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GERead.m
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GERead.m
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function MRS_struct = GERead(MRS_struct, fname)
% 141007: RTN edits to accommodate Noeske version
% 160916: MM & RTN edits to accommodate different encoding schemes
% 180404: RTN edits for more flexible handling of different P-file header
% revisions; added support for rdbm_rev_num 26.002
ii = MRS_struct.ii;
fid = fopen(fname, 'r', 'ieee-be');
fseek(fid, 0, 'bof');
rdbm_rev_num = fread(fid, 1, 'real*4');
if rdbm_rev_num == 7.0
pfile_header_size = 39984; % LX
elseif rdbm_rev_num == 8.0
pfile_header_size = 60464; % Cardiac / MGD
elseif rdbm_rev_num > 5.0 && rdbm_rev_num < 6.0
pfile_header_size = 39940; % Signa 5.5
else
% In 11.0 and later the header and data are stored as little-endian
fclose(fid);
fid = fopen(fname, 'r', 'ieee-le');
fseek(fid, 0, 'bof');
rdbm_rev_num = fread(fid, 1, 'real*4');
if rdbm_rev_num == 9.0 % 11.0 product release
pfile_header_size = 61464;
elseif rdbm_rev_num == 11.0 % 12.0 product release
pfile_header_size = 66072;
end
end
MRS_struct.p.GE.rdbm_rev_num(ii) = rdbm_rev_num;
chkRev = {'14.3', '16', '24', '20.006', '20.007', '26.002'}; % GERead mods tested with these revisions only
if ~any(strcmp(num2str(rdbm_rev_num), chkRev))
warning('GERead not fully functional with header revision number %g!', rdbm_rev_num);
end
% RTN 2018
% Added flexible P-file revision support
% Values are read from rdb_hdr and image sub-headers
% Position can be found in rdbm.h (RDB_HEADER_REC) and imagedb.h (MRIMAGEDATATYPE)
% RTN 2018
% unsigned int rdb_hdr_ps_mps_freq
% float rdb_hdr_user0
% float rdb_hdr_user4
% float rdb_hdr_user19
% short rdb_hdr_nechoes
% short rdb_hdr_navs
% short rdb_hdr_nframes
% short rdb_hdr_point_size
% unsigned short rdb_hdr_da_xres
% short rdb_hdr_da_yres
% short rdb_hdr_dab[0].start_rcv
% short rdb_hdr_dab[0].stop_rcv
% int rdb_hdr_off_image
% int rdb_hdr_off_data
%
% image sub-header
% int te
% int tr
% float user8-10 voxel dimensions
% float user19 rf waveform
% float user20-21 offset frequencies
% float user22 pulse width (-1 default)
switch num2str(rdbm_rev_num)
case '14.3'
% int
rdb_hdr_off_image = 377;
rdb_hdr_off_data = 368;
rdb_hdr_ps_mps_freq = 107;
% float
rdb_hdr_user0 = 55;
rdb_hdr_user4 = 59;
rdb_hdr_user19 = 74;
% short
rdb_hdr_nechoes = 36;
rdb_hdr_navs = 37;
rdb_hdr_nframes = 38;
rdb_hdr_point_size = 42;
rdb_hdr_da_xres = 52;
rdb_hdr_da_yres = 53;
rdb_hdr_dab_start_rcv = 101;
rdb_hdr_dab_stop_rcv = 102;
% int
image_te = 181;
image_tr = 179;
% float
image_user8 = 38;
image_user19 = 49;
image_user20 = 50;
image_user22 = 52;
case '16'
% int
rdb_hdr_off_image = 377;
rdb_hdr_off_data = 368;
rdb_hdr_ps_mps_freq = 107;
% float
rdb_hdr_user0 = 55;
rdb_hdr_user4 = 59;
rdb_hdr_user19 = 74;
% short
rdb_hdr_nechoes = 36;
rdb_hdr_navs = 37;
rdb_hdr_nframes = 38;
rdb_hdr_point_size = 42;
rdb_hdr_da_xres = 52;
rdb_hdr_da_yres = 53;
rdb_hdr_dab_start_rcv = 101;
rdb_hdr_dab_stop_rcv = 102;
% int
image_te = 193;
image_tr = 191;
% float
image_user8 = 50;
image_user19 = 61;
image_user20 = 62;
image_user22 = 64;
case {'20.006','20.007','24'}
% int
rdb_hdr_off_image = 377;
rdb_hdr_off_data = 368;
rdb_hdr_ps_mps_freq = 107;
% float
rdb_hdr_user0 = 55;
rdb_hdr_user4 = 59;
rdb_hdr_user19 = 74;
% short
rdb_hdr_nechoes = 36;
rdb_hdr_navs = 37;
rdb_hdr_nframes = 38;
rdb_hdr_point_size = 42;
rdb_hdr_da_xres = 52;
rdb_hdr_da_yres = 53;
rdb_hdr_dab_start_rcv = 101;
rdb_hdr_dab_stop_rcv = 102;
% int
image_te = 267;
image_tr = 265;
% float
image_user8 = 98;
image_user19 = 109;
image_user20 = 110;
image_user22 = 112;
case '26.002'
% int
rdb_hdr_off_image = 11;
rdb_hdr_off_data = 2;
rdb_hdr_ps_mps_freq = 123;
% float
rdb_hdr_user0 = 71;
rdb_hdr_user4 = 75;
rdb_hdr_user19 = 90;
% short
rdb_hdr_nechoes = 74;
rdb_hdr_navs = 75;
rdb_hdr_nframes = 76;
rdb_hdr_point_size = 80;
rdb_hdr_da_xres = 90;
rdb_hdr_da_yres = 91;
rdb_hdr_dab_start_rcv = 133;
rdb_hdr_dab_stop_rcv = 134;
% int
image_te = 267;
image_tr = 265;
% float
image_user8 = 98;
image_user19 = 109;
image_user20 = 110;
image_user22 = 112;
end
% Read rdb header as short, int and float
fseek(fid, 0, 'bof');
hdr_value = fread(fid, rdb_hdr_dab_stop_rcv, 'integer*2');
fseek(fid, 0, 'bof');
f_hdr_value = fread(fid, rdb_hdr_user19, 'real*4');
fseek(fid, 0, 'bof');
i_hdr_value = fread(fid, max(rdb_hdr_off_image, rdb_hdr_ps_mps_freq), 'integer*4');
if rdbm_rev_num > 11.0
pfile_header_size = i_hdr_value(rdb_hdr_off_data);
end
MRS_struct.p.LarmorFreq(ii) = i_hdr_value(rdb_hdr_ps_mps_freq)/1e7;
MRS_struct.p.sw(ii) = f_hdr_value(rdb_hdr_user0);
nechoes = hdr_value(rdb_hdr_nechoes);
MRS_struct.p.GE.nechoes = nechoes;
nex = hdr_value(rdb_hdr_navs);
MRS_struct.p.GE.NEX = nex;
nframes = hdr_value(rdb_hdr_nframes);
point_size = hdr_value(rdb_hdr_point_size);
MRS_struct.p.npoints(ii) = hdr_value(rdb_hdr_da_xres);
MRS_struct.p.nrows(ii) = hdr_value(rdb_hdr_da_yres);
start_recv = hdr_value(rdb_hdr_dab_start_rcv);
stop_recv = hdr_value(rdb_hdr_dab_stop_rcv);
nreceivers = (stop_recv - start_recv) + 1;
% RTN 2018
dataframes = f_hdr_value(rdb_hdr_user4)/nex;
refframes = f_hdr_value(rdb_hdr_user19);
% Read image header as int and float
% MM (170118): Find TE/TR
fseek(fid, i_hdr_value(rdb_hdr_off_image), 'bof');
t_hdr_value = fread(fid, image_te, 'integer*4');
fseek(fid, i_hdr_value(rdb_hdr_off_image), 'bof');
o_hdr_value = fread(fid, image_user22, 'real*4');
MRS_struct.p.TE(ii) = t_hdr_value(image_te)/1e3;
MRS_struct.p.TR(ii) = t_hdr_value(image_tr)/1e3;
% MM (170127): Find voxel dimensions and edit pulse parameters
MRS_struct.p.voxdim(ii,:) = o_hdr_value(image_user8:image_user8+2)';
MRS_struct.p.GE.editRF.waveform(ii) = o_hdr_value(image_user19);
MRS_struct.p.GE.editRF.freq_Hz(ii,:) = o_hdr_value(image_user20:image_user20+1)';
MRS_struct.p.GE.editRF.freq_ppm(ii,:) = (MRS_struct.p.GE.editRF.freq_Hz(ii,:) / MRS_struct.p.LarmorFreq(ii)) + 4.68;
MRS_struct.p.GE.editRF.dur(ii) = o_hdr_value(image_user22)/1e3;
% RTN 2018: check for default value (-1) of pulse length
if MRS_struct.p.GE.editRF.dur(ii) <= 0
MRS_struct.p.GE.editRF.dur(ii) = 16;
end
% Spectro prescan pfiles
if MRS_struct.p.npoints(ii) == 1 && MRS_struct.p.nrows(ii) == 1
MRS_struct.p.npoints(ii) = 2048;
end
% Compute size (in bytes) of data
data_elements = MRS_struct.p.npoints(ii) * 2;
totalframes = MRS_struct.p.nrows(ii) * nechoes; % RTN nechoes mulitply
MRS_struct.p.nrows(ii) = totalframes;
data_elements = data_elements * totalframes * nreceivers;
fseek(fid, pfile_header_size, 'bof');
% Read data: point_size = 2 means 16-bit data, point_size = 4 means EDR
if point_size == 2
raw_data = fread(fid, data_elements, 'integer*2');
else
raw_data = fread(fid, data_elements, 'integer*4');
end
fclose(fid);
% 110303 CJE
% Calculate Navg from nframes, 8 water frames, 2 phase cycles
% Needs to be specific to single experiment - for frame rejection
% RTN edits to accommodate Noeske version raee 20141007
% MM (160916): Incorporating more edits from RTN to handle dual-echo data
% acquired with one of four possible encoding schemes:
% NEX=2/noadd=0, NEX=2/noadd=1, NEX=8/noadd=0, NEX=8/noadd=1
% MM (171120): RTN edits to accomodate HERMES aquisitions; better looping
% over phase cycles
if nechoes == 1
MRS_struct.p.Navg(ii) = (nframes - 8) * 2;
MRS_struct.p.Nwateravg(ii) = 8;
ShapeData = reshape(raw_data, [2 MRS_struct.p.npoints(ii) totalframes nreceivers]);
WaterData = ShapeData(:,:,2:9,:);
MetabData = ShapeData(:,:,10:end,:);
totalframes = totalframes - 9;
MRS_struct.p.nrows(ii) = totalframes;
waterframes = 8;
else
MRS_struct.p.Navg(ii) = dataframes * nex * nechoes; % RTN 2017
if (dataframes + refframes) ~= nframes
mult = nex/2; % RTN 2016
multw = nex; % RTN 2016
%mult = 1; % RTN 2017
%multw = 1; % RTN 2017
MRS_struct.p.GE.noadd = 1;
dataframes = dataframes * nex;
refframes = nframes - dataframes;
else
mult = nex/2; % RTN 2016
multw = 1; % RTN 2016
%mult = 1; % RTN 2017
%multw = 1/nex; % RTN 2017
MRS_struct.p.GE.noadd = 0;
end
MRS_struct.p.Nwateravg(ii) = refframes * nechoes; % RTN 2017
if totalframes ~= (dataframes + refframes + 1) * nechoes % RTN 2017
error('# of totalframes not same as (dataframes + refframes + 1) * nechoes');
end
ShapeData = reshape(raw_data, [2 MRS_struct.p.npoints(ii) totalframes nreceivers]);
% MM (180404)
[X1,X2] = ndgrid(1:refframes, 1:nechoes);
X1 = X1'; X1 = X1(:);
X2 = X2'; X2 = X2(:);
Y1 = (-1).^(MRS_struct.p.GE.noadd * (X1-1));
Y1 = permute(repmat(Y1, [1 MRS_struct.p.npoints(ii) 2 nreceivers]), [3 2 1 4]);
Y2 = 1 + (totalframes/nechoes) * (X2-1) + X1;
WaterData = Y1 .* ShapeData(:,:,Y2,:) * multw;
[X1,X2] = ndgrid(1:dataframes, 1:nechoes);
X1 = X1'; X1 = X1(:);
X2 = X2'; X2 = X2(:);
Y1 = (-1).^(MRS_struct.p.GE.noadd * (X1-1));
Y1 = permute(repmat(Y1, [1 MRS_struct.p.npoints(ii) 2 nreceivers]), [3 2 1 4]);
Y2 = 1 + refframes + (totalframes/nechoes) * (X2-1) + X1;
MetabData = Y1 .* ShapeData(:,:,Y2,:) * mult;
totalframes = totalframes - (refframes + 1) * nechoes; % RTN 2017
MRS_struct.p.nrows(ii) = totalframes;
waterframes = refframes * nechoes; % RTN 2017
end
MetabData = MetabData .* repmat([1; 1i], [1 MRS_struct.p.npoints(ii) totalframes nreceivers]);
MetabData = squeeze(sum(MetabData,1));
MetabData = permute(MetabData, [3 1 2]);
WaterData = WaterData .* repmat([1; 1i], [1 MRS_struct.p.npoints(ii) waterframes nreceivers]);
WaterData = squeeze(sum(WaterData,1));
WaterData = permute(WaterData, [3 1 2]);
firstpoint_water = conj(WaterData(:,1,:));
channels_scale = squeeze(sqrt(sum(firstpoint_water .* conj(firstpoint_water),1)));
channels_scale = repmat(channels_scale, [1 nreceivers MRS_struct.p.npoints(ii)]);
channels_scale = permute(channels_scale, [2 3 1]);
firstpoint_water = repmat(firstpoint_water, [1 MRS_struct.p.npoints(ii) 1]) ./ channels_scale;
WaterData = WaterData .* firstpoint_water;
WaterData = squeeze(sum(WaterData,1));
MRS_struct.fids.data_water = WaterData;
firstpoint = mean(firstpoint_water,3);
firstpoint = repmat(firstpoint, [1 1 size(MetabData,3)]);
MetabData = MetabData .* firstpoint;
MetabData = squeeze(sum(MetabData,1));
MRS_struct.fids.data = MetabData;
% Rescale, otherwise numbers blow up
MRS_struct.fids.data = MRS_struct.fids.data/1e11;
MRS_struct.fids.data_water = MRS_struct.fids.data_water/1e11;
% % Generalized least squares method (MM: under dev.)
% % Align water signal over each avg. for each coil element
% lsqnonlinopts = optimoptions(@lsqnonlin);
% lsqnonlinopts = optimoptions(lsqnonlinopts,'Algorithm','levenberg-marquardt','Display','off');
% t1 = 0:(1/MRS_struct.p.sw(ii)):(size(WaterData,2)-1)*(1/MRS_struct.p.sw(ii));
% tMax = find(t1 <= 0.2,1,'last');
% t2 = 0:(1/MRS_struct.p.sw(ii)):(tMax-1)*(1/MRS_struct.p.sw(ii));
%
% for jj = 1:size(WaterData,1)
% flatdata(:,1,:) = real(WaterData(jj,1:tMax,:));
% flatdata(:,2,:) = imag(WaterData(jj,1:tMax,:));
% target = squeeze(flatdata(:,:,1));
% target = target(:);
% for kk = 2:size(WaterData,3)
% transient = squeeze(flatdata(:,:,kk));
% fun = @(x) SpecReg(double(transient(:)), double(target), t2, x);
% p = lsqnonlin(fun, [0 0], [], [], lsqnonlinopts);
% WaterData(jj,:,kk) = WaterData(jj,:,kk) .* ...
% exp(1i*p(1)*2*pi*t1) * exp(1i*pi/180*p(2));
% end
% end
%
% WaterData_avg = mean(WaterData,3);
% e = WaterData_avg(:,ceil(0.75*size(WaterData_avg,2)):end);
% Psi = e*e';
% [~,ind] = max(abs(WaterData_avg),[],2);
% ind = mode(ind);
% S = WaterData_avg(:,ind);
% w = (S'*(Psi\S))^-1 * S' / Psi;
% WaterData = w.' .* WaterData;
% MRS_struct.fids.data_water = squeeze(sum(WaterData,1));
%
% MetabData_avg = mean(MetabData,3);
% e = MetabData_avg(:,ceil(0.75*size(MetabData_avg,2)):end);
% Psi = e*e';
% w = (S'*(Psi\S))^-1 * S' / Psi;
% MetabData = w.' .* MetabData;
% MRS_struct.fids.data = squeeze(sum(MetabData,1));
end