-
Notifications
You must be signed in to change notification settings - Fork 13
/
read_dcm_header.m
260 lines (248 loc) · 11.3 KB
/
read_dcm_header.m
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
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
function DicomHeader = read_dcm_header(fid)
% DicomHeader = read_dcm_header(fid)
% Reads header information from a DICOM file.
%
% Example:
% dcmHeader = read_dcm_header('file0001.dcm')
%
% Author:
% Dr. Georg Oeltzschner (Johns Hopkins University, 2018-04-24)
% goeltzs1@jhmi.edu
%
% Credits:
%
% Version history:
% 0.9: First version (2018-04-24)
% 0.91: Several sequence-specific loading fixes (2018-05-13)
% 0.92: Added support for sLASER sequence (2018-07-18)
% 0.93: Bug fix for invalid field names (thanks to Meredith Reid) (2022-04-27)
% 0.94: Added CMRR PRESS sequence type (2022-10-13)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% HEADER INFO PARSING %%%
% Simply open the dicom file, the information should all be the same.
fid = fopen(fid);
% Start looking for a convenient parameter block. The line before will
% start with ### ASCCONV BEGIN and end with ### ASCCONV END.
% This is defined here.
head_start_text = '### ASCCONV BEGIN';
head_end_text = '### ASCCONV END';
tline = fgets(fid); % get first line
% Keep looking until start of the parameter block is found.
while isempty(strfind(tline, head_start_text)) %#ok<*STREMP>
tline = fgets(fid);
end
% Look for regular expression containing the 'equal' signs
while isempty(strfind(tline, head_end_text))
[tokens, ~] = regexp(tline,'([\w\[\].]*)\s*=\s*([\w.-\"\\]*)','tokens','match');
% When a matching string is found, parse the results into a struct
if length(tokens) == 1
fieldname = regexprep(tokens{1}{1}, '\[|\]|_',''); % delete invalid characters
if isempty(strfind(tokens{1}{2},'"'))
if strcmp(tokens{1}{2},'0x1')
value = 0;
elseif strcmp(tokens{1}{2},'1x1')
value = 1;
else
value = str2double(tokens{1}{2});
end
else
value = tokens{1}{2};
end
C = strsplit(fieldname,'.'); % check for nested variable names
switch length(C)
case 1
try
dcmHeader.(C{1}) = value;
catch
tline = fgets(fid);
continue;
end
case 2
try
dcmHeader.(C{1}).(C{2}) = value;
catch
tline = fgets(fid);
continue;
end
case 3
dcmHeader.(C{1}).(C{2}).(C{3}) = value;
case 4
dcmHeader.(C{1}).(C{2}).(C{3}).(C{4}) = value;
case 5
dcmHeader.(C{1}).(C{2}).(C{3}).(C{4}).(C{5}) = value;
case 6
dcmHeader.(C{1}).(C{2}).(C{3}).(C{4}).(C{5}).(C{6}) = value;
case 7
dcmHeader.(C{1}).(C{2}).(C{3}).(C{4}).(C{5}).(C{6}).(C{7}) = value;
end
end
tline = fgets(fid);
end
fclose(fid);
% Determine sequence name and type
DicomHeader.sequenceFileName = dcmHeader.tSequenceFileName; % Full sequence name
% Determine the origin of the sequence
if strfind(DicomHeader.sequenceFileName,'svs_edit')
DicomHeader.seqtype = 'MEGAPRESS';
if strfind(DicomHeader.sequenceFileName(end-3:end),'univ') %#ok<STRIFCND>
DicomHeader.seqorig = 'Universal'; % Universal sequence
else
DicomHeader.seqorig = 'WIP'; % Siemens WIP
end
elseif strfind(DicomHeader.sequenceFileName,'JEdit')
DicomHeader.seqtype = 'MEGAPRESS';
DicomHeader.seqorig = 'Utah'; % Utah sequence
elseif strfind(DicomHeader.sequenceFileName,'jn_')
DicomHeader.seqtype = 'MEGAPRESS';
DicomHeader.seqorig = 'JN'; % Jamie Near's sequence
elseif strfind(DicomHeader.sequenceFileName,'eja_svs_mpress')
DicomHeader.seqtype = 'MEGAPRESS';
DicomHeader.seqorig = 'CMRR'; % Minnesota sequence
elseif strfind(DicomHeader.sequenceFileName,'eja_svs_press')
DicomHeader.seqtype = 'PRESS';
DicomHeader.seqorig = 'CMRR'; % Minnesota sequence
elseif strfind(DicomHeader.sequenceFileName,'svs_se')
DicomHeader.seqtype = 'PRESS'; % PRESS
elseif strfind(DicomHeader.sequenceFileName,'svs_slaser')
DicomHeader.seqtype = 'sLASER'; % sLASER
elseif strfind(DicomHeader.sequenceFileName,'st_vapor_643')
DicomHeader.seqtype = 'STEAM'; % STEAM
elseif strfind(DicomHeader.sequenceFileName, '%SiemensSeq%\svs_st')
DicomHeader.seqtype = 'STEAM'; % Siemens 7T Terra.X product STEAM sequence
else
DicomHeader.seqorig = DicomHeader.sequenceFileName;
error(['Unknown sequence: ' DicomHeader.seqorig '. Please consult the Gannet team for support.'])
end
% Read information
DicomHeader.TR = dcmHeader.alTR0 * 1e-3; % TR [ms]
DicomHeader.TE = dcmHeader.alTE0 * 1e-3; % TE [ms]
if isfield(dcmHeader, 'lAverages')
DicomHeader.nAverages = dcmHeader.lAverages;
else
% Minnesota sequence (CMRR, Eddy Auerbach) may store numbers of averages in a
% different field. GO 112017. Spelling may vary as well...
if isfield(dcmHeader, 'sWipMemBlock')
DicomHeader.nAverages = dcmHeader.sWipMemBlock.alFree2;
elseif isfield(dcmHeader, 'sWiPMemBlock')
DicomHeader.nAverages = dcmHeader.sWiPMemBlock.alFree2;
end
end
DicomHeader.removeOS = dcmHeader.sSpecPara.ucRemoveOversampling; % Is the oversampling removed in the RDA files?
DicomHeader.vectorSize = dcmHeader.sSpecPara.lVectorSize; % Data points specified on exam card
% GO180424: If a parameter is set to zero (e.g. if no voxel rotation is
% performed), the respective field does not show up in the dicom file. This
% case needs to be intercepted. Setting to the minimum possible value.
if ~isfield(dcmHeader.sSpecPara.sVoI, 'dInPlaneRot')
dcmHeader.sSpecPara.sVoI.dInPlaneRot = realmin('double');
end
VoI_Params = {'dCor','dSag','dTra'};
for pp = 1:length(VoI_Params)
if ~isfield(dcmHeader.sSpecPara.sVoI.sNormal, VoI_Params{pp})
dcmHeader.sSpecPara.sVoI.sNormal.(VoI_Params{pp}) = realmin('double');
end
if ~isfield(dcmHeader.sSpecPara.sVoI.sPosition, VoI_Params{pp})
dcmHeader.sSpecPara.sVoI.sPosition.(VoI_Params{pp}) = realmin('double');
end
end
DicomHeader.VoI_InPlaneRot = dcmHeader.sSpecPara.sVoI.dInPlaneRot; % Voxel rotation in plane
DicomHeader.VoI_RoFOV = dcmHeader.sSpecPara.sVoI.dReadoutFOV; % Voxel size in readout direction [mm]
DicomHeader.VoI_PeFOV = dcmHeader.sSpecPara.sVoI.dPhaseFOV; % Voxel size in phase encoding direction [mm]
DicomHeader.VoIThickness = dcmHeader.sSpecPara.sVoI.dThickness; % Voxel size in slice selection direction [mm]
DicomHeader.NormCor = dcmHeader.sSpecPara.sVoI.sNormal.dCor; % Coronal component of normal vector of voxel
DicomHeader.NormSag = dcmHeader.sSpecPara.sVoI.sNormal.dSag; % Sagittal component of normal vector of voxel
DicomHeader.NormTra = dcmHeader.sSpecPara.sVoI.sNormal.dTra; % Transversal component of normal vector of voxel
DicomHeader.PosCor = dcmHeader.sSpecPara.sVoI.sPosition.dCor; % Coronal coordinate of voxel [mm]
DicomHeader.PosSag = dcmHeader.sSpecPara.sVoI.sPosition.dSag; % Sagittal coordinate of voxel [mm]
DicomHeader.PosTra = dcmHeader.sSpecPara.sVoI.sPosition.dTra; % Transversal coordinate of voxel [mm]
% delta frequency (center of slice selection)
if isfield(dcmHeader.sSpecPara, 'dDeltaFrequency')
DicomHeader.deltaFreq = dcmHeader.sSpecPara.dDeltaFrequency;
else
DicomHeader.deltaFreq = 0;
end
if isfield(dcmHeader.sProtConsistencyInfo, 'flNominalB0')
DicomHeader.B0 = dcmHeader.sProtConsistencyInfo.flNominalB0; % Nominal B0 [T]
end
DicomHeader.dwellTime = dcmHeader.sRXSPEC.alDwellTime0; % Dwell time [ns]
DicomHeader.tx_freq = dcmHeader.sTXSPEC.asNucleusInfo0.lFrequency; % Transmitter frequency [Hz]
% These may only be extractable from a few sequences and MEGA-PRESS
% versions:
% Editing pulse parameters
if isfield(DicomHeader, 'seqorig')
if strcmp(DicomHeader.seqorig, 'CMRR')
if isfield(dcmHeader, 'sWipMemBlock')
if isfield(dcmHeader.sWipMemBlock, 'adFree3')
DicomHeader.editRF.freq(1) = dcmHeader.sWipMemBlock.adFree3;
end
if isfield(dcmHeader.sWipMemBlock, 'adFree2')
DicomHeader.editRF.freq(2) = dcmHeader.sWipMemBlock.adFree2;
end
if isfield(dcmHeader.sWipMemBlock, 'adFree6')
DicomHeader.editRF.bw = dcmHeader.sWipMemBlock.adFree8;
end
elseif isfield(dcmHeader, 'sWiPMemBlock')
if isfield(dcmHeader.sWiPMemBlock, 'adFree3')
DicomHeader.editRF.freq(1) = dcmHeader.sWiPMemBlock.adFree3;
end
if isfield(dcmHeader.sWiPMemBlock, 'adFree2')
DicomHeader.editRF.freq(2) = dcmHeader.sWiPMemBlock.adFree2;
end
if isfield(dcmHeader.sWiPMemBlock, 'adFree6')
DicomHeader.editRF.bw = dcmHeader.sWiPMemBlock.adFree8;
end
end
elseif strcmp(DicomHeader.seqorig, 'Utah')
if isfield(dcmHeader, 'sWipMemBlock')
if isfield(dcmHeader.sWipMemBlock, 'adFree8')
DicomHeader.editRF.centerFreq = dcmHeader.sWipMemBlock.adFree8;
end
if isfield(dcmHeader.sWipMemBlock, 'adFree3')
DicomHeader.editRF.freq(1) = dcmHeader.sWipMemBlock.adFree3;
end
if isfield(dcmHeader.sWipMemBlock, 'adFree4')
DicomHeader.editRF.freq(2) = dcmHeader.sWipMemBlock.adFree4;
end
if isfield(dcmHeader.sWipMemBlock, 'adFree0')
DicomHeader.editRF.bw = dcmHeader.sWipMemBlock.adFree0;
end
elseif isfield(dcmHeader, 'sWiPMemBlock')
if isfield(dcmHeader.sWipMemBlock, 'adFree8')
DicomHeader.editRF.centerFreq = dcmHeader.sWipMemBlock.adFree8;
end
if isfield(dcmHeader.sWipMemBlock, 'adFree3')
DicomHeader.editRF.freq(1) = dcmHeader.sWipMemBlock.adFree3;
end
if isfield(dcmHeader.sWipMemBlock, 'adFree4')
DicomHeader.editRF.freq(2) = dcmHeader.sWipMemBlock.adFree4;
end
if isfield(dcmHeader.sWipMemBlock, 'adFree0')
DicomHeader.editRF.bw = dcmHeader.sWipMemBlock.adFree0;
end
end
else
if isfield(dcmHeader, 'sWipMemBlock')
if isfield(dcmHeader.sWipMemBlock, 'adFree9')
DicomHeader.editRF.centerFreq = dcmHeader.sWipMemBlock.adFree9;
end
if isfield(dcmHeader.sWipMemBlock, 'adFree7')
DicomHeader.editRF.freq(1) = dcmHeader.sWipMemBlock.adFree7;
DicomHeader.editRF.freq(2) = DicomHeader.editRF.centerFreq + (DicomHeader.editRF.centerFreq - DicomHeader.editRF.freq(1));
end
if isfield(dcmHeader.sWipMemBlock, 'adFree8')
DicomHeader.editRF.bw = dcmHeader.sWipMemBlock.adFree8;
end
elseif isfield(dcmHeader, 'sWiPMemBlock')
if isfield(dcmHeader.sWiPMemBlock, 'adFree9')
DicomHeader.editRF.centerFreq = dcmHeader.sWiPMemBlock.adFree9;
end
if isfield(dcmHeader.sWiPMemBlock, 'adFree7')
DicomHeader.editRF.freq(1) = dcmHeader.sWiPMemBlock.adFree7;
DicomHeader.editRF.freq(2) = DicomHeader.editRF.centerFreq + (DicomHeader.editRF.centerFreq - DicomHeader.editRF.freq(1));
end
if isfield(dcmHeader.sWiPMemBlock, 'adFree8')
DicomHeader.editRF.bw = dcmHeader.sWiPMemBlock.adFree8;
end
end
end
end