI_MAGIC_EMBEDDED_HDR then
lHdr.magic := kNIFTI2_MAGIC_EMBEDDED_HDR;
if lHdr.magic = kNIFTI_MAGIC_SEPARATE_HDR then
lHdr.magic := kNIFTI2_MAGIC_SEPARATE_HDR;
lOverwrite := false; //will we overwrite existing file?
result := false; //assume failure
if lHdr.magic = kNIFTI2_MAGIC_EMBEDDED_HDR then begin
lExt := UpCaseExt(lFileName);
if (lExt = '.GZ') or (lExt = '.NII.GZ') then begin
ShowMessage('Unable to save .nii.gz headers (first ungzip your image if you wish to edit the header)');
exit;
end;
lFilename := changefileext(lFilename,'.nii')
end else
lFilename := changefileext(lFilename,'.hdr');
if ((sizeof(TNIFTIhdr))> DiskFreeEx(lFileName)) then begin
ShowMessage('There is not enough free space on the destination disk to save the header. '+kCR+
lFileName+ kCR+' Bytes Required: '+inttostr(sizeof(TNIFTIhdr)) );
exit;
end;
if Fileexists(lFileName) then begin
if lAllowOverwrite then begin
case MessageDlg('Do you wish to modify the existing file '+lFilename+'?', mtConfirmation,[mbYes, mbNo], 0) of { produce the message dialog box }
6: lOverwrite := true; //6= mrYes, 7=mrNo... not sure what this is for Linux. Hardcoded as we do not include Form values
end;//case
end else
showmessage('Error: the file '+lFileName+' already exists.');
if not lOverwrite then Exit;
end;
if lHdr.magic = kNIFTI2_MAGIC_EMBEDDED_HDR then
if lHdr.vox_offset < sizeof(TNIFTIHdr) then
lHdr.vox_offset := sizeof(TNIFTIHdr); //embedded images MUST start after header
if lHdr.magic = kNIFTI2_MAGIC_SEPARATE_HDR then
lHdr.vox_offset := 0; //embedded images MUST start after header
if lSPM2 then begin //SPM2 does not recognize NIfTI - origin values will be wrong
lHdr.magic := 0;
{lHdr.qform_code := 0;
lHdr.sform_code:= 0;
lHdr.quatern_b := 0;
lHdr.quatern_c := 0;
lHdr.quatern_d := 0;
lHdr.qoffset_x := 0;
lHdr.qoffset_y := 0;
lHdr.qoffset_z := 0; }
end;
result := true;
move(lHdr, lOutHdr, sizeof(lOutHdr));
Filemode := 1;
AssignFile(lF, lFileName); {WIN}
if lOverwrite then //this allows us to modify just the 348byte header of an existing NII header without touching image data
Reset(lF,sizeof(TNIFTIhdr))
else
Rewrite(lF,sizeof(TNIFTIhdr));
BlockWrite(lF,lOutHdr, 1 );
CloseFile(lF);
Filemode := 2;
end; //func NIFTIhdr_SaveHdr
function NIFTIhdr_SaveHdr (var lFilename: string; var lHdr: TNIFTIHdr; lAllowOverwrite,lSPM2: boolean): boolean; overload;
var lOutHdr: TNIFTIhdr;
lExt: string;
lF: File;
lOverwrite: boolean;
begin
if (lHdr.magic = kNIFTI2_MAGIC_EMBEDDED_HDR) or (lHdr.Magic = kNIFTI2_MAGIC_SEPARATE_HDR) then begin
result := NIFTIhdr_SaveHdr2(lFilename,lHdr,lAllowOverwrite,lSPM2);
exit;
end;
lOverwrite := false; //will we overwrite existing file?
result := false; //assume failure
if lHdr.magic = kNIFTI_MAGIC_EMBEDDED_HDR then begin
lExt := UpCaseExt(lFileName);
if (lExt = '.GZ') or (lExt = '.NII.GZ') then begin
ShowMessage('Unable to save .nii.gz headers (first ungzip your image if you wish to edit the header)');
exit;
end;
lFilename := changefileext(lFilename,'.nii')
end else
lFilename := changefileext(lFilename,'.hdr');
if ((sizeof(TNIFTIhdr))> DiskFreeEx(lFileName)) then begin
ShowMessage('There is not enough free space on the destination disk to save the header. '+kCR+
lFileName+ kCR+' Bytes Required: '+inttostr(sizeof(TNIFTIhdr)) );
exit;
end;
if Fileexists(lFileName) then begin
if lAllowOverwrite then begin
case MessageDlg('Do you wish to modify the existing file '+lFilename+'?', mtConfirmation,[mbYes, mbNo], 0) of { produce the message dialog box }
6: lOverwrite := true; //6= mrYes, 7=mrNo... not sure what this is for Linux. Hardcoded as we do not include Form values
end;//case
end else
showmessage('Error: the file '+lFileName+' already exists.');
if not lOverwrite then Exit;
end;
if lHdr.magic = kNIFTI_MAGIC_EMBEDDED_HDR then
if lHdr.vox_offset < sizeof(TNIFTIHdr) then
lHdr.vox_offset := sizeof(TNIFTIHdr); //embedded images MUST start after header
if lHdr.magic = kNIFTI_MAGIC_SEPARATE_HDR then
lHdr.vox_offset := 0; //embedded images MUST start after header
if lSPM2 then begin //SPM2 does not recognize NIfTI - origin values will be wrong
lHdr.magic := 0;
end;
result := true;
move(lHdr, lOutHdr, sizeof(lOutHdr));
Filemode := 1;
AssignFile(lF, lFileName); {WIN}
if lOverwrite then //this allows us to modify just the 348byte header of an existing NII header without touching image data
Reset(lF,sizeof(TNIFTIhdr))
else
Rewrite(lF,sizeof(TNIFTIhdr));
BlockWrite(lF,lOutHdr, 1 {, NumWritten});
CloseFile(lF);
Filemode := 2;
end; //func NIFTIhdr_SaveHdr
function NIFTIhdr_SaveHdr (var lFilename: string; var lHdr: TMRIcroHdr; lAllowOverwrite: boolean): boolean; overload;
var lOutHdr: TNIFTIhdr;
lExt: string;
lF: File;
lOverwrite: boolean;
begin
if (lHdr.NIFTIVersion = 2) or (lHdr.NIFTIhdr.magic = kNIFTI2_MAGIC_EMBEDDED_HDR) or (lHdr.NIFTIhdr.Magic = kNIFTI2_MAGIC_SEPARATE_HDR) then begin
result := NIFTIhdr_SaveHdr2(lFilename,lHdr.NIFTIhdr,lAllowOverwrite,false); //666 byte swapping
exit;
end;
lOverwrite := false; //will we overwrite existing file?
result := false; //assume failure
if lHdr.NIFTIhdr.magic = kNIFTI_MAGIC_EMBEDDED_HDR then begin
lExt := UpCaseExt(lFileName);
if (lExt = '.GZ') or (lExt = '.NII.GZ') then begin
showmessage('Unable to save .nii.gz headers (first ungzip your image if you wish to edit the header)');
exit;
end;
lFilename := changefileext(lFilename,'.nii')
end else
lFilename := changefileext(lFilename,'.hdr');
if ((sizeof(TNIFTIhdr))> DiskFreeEx(lFileName)) then begin
ShowMessage('There is not enough free space on the destination disk to save the header. '+kCR+
lFileName+ kCR+' Bytes Required: '+inttostr(sizeof(TNIFTIhdr)) );
exit;
end;
if Fileexists(lFileName) then begin
if lAllowOverwrite then begin
case MessageDlg('Do you wish to modify the existing file '+lFilename+'?', mtConfirmation,[mbYes, mbNo], 0) of { produce the message dialog box }
6: lOverwrite := true; //6= mrYes, 7=mrNo... not sure what this is for unix. Hardcoded as we do not include Form values
end;//case
end else
showmessage('Error: the file '+lFileName+' already exists.');
if not lOverwrite then Exit;
end;
if lHdr.NIFTIhdr.magic = kNIFTI_MAGIC_EMBEDDED_HDR then
if lHdr.NIFTIhdr.vox_offset < sizeof(TNIFTIHdr) then
lHdr.NIFTIhdr.vox_offset := sizeof(TNIFTIHdr); //embedded images MUST start after header
if lHdr.NIFTIhdr.magic = kNIFTI_MAGIC_SEPARATE_HDR then
lHdr.NIFTIhdr.vox_offset := 0; //embedded images MUST start after header
result := true;
move(lHdr.NIFTIhdr, lOutHdr, sizeof(lOutHdr));
if lHdr.DiskDataNativeEndian= false then
NIFTIhdr_SwapBytes (lOutHdr);{swap to big-endianformat}
Filemode := 1;
AssignFile(lF, lFileName); {WIN}
if lOverwrite then //this allows us to modify just the 348byte header of an existing NII header without touching image data
Reset(lF,sizeof(TNIFTIhdr))
else
Rewrite(lF,sizeof(TNIFTIhdr));
BlockWrite(lF,lOutHdr, 1 {, NumWritten});
CloseFile(lF);
Filemode := 2;
end; //func NIFTIhdr_SaveHdr
procedure NIFTIhdr_SwapBytes (var lAHdr: TNIFTIhdr); //Swap Byte order for the Analyze type
var
lInc: integer;
begin
with lAHdr do begin
swap4(hdrsz);
swap4(extents);
session_error := swap(session_error);
for lInc := 0 to 7 do
dim[lInc] := swap(dim[lInc]);
Xswap4r(intent_p1);
Xswap4r(intent_p2);
Xswap4r(intent_p3);
intent_code:= swap(intent_code);
datatype:= swap(datatype);
bitpix := swap(bitpix);
slice_start:= swap(slice_start);
for lInc := 0 to 7 do
Xswap4r(pixdim[linc]);
Xswap4r(vox_offset);
Xswap4r(scl_slope);
Xswap4r(scl_inter);
slice_end := swap(slice_end);
Xswap4r(cal_max);
Xswap4r(cal_min);
Xswap4r(slice_duration);
Xswap4r(toffset);
swap4(glmax);
swap4(glmin);
qform_code := swap(qform_code);
sform_code:= swap(sform_code);
Xswap4r(quatern_b);
Xswap4r(quatern_c);
Xswap4r(quatern_d);
Xswap4r(qoffset_x);
Xswap4r(qoffset_y);
Xswap4r(qoffset_z);
for lInc := 0 to 3 do //alpha
Xswap4r(srow_x[lInc]);
for lInc := 0 to 3 do //alpha
Xswap4r(srow_y[lInc]);
for lInc := 0 to 3 do //alpha
Xswap4r(srow_z[lInc]);
end; //with NIFTIhdr
end; //proc NIFTIhdr_SwapBytes
end.
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