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GERead.m
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GERead.m
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function [ MRS_struct ] = GERead(MRS_struct, fname)
ii=MRS_struct.ii;
MRS_struct.p.global_rescale=1;
%121106 RAEE moving code from GAnnetLoad to GERead (to match other file
%formats and tidy things up some.
%RTN edits to accommodate Noeske version RAEE 141007
fid = fopen(fname,'r', 'ieee-be');
if fid == -1
tmp = [ 'Unable to locate Pfile ' fname ];
disp(tmp);
return;
end
% return error message if unable to read file type.
% Determine size of Pfile header based on Rev number
status = fseek(fid, 0, 'bof');
[f_hdr_value, count] = fread(fid, 1, 'real*4');
rdbm_rev_num = f_hdr_value(1);
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');
status = fseek(fid, 0, 'bof');
[f_hdr_value, count] = fread(fid, 1, 'real*4');
if (f_hdr_value == 9.0) % 11.0 product release
pfile_header_size= 61464;
elseif (f_hdr_value == 11.0); % 12.0 product release
pfile_header_size= 66072;
elseif (f_hdr_value > 11.0) & (f_hdr_value < 100.0) % 14.0 and later
status = fseek(fid, 1468, 'bof');
pfile_header_size = fread(fid,1,'integer*4');
else
err_msg = sprintf('Invalid Pfile header revision: %f', f_hdr_value );
return;
end
end
% Read header information
status = fseek(fid, 0, 'bof');
[hdr_value, count] = fread(fid, 102, 'integer*2');
% RTN - read rhuser
status = fseek(fid, 0, 'bof');
[f_hdr_value, count] = fread(fid, 74, 'real*4');
npasses = hdr_value(33);
nslices = hdr_value(35);
nechoes = hdr_value(36);
%RTN - number of phase cycles
navs = hdr_value(37);
nframes = hdr_value(38);
point_size = hdr_value(42);
MRS_struct.p.npoints = hdr_value(52);
MRS_struct.p.nrows = hdr_value(53);
rc_xres = hdr_value(54);
rc_yres = hdr_value(55);
start_recv = hdr_value(101);
stop_recv = hdr_value(102);
nreceivers = (stop_recv - start_recv) + 1;
% Specto Prescan pfiles
if (MRS_struct.p.npoints == 1) & (MRS_struct.p.nrows == 1)
MRS_struct.p.npoints = 2048;
end
% Determine number of slices in this Pfile: this does not work for all cases.
slices_in_pass = nslices/npasses;
% Compute size (in bytes) of each frame, echo and slice
data_elements = MRS_struct.p.npoints*2;
frame_size = data_elements*point_size;
echo_size = frame_size*MRS_struct.p.nrows;
slice_size = echo_size*nechoes;
mslice_size = slice_size*slices_in_pass;
my_slice = 1;
my_echo = 1;
my_frame = 1;
FullData=zeros(nreceivers, MRS_struct.p.npoints , (MRS_struct.p.nrows-my_frame+1)*nechoes); %RTN nechoes multiplication;
%Start to read data into Eightchannel structure.
totalframes=(MRS_struct.p.nrows-my_frame+1)*nechoes; % RTN nechoes mulitply;
MRS_struct.p.nrows=totalframes;
data_elements2 = data_elements*totalframes*nreceivers;
% % Compute offset in bytes to start of frame.
file_offset = pfile_header_size + ((my_frame-1)*frame_size);
status = fseek(fid, file_offset, 'bof');
% read data: point_size = 2 means 16 bit data, point_size = 4 means EDR )
if (point_size == 2 )
[raw_data, count] = fread(fid, data_elements2, 'integer*2');
else
[raw_data, count] = fread(fid, data_elements2, '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
if (nechoes == 1)
MRS_struct.p.Navg(ii) = (nframes-8)*2;
MRS_struct.p.Nwateravg = 8; %moved from MRSGABAinstunits RE 110726
ShapeData = reshape(raw_data,[2 MRS_struct.p.npoints totalframes nreceivers]);
ZeroData = ShapeData(:,:,1,:);
WaterData = ShapeData(:,:,2:9,:);
FullData = ShapeData(:,:,10:end,:);
totalframes = totalframes-9;
MRS_struct.p.nrows=totalframes;
Frames_for_Water = 8;
else
dataframes = f_hdr_value(59)/navs
refframes = f_hdr_value(74)
MRS_struct.p.Navg(ii) = dataframes*navs;
MRS_struct.p.Nwateravg = refframes*2;
MRS_struct.p.TR = 1.8;
if ((dataframes+refframes) ~= nframes)
noadd = 1;
dataframes = dataframes*navs;
refframes = refframes*navs;
else
noadd = 0;
end
if (totalframes ~= ((dataframes+refframes+1)*2))
error('# of totalframes not same as (dataframes+refframes+1)*2');
end
ShapeData = reshape(raw_data,[2 MRS_struct.p.npoints totalframes nreceivers]);
ZeroData = ShapeData(:,:,1,:);
WaterData = zeros([2 MRS_struct.p.npoints refframes*2 nreceivers]);
for loop = 1:refframes
WaterData(:,:,2*loop,:)=(-1)^(noadd*(loop-1))*ShapeData(:,:,1+loop,:);
WaterData(:,:,2*loop-1,:)=(-1)^(noadd*(loop-1))*ShapeData(:,:,totalframes/2+1+loop,:);
end
FullData = zeros([2 MRS_struct.p.npoints dataframes*2 nreceivers]);
for loop = 1:dataframes
FullData(:,:,2*loop,:)=(-1)^(noadd*(loop-1))*ShapeData(:,:,1+refframes+loop,:);
FullData(:,:,2*loop-1,:)=(-1)^(noadd*(loop-1))*ShapeData(:,:,totalframes/2+refframes+1+loop,:);
end
totalframes=totalframes-refframes*2-2;
MRS_struct.p.nrows=totalframes;
Frames_for_Water=refframes*2;
end
FullData = FullData.*repmat([1;i],[1 MRS_struct.p.npoints totalframes nreceivers]);
WaterData = WaterData.*repmat([1;i],[1 MRS_struct.p.npoints Frames_for_Water nreceivers]);
FullData = squeeze(sum(FullData,1));
FullData = permute(FullData,[3 1 2]);
WaterData = squeeze(sum(WaterData,1));
WaterData = permute(WaterData,[3 1 2]);
% at this point, FullData(rx_channel, point, average)
firstpoint=conj(WaterData(:,1,:));
firstpoint=repmat(firstpoint, [1 MRS_struct.p.npoints 1]);
% here firstpoint(rx_channel,[], average)
% CJE March 10 - correct phase of each Water avg independently
WaterData=WaterData.*firstpoint*MRS_struct.p.global_rescale;
%Multiply the Eightchannel data by the firstpointvector
% zeroth order phasing of spectra
% CJE Nov 09: do global rescaling here too
% don't really need the phasing step here if performing frame-by-frame phasing
for receiverloop = 1:nreceivers
FullData(receiverloop,:) = FullData(receiverloop,:)*firstpoint(receiverloop,1,1)*MRS_struct.p.global_rescale;
% WaterData(receiverloop,:) = WaterData(receiverloop,:)*firstpoint(receiverloop,1,1)*MRS_struct.global_rescale;
end
% sum over Rx channels
FullData = squeeze(sum(FullData,1));
MRS_struct.fids.data =FullData;
WaterData = squeeze(sum(WaterData,1));
MRS_struct.fids.data_water=WaterData;
MRS_struct.p.sw = 5000; %should really pick this up from the header
%%%%%% end of GE specific load
rescale=1/1e11;%necessary for GE data or numbers blow up.
MRS_struct.fids.data =MRS_struct.fids.data*rescale;
MRS_struct.fids.data_water =MRS_struct.fids.data_water*rescale;
end