SIEMENS_IMA_READ - read Siemens .ima data file (*.ima)
[ ima, machine ] = siemens_ima_read(fileprefix, orient, machine)
fileprefix - a string, the filename without the .ima extension
orient - force reading of specified orientation, integer values:
'', read header history orient field
0, transverse/axial unflipped
1, coronal unflipped
2, sagittal unflipped
3, transverse/axial flipped
4, coronal flipped
5, sagittal flipped
machine - a string, see machineformat in fread for details.
The default here is 'ieee-be' but the routine
will automatically switch between little and big
endian. It reports the appropriate machine
format and can return the machine value.
Returned values:
ima.hdr - a struct with image data parameters.
ima.img - a 3D matrix of image data (double precision).
See also: IMA_HDR_READ (called by this function)0001 function [ ima, machine ] = siemens_ima_read(fileprefix,IMGorient) 0002 0003 % SIEMENS_IMA_READ - read Siemens .ima data file (*.ima) 0004 % 0005 % [ ima, machine ] = siemens_ima_read(fileprefix, orient, machine) 0006 % 0007 % fileprefix - a string, the filename without the .ima extension 0008 % 0009 % orient - force reading of specified orientation, integer values: 0010 % 0011 % '', read header history orient field 0012 % 0, transverse/axial unflipped 0013 % 1, coronal unflipped 0014 % 2, sagittal unflipped 0015 % 3, transverse/axial flipped 0016 % 4, coronal flipped 0017 % 5, sagittal flipped 0018 % 0019 % machine - a string, see machineformat in fread for details. 0020 % The default here is 'ieee-be' but the routine 0021 % will automatically switch between little and big 0022 % endian. It reports the appropriate machine 0023 % format and can return the machine value. 0024 % 0025 % Returned values: 0026 % 0027 % ima.hdr - a struct with image data parameters. 0028 % ima.img - a 3D matrix of image data (double precision). 0029 % 0030 % See also: IMA_HDR_READ (called by this function) 0031 % 0032 0033 % $Revision: 1.1 $ $Date: 2004/11/12 01:32:35 $ 0034 0035 % Licence: GNU GPL, no express or implied warranties 0036 % History: 10/2002, Darren.Weber@flinders.edu.au 0037 % 0038 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0039 0040 0041 fprintf('\n\nUnder development - not functional yet...sorry.\n\n'); 0042 return 0043 0044 0045 if ~exist('fileprefix','var'), 0046 fprintf('SIEMENS_IMA_READ: No input fileprefix - see help siemens_ima_read\n'); 0047 return; 0048 end 0049 if ~exist('IMGorient','var'), IMGorient = ''; end 0050 if ~exist('machine','var'), machine = 'ieee-le'; end 0051 0052 0053 % MAIN 0054 0055 fid = fopen(sprintf('%s.ima',fileprefix),'r',machine); 0056 if fid < 0, 0057 msg = sprintf('Cannot open file %s.ima\n',fileprefix); 0058 error(msg); 0059 else 0060 ima = read_image(fid,fileprefix,IMGorient,machine); 0061 ima.fileprefix = fileprefix; 0062 end 0063 0064 return 0065 0066 0067 0068 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0069 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0070 function [ ima ] = read_image(fid,fileprefix,IMGorient,machine) 0071 0072 % Read the file header 0073 [ ima, machine ] = ima_hdr_read(fileprefix,machine); 0074 0075 if ~isequal(ima.hdr.hk.sizeof_hdr,6144), 0076 fprintf('SIEMENS_IMA_READ: Failed reading %s Analyze image\n',fileprefix); 0077 ima.img = []; 0078 fclose(fid); 0079 return 0080 end 0081 0082 0083 % read the whole .img file into matlab (faster) 0084 fprintf('SIEMENS_IMA_READ: Reading Siemens image data.\n'); 0085 fseek(fid,6144,'bof'); 0086 precision = 'double'; 0087 tmp = fread(fid,inf,sprintf('%s=>double',precision)); 0088 fclose(fid); 0089 0090 % Now partition the img data into xyz 0091 0092 0093 0094 PixelDim = double(ima.hdr.dime.dim(2)); 0095 RowDim = double(ima.hdr.dime.dim(3)); 0096 SliceDim = double(ima.hdr.dime.dim(4)); 0097 0098 0099 0100 if ~isempty(IMGorient), ima.hdr.hist.orient = IMGorient; end, 0101 0102 0103 switch double(ima.hdr.hist.orient), 0104 0105 case 0, % transverse/axial unflipped 0106 0107 % For the 'transverse unflipped' type, the voxels are stored with 0108 % Pixels in 'x' axis (varies fastest) - from patient right to left 0109 % Rows in 'y' axis - from patient posterior to anterior 0110 % Slices in 'z' axis - from patient inferior to superior 0111 0112 fprintf('SIEMENS_IMA_READ: Image orient appears to be axial unflipped\n'); 0113 0114 ima.img = zeros(PixelDim,RowDim,SliceDim); 0115 0116 n = 1; 0117 for z = 1:SliceDim, 0118 for y = 1:RowDim, 0119 x = 1:PixelDim; 0120 ima.img(x,y,z) = tmp(n:n+(PixelDim-1)); 0121 n = n + PixelDim; 0122 end 0123 end 0124 0125 end 0126 return 0127 0128 0129 function [ ima, machine ] = ima_hdr_read(fileprefix,machine) 0130 0131 0132 0133 % Siemens Magnetom Vision Native Format 0134 % 0135 % The exact details of the format are not known, but 0136 % a little guess work has determined what follows. The 0137 % data types are Sun, hence the byte order is big-endian 0138 % and the all the floats I have found are doubles. Offsets 0139 % here are in bytes from the start of the header. The 0140 % uncompressed image data starts at offset 6144. 0141 % 0142 % 0 u_int SiemensStudyDateYYYY 0143 % 4 u_int SiemensStudyDateMM 0144 % 8 u_int SiemensStudyDateDD 0145 % 12 u_int AcquisitionDateYYYY 0146 % 16 u_int AcquisitionDateMM 0147 % 20 u_int AcquisitionDateDD 0148 % 24 u_int ImageDateYYYY 0149 % 28 u_int ImageDateMM 0150 % 32 u_int ImageDateDD 0151 % 36 u_int SiemensStudyTimeHH 0152 % 40 u_int SiemensStudyTimeMM 0153 % 44 u_int SiemensStudyTimeSS 0154 % 52 u_int AcquisitionTimeHH 0155 % 56 u_int AcquisitionTimeMM 0156 % 60 u_int AcquisitionTimeSS 0157 % 68 u_int ImageTimeHH 0158 % 72 u_int ImageTimeMM 0159 % 76 u_int ImageTimeSS 0160 % 96 char[7] Manufacturer 0161 % 105 char[25] InstitutionName 0162 % 186 char[4] Annotation 0163 % 281 char[15] ModelName 0164 % 412 u_int LastMoveDateYYYY 0165 % 416 u_int LastMoveDateMM 0166 % 420 u_int LastMoveDateDD 0167 % 424 u_int LastMoveTimeHH 0168 % 428 u_int LastMoveTimeMM 0169 % 432 u_int LastMoveTimeSS 0170 % 768 char[25] PatientName 0171 % 795 char[12] PatientID 0172 % 808 u_int DOBYYYY 0173 % 812 u_int DOBMM 0174 % 816 u_int DOBDD 0175 % 851 char[3] PatientAge 0176 % 854 char PatientAgeUnits ('Y'=years) 0177 % 1052 u_int RegistrationDateYYYY 0178 % 1056 u_int RegistrationDateMM 0179 % 1060 u_int RegistrationDateDD 0180 % 1064 u_int RegistrationTimeHH 0181 % 1068 u_int RegistrationTimeMM 0182 % 1072 u_int RegistrationTimeSS 0183 % 1544 double SliceThickness 0184 % 1560 double RepetitionTime 0185 % 1568 double EchoTime 0186 % 1592 double FrequencyMHz 0187 % 1639 char[5] Station 0188 % 1712 u_int CalibrationDateYYYY 0189 % 1716 u_int CalibrationDateMM 0190 % 1720 u_int CalibrationDateDD 0191 % 1724 u_int CalibrationTimeHH 0192 % 1728 u_int CalibrationTimeMM 0193 % 1732 u_int CalibrationTimeSS 0194 % 1767 char[16] ReceivingCoil 0195 % 1828 char[4] ImagedNucleus 0196 % 2112 double FlipAngle 0197 % 2560 double MagneticFieldStrength 0198 % 2864 u_int DisplayMatrixSize 0199 % 2944 char[65] SequencePrgName 0200 % 3009 char[65] SequenceWkcName 0201 % 3074 char[9] SequenceAuthor 0202 % 3083 char[8] SequenceType 0203 % 3744 double FOVRow 0204 % 3752 double FOVColumn 0205 % 3768 double CenterPointX 0206 % 3776 double CenterPointY 0207 % 3784 double CenterPointZ 0208 % 3792 double NormalVectorX 0209 % 3800 double NormalVectorY 0210 % 3808 double NormalVectorZ 0211 % 3816 double DistanceFromIsocenter 0212 % 3832 double RowVectorX 0213 % 3840 double RowVectorY 0214 % 3848 double RowVectorZ 0215 % 3856 double ColumnVectorX 0216 % 3864 double ColumnVectorY 0217 % 3872 double ColumnVectorZ 0218 % 3880 char[3] OrientationSet1Top 0219 % 3884 char[3] OrientationSet1Left 0220 % 3888 char[3] OrientationSet1Back 0221 % 3892 char[3] OrientationSet2Down 0222 % 3896 char[3] OrientationSet2Right 0223 % 3900 char[3] OrientationSet2Front 0224 % 3904 char[32] SequenceName 0225 % 0226 % 4136 double GapRatio (see below) 0227 % 0228 % 5000 double PixelSizeRow 0229 % 5008 double PixelSizeColumn 0230 % 0231 % 5504 char[12] TextPatientID 0232 % 5517 char TextPatientSex 0233 % 5518 char[3] TextPatientAge 0234 % 5521 char TextPatientAgeUnits ('Y'=years) 0235 % 5529 char[7] TextPatientPosition 0236 % 5541 char[5] TextImageNumberFlag ('IMAGE'=image) 0237 % 5546 char[3] TextImageNumber 0238 % 5559 char[2] TextDateDD 0239 % 5562 char[3] TextDateMM 0240 % 5566 char[4] TextDateYYYY 0241 % 5571 char[2] TextTimeHH 0242 % 5574 char[2] TextTimeMM 0243 % 5577 char[2] TextAcquisitionTimeFlag ('TA'=acquisition time) 0244 % 5583 char[2] TextAcquisitionTimeMM 0245 % 5586 char[2] TextAcquisitionTimeSS 0246 % 5601 char[4] TextAnnotation 0247 % 5655 char[25] TextOrganization 0248 % 5682 char[5] TextStation 0249 % 5695 char[3] TextAcquisitionMatrixPhase 0250 % 5698 char TextAcquisitionMatrixPhaseAxis ('h'=horizontal,' '=vertical) 0251 % 5700 char[3] TextAcquisitionMatrixFreq 0252 % 5703 char TextAcquisitionMatrixFreqO ('o'=o,' '=blank) 0253 % 5704 char TextAcquisitionMatrixFreqS ('s'=s,' '=blank) 0254 % 5706 char[8] TextSequence 0255 % 5714 char[3] TextFlipAngle 0256 % 5718 char[4] TextScanNumberFlag ('SCAN'=scan) 0257 % 5723 char[3] TextScanNumberA 0258 % 5726 char[3] TextScanNumberB 0259 % 5730 char[2] TextRepetitionTimeFlag ('TR'=tr) 0260 % 5734 char[7] TextRepetitionTime 0261 % 5742 char[2] TextEchoTimeFlag ('TE'=te) 0262 % 5746 char[5] TextEchoTime 0263 % 5752 char TextEchoNumber 0264 % 5790 char[2] TextSliceThicknessFlag ('SL'=slice thickness) 0265 % 5794 char[7] TextSliceThickness 0266 % 5802 char[2] TextSlicePositionFlag ('SP'=slice position) 0267 % 5806 char[7] TextSlicePosition 0268 % 5814 char[3] TextAngleFlag1 ('Sag'=sagittal,'Cor'=coronal,'Tra'=transverse) 0269 % 5817 char TextAngleFlag2 ('>'=gt,'<'=lt) 0270 % 5818 char[3] TextAngleFlag3 ('Sag'=sagittal,'Cor'=coronal,'Tra'=transverse) 0271 % 5821 char[4] TextAngle 0272 % 5838 char[3] TextFOVFlag ('FoV'=field of view) 0273 % 5842 char[3] TextFOVH 0274 % 5846 char[3] TextFOVV 0275 % 5874 char[2] TextTablePositionFlag ('TP'=table position) 0276 % 5878 char[7] TextTablePosition 0277 % 5938 char[5] TextStudyNumberFlag ('STUDY'=study) 0278 % 5943 char[2] TextStudyNumber 0279 % 5956 char[2] TextDOBDD 0280 % 5959 char[3] TextDOBMM 0281 % 5963 char[4] TextDOBYYYY 0282 % 5992 char[3] TextStudyNumberFlag2 ('STU'=study) 0283 % 5996 char[3] TextImageNumberFlag2 ('IMA'=study) 0284 % 5999 char[2] TextStudyNumber2 0285 % 6002 char[2] TextImageNumber2 0286 % 6013 char[5] TextStudyImageNumber3 0287 % 6031 char[15] TextModelName 0288 % 6058 char[25] TextPatientName 0289 % 6085 char[2] TextScanStartTimeHH 0290 % 6088 char[2] TextScanStartTimeMM 0291 % 6091 char[2] TextScanStartTimeSS 0292 0293 0294 % I have asked David Clunie to update his FAQ to include information for 0295 % finding size of the gap given a Siemens Vision format image. For the record 0296 % the answer is: GapRatio is at byte 4136 (measured from the beginning of 0297 % the file) and it is of type double (8-byte float, Big Endian). For example, 0298 % if SliceThickness is 8mm and the GapRatio is 0.25, then the Gap is 0299 % (8x0.25=) 2mm, and the interslice distance is (8+2=) 10mm. 0300 0301 0302 return