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hmri_create_b1map.m
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hmri_create_b1map.m
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function P_trans = hmri_create_b1map(jobsubj)
%% Processing of B1 maps for B1 bias correction
% FORMAT P_trans = hmri_create_b1map(jobsubj)
% jobsubj - are parameters for one subject out of the job list.
% NB: ONE SINGLE DATA SET FROM ONE SINGLE SUBJECT IS PROCESSED HERE,
% LOOP OVER SUBJECTS DONE AT HIGHER LEVEL.
% P_trans - a vector of file names with P_trans(1,:) = anatomical volume
% for coregistration and P_trans(2,:) = B1 map in percent units.
%_______________________________________________________________________
% Written by E. Balteau, 2014.
% Cyclotron Research Centre, University of Liege, Belgium
%_______________________________________________________________________
% Modified by T. Leutritz in 2016 in order to use the SIEMENS product
% sequences 'rf_map' and 'tfl_b1map'. The latter produces essentially
% a FLASH like image and a flip angle map (multiplied by 10) based on
% Chung S. et al.: "Rapid B1+ Mapping Using a Preconditioning RF Pulse with
% TurboFLASH Readout", MRM 64:439-446 (2010).
%_______________________________________________________________________
flags = jobsubj.log.flags;
flags.PopUp = false;
hmri_log(sprintf('\t============ CREATE B1 MAP - %s.m (%s) ============', mfilename, datetime('now')),flags);
% retrieve effective acquisition & processing parameters, alternatively
% use defaults
b1map_params = get_b1map_params(jobsubj);
% save b1map_params as json-file
spm_jsonwrite(fullfile(jobsubj.path.supplpath,'hMRI_map_creation_b1map_params.json'),b1map_params,struct('indent','\t'));
% init output
P_trans = [];
% return if nothing else to be done (no B1 correction or UNICORT cases)
if ~b1map_params.b1avail
return;
end
% calculate B1 map according to b1 data type
switch(b1map_params.b1type)
case 'i3D_AFI'
% processing B1 map from AFI data
P_trans = calc_AFI_b1map(jobsubj, b1map_params);
case 'i3D_EPI'
% processing B1 map from SE/STE EPI data
P_trans = calc_SESTE_b1map(jobsubj, b1map_params);
case 'DAM'
% processing B1 map from DAM data
P_trans = calc_DAM_b1map(jobsubj, b1map_params);
case 'tfl_b1_map'
% processing B1 map from tfl_b1map data
P = b1map_params.b1input(2,:); % scaled FA map from tfl_b1map sequence
alphanom = get_metadata_val(P,'FlipAngle');
scaling = 10/alphanom;
offset = 0;
descrip = 'SIEMENS tfl_b1map protocol';
P_trans = calc_scaled_b1map(jobsubj, b1map_params, offset, scaling, descrip);
case 'rf_map'
% processing B1 map from rf_map data
P = b1map_params.b1input(2,:); % scaled FA map from rf_map sequence
% the formula (abs(Vol1)-2048)*180/2048 would result in an absolute FA map
alphanom = get_metadata_val(P,'FlipAngle');
scaling = 180*100/(alphanom*2048); % *100/alpha to get p.u.
offset = -2048;
descrip = 'SIEMENS rf_map protocol';
P_trans = calc_scaled_b1map(jobsubj, b1map_params, offset, scaling, descrip);
case 'pre_processed_B1'
P_trans = calc_scaled_b1map(jobsubj, b1map_params, 0, b1map_params.scafac, sprintf('Pre-processed B1 map rescaled with factor %f', b1map_params.scafac));
otherwise
hmri_log(sprintf('WARNING: unknown B1 type, no B1 map calculation performed.'),b1map_params.defflags);
end
% copy P_trans output to Results/Supplementary directory (nii & json!) and
% make P_trans point to the copied files (so coregistration is applied to
% them).
%
% NOTES:
% - if "cleanup" set to true, the B1mapCalc directory is deleted when the
% Map Calculation completes...
% - just in case no json files have been saved with the output, the
% copyfile is called in "try" mode...
% - must strip the ',1' (at the end of the file extension '.nii,1')
% otherwise copyfile does not find the files!!
if ~isempty(P_trans)
P_trans = spm_file(P_trans,'number','');
P_trans_copy{1} = fullfile(jobsubj.path.b1respath, spm_file(P_trans(1,:), 'filename'));
P_trans_copy{2} = fullfile(jobsubj.path.b1respath, spm_file(P_trans(2,:), 'filename'));
copyfile(deblank(P_trans(1,:)), P_trans_copy{1});
try copyfile([spm_str_manip(P_trans(1,:),'r') '.json'],[spm_str_manip(P_trans_copy{1},'r') '.json']); end %#ok<*TRYNC>
copyfile(deblank(P_trans(2,:)), P_trans_copy{2});
try copyfile([spm_str_manip(P_trans(2,:),'r') '.json'],[spm_str_manip(P_trans_copy{2},'r') '.json']); end
P_trans = char(P_trans_copy{1},P_trans_copy{2});
end
hmri_log(sprintf('\t============ CREATE B1 MAP: completed (%s) ============', datetime('now')),b1map_params.nopuflags);
end
%% =======================================================================%
% B1 map calculation - AFI protocol
%=========================================================================%
function P_trans = calc_AFI_b1map(jobsubj, b1map_params)
% default format specifications for the output metadata
json = hmri_get_defaults('json');
% define output dir
outpath = jobsubj.path.b1path;
b1map_params.outpath = outpath;
% NB: both phase and magnitude images can be provided but only the
% magnitude images (first series) are used. Phase images (second series)
% are not used. In each series, first image = TR2 (long TR) and second
% image = TR1 (short TR).
fileTR1 = b1map_params.b1input(1,:);
fileTR2 = b1map_params.b1input(2,:);
V1 = spm_vol(fileTR1);
V2 = spm_vol(fileTR2);
Y1 = spm_read_vols(V1);
Y2 = spm_read_vols(V2);
sname = spm_file(V1.fname,'basename');
% copy and rename anatomical reference for uniformity between protocols
B1ref = fullfile(outpath, [sname '_B1ref.nii']);
copyfile(char(V1.fname),B1ref);
try copyfile([spm_str_manip(char(V1.fname),'r') '.json'],[spm_str_manip(B1ref,'r') '.json']); end %#ok<*TRYNC>
TR1 = 1; % only the ratio [TR2/TR1=n] matters
TR2 = b1map_params.b1acq.TR2TR1ratio;
alphanom = b1map_params.b1acq.alphanom; % degrees
% compute B1 map
FAfun=@(r,n) acosd((r*n-1)./(n-r)); % Eq. (6) in Yarnykh, MRM (2007)
r=Y2./Y1;
n=b1map_params.b1acq.TR2TR1ratio;
FAmap = FAfun(r,n); % flip angle map in degrees
% print warning if images might have been input in the wrong order
% This is determined by comparing the number of complex values in the B1
% map to the number obtained with the images in reverse order.
if nnz(imag(FAmap))>nnz(imag(FAfun(1./r,n)))
warn_message = sprintf(...
['unusually many complex values detected in the AFI \n'...
'B1 map. Please perform a visual check of the output B1 map and \n'...
'carefully check the order of the input AFI images.']);
% avoid printing both matlab warning and log message to command window
local_defflags = b1map_params.defflags;
local_defflags.ComWin = 0;
hmri_log(['WARNING: ',warn_message],local_defflags);
warning('hmri:afiTooManyImag',warn_message) %#ok<SPWRN>
end
% normalise B1 map
% Take the real part because the imaginary component is erroneous and
% should only appear in background voxels. Too many would be a sign of
% incorrect file order.
B1map_norm = real(FAmap)*100/alphanom;
% masking; mask is written out to folder of B1ref
mask = mask_for_B1(spm_vol(B1ref),b1map_params.b1mask);
% smoothed map
smB1map_norm = smoothB1(V1,B1map_norm,b1map_params.b1proc.B1FWHM,mask);
% save output images
VB1 = V1;
VB1.pinfo(1) = max(smB1map_norm(:))/spm_type(VB1.dt(1),'maxval');
VB1.descrip = ['B1+ map - smoothed ( ' sprintf('%d ',b1map_params.b1proc.B1FWHM) 'mm ) and normalised (p.u.) - AFI protocol'];
VB1.fname = fullfile(outpath, [sname '_B1map.nii']);
spm_write_vol(VB1,smB1map_norm);
% set and write metadata
input_files = b1map_params.b1input;
Output_hdr = init_b1_output_metadata(input_files, b1map_params);
Output_hdr.history.procstep.descrip = [Output_hdr.history.procstep.descrip ' (AFI protocol)'];
Output_hdr.history.output.imtype = 'B1+ map (AFI protocol)';
set_metadata(VB1.fname,Output_hdr,json);
% requires anatomic image + map
P_trans = char(B1ref,char(VB1.fname));
end
%% =======================================================================%
% B1 map calculation - DAM protocol % TL copied and adapted from AFI_b1map
%=========================================================================%
function P_trans = calc_DAM_b1map(jobsubj, b1map_params)
% default format specifications for the output metadata
json = hmri_get_defaults('json');
% define output dir
outpath = jobsubj.path.b1path;
b1map_params.outpath = outpath;
% first image = 2alpha (2*alpha) and second image = alpha.
file_alpha = b1map_params.b1input(2,:);
file_2alpha = b1map_params.b1input(1,:);
V1 = spm_vol(file_alpha);
V2 = spm_vol(file_2alpha);
Y1 = spm_read_vols(V1);
Y2 = spm_read_vols(V2);
sname = spm_file(V1.fname,'basename');
% copy and rename anatomical reference for uniformity between protocols
B1ref = fullfile(outpath, [sname '_B1ref.nii']);
copyfile(char(V1.fname),B1ref);
try copyfile([spm_str_manip(char(V1.fname),'r') '.json'],[spm_str_manip(B1ref,'r') '.json']); end %#ok<*TRYNC>
alphanom = b1map_params.b1acq.alphanom;
% compute B1 map
% Note: imaginary component is erroneous and should only appear in
% background voxels. Too many would be a sign of incorrect file order.
B1map = acosd(Y2./(2*Y1))/alphanom;
% normalise B1 map
B1map_norm = real(B1map)*100;
% masking; mask is written out to folder of B1ref
mask = mask_for_B1(spm_vol(B1ref),b1map_params.b1mask);
% smoothed map
smB1map_norm = smoothB1(V1,B1map_norm,b1map_params.b1proc.B1FWHM,mask);
% save output images
VB1 = V1;
VB1.pinfo(1) = max(smB1map_norm(:))/spm_type(VB1.dt(1),'maxval');
VB1.descrip = ['B1+ map - smoothed ( ' sprintf('%d ',b1map_params.b1proc.B1FWHM) 'mm ) and normalised (p.u.) - DAM protocol'];
VB1.fname = fullfile(outpath, [sname '_B1map.nii']);
spm_write_vol(VB1,smB1map_norm);
% set and write metadata
input_files = b1map_params.b1input;
Output_hdr = init_b1_output_metadata(input_files, b1map_params);
Output_hdr.history.procstep.descrip = [Output_hdr.history.procstep.descrip ' (DAM protocol)'];
Output_hdr.history.output.imtype = 'B1+ map (DAM protocol)';
set_metadata(VB1.fname,Output_hdr,json);
% requires anatomic image + map
P_trans = char(B1ref,char(VB1.fname));
end
%% =======================================================================%
% B1 map calculation - SE/STE EPI protocol
%=========================================================================%
function P_trans = calc_SESTE_b1map(jobsubj, b1map_params)
% Calculation of B1 maps based on 3D EPI spin echo (SE) and stimulated
% (STE) echo images (see Jiru and Klose MRM 2006).
% Corresponding scanning protocol/sequence: al_B1mapping
% Input: 11 pairs of (SE, STE) images for B1 map calculation and 3 images
% for B0 map calculation.
% This macro calls the functions hmri_create_B1Map_unwarp and
% hmri_create_B1Map_process for correction of image distortions, padding
% and smoothing of the images.
% Output:
% - distorted B1 (B1map_*) and error (SDmap_*) maps
% - undistorted B1 (uB1map_*) and error (uSDmap_*) maps
% - undistorted, masked and padded B1 maps (muB1map_*)
% - undistorted, masked, padded and smoothed B1 maps (smuB1map_*)
% i.e. FULLY PROCESSED
% At each voxel, this macro selects the 5 pairs of (SE,STE image) (out of
% 11) with maximum signal amplitude in the SE images.
% The sum of square image of all SE images is created (SumOfSq) and
% undistorted (uSumOfSq) for coregistration of the B1 map to an anatomical
% dataset.
%
% For coherence among B1 protocols, the fully processed B1 map (smuB1map_*)
% is renamed *_B1map.nii, while the undistorted SoS image (uSumOfSq) is
% renamed *_B1ref for anatomical reference.
json = hmri_get_defaults('json');
b0input = b1map_params.b0input; % B0 data - 3 volumes
V_SE = spm_vol(b1map_params.SEinput);
V_STE = spm_vol(b1map_params.STEinput);
% calc_SESTE_b1map expects fa in decreasing order
[b1map_params.b1acq.beta, fa_order] = sort(b1map_params.b1acq.beta, 'descend');
% rearrange volumes in decreasing fa
V_SE = V_SE(fa_order);
V_STE = V_STE(fa_order);
n = 2*length(V_SE);
% Because we use magnitude images and trigonometric functions are periodic,
% there is ambiguity in the calculated angles. The number of ambiguous
% angles to try is determined by how high the actual flip angle is; if less
% than 90°, only one angle would be needed, less than 180°, 2, and greater
% than 180°, 3. Note that the number of permutations to test will scale
% combinatorically with the number of ambiguous angles to test!
nAmbiguousAngles=b1map_params.b1proc.nAmbiguousAngles;
if nAmbiguousAngles<2 % Use at least as many as Lutti, et al. (MRM, 2010)
nAmbiguousAngles=2;
end
Y_tmptmp = zeros([V_SE(1).dim(1:2) n/2 nAmbiguousAngles]);
Y_mn_out = zeros(V_SE(1).dim(1:3));
Y_sd_out = zeros(V_SE(1).dim(1:3));
real_Y_tmp = zeros([V_SE(1).dim(1:2) b1map_params.b1proc.Nonominalvalues nAmbiguousAngles]);
Ssq_matrix = sqrt(sum(spm_read_vols(V_SE).^2,4));
%-Define output directory
%-----------------------------------------------------------------------
outpath = jobsubj.path.b1path;
b1map_params.outpath = outpath;
%-Start progress plot
%-----------------------------------------------------------------------
spm_progress_bar('Init',V_SE(1).dim(3),'B1 map fit','planes completed');
%-Loop over planes computing result Y
%-----------------------------------------------------------------------
corr_fact = exp(b1map_params.b1acq.TM/b1map_params.b1proc.T1);
interp = 0; % nearest neighbor interpolation
for p = 1:V_SE(1).dim(3) %loop over the partition dimension of the data set
SE_intensities = zeros([V_SE(1).dim(1:2),n/2]);
for i = 1:n/2
% SE image intensities to determine which estimates to trust
SE_intensities(:,:,i) = hmri_read_vols(V_SE(i),V_SE(1),p,interp);
% B1 estimates
Y_tmptmp(:,:,i,1) = real(acosd(corr_fact * ...
hmri_read_vols(V_STE(i),V_SE(1),p,interp) ./ ...
(SE_intensities(:,:,i)+b1map_params.b1proc.eps)) / ...
b1map_params.b1acq.beta(i));
% Alternative B1 estimates due to pi/2 ambiguity of acos for magnitude images
Y_tmptmp(:,:,i,2) = 180/b1map_params.b1acq.beta(i) - Y_tmptmp(:,:,i,1);
% We can keep adding pi to the angles, reflecting ambiguity in acos for larger actual flip angles
for j=3:nAmbiguousAngles
Y_tmptmp(:,:,i,j) = 180/b1map_params.b1acq.beta(i) + Y_tmptmp(:,:,i,j-2);
end
end
% We trust values with highest SE intensity
[~,indexes] = sort(SE_intensities,3,'descend');
for x_nr = 1:V_SE(1).dim(1)
for y_nr = 1:V_SE(1).dim(2)
real_Y_tmp(x_nr,y_nr,:,:) = Y_tmptmp(x_nr,y_nr,indexes(x_nr,y_nr,1:b1map_params.b1proc.Nonominalvalues),:);
end
end
% Test all permutations of the different ambiguous-angle B1 estimates
% to find the combination with the lowest standard deviation
% The algorithm below treats the combinations as (nAmbiguousAngles)-ary
% numbers from 00...0 to NN...N to index all possible combinations
Nperms=nAmbiguousAngles^b1map_params.b1proc.Nonominalvalues;
Y_sd = zeros([V_SE(1).dim(1:2) Nperms]);
Y_mn = zeros([V_SE(1).dim(1:2) Nperms]);
for i = 1:Nperms
perm=(dec2base(i-1, nAmbiguousAngles, b1map_params.b1proc.Nonominalvalues)-'0') + 1; % difference between char 'N' and char '0' is integer N
idxs=sub2ind([b1map_params.b1proc.Nonominalvalues,nAmbiguousAngles],1:b1map_params.b1proc.Nonominalvalues,perm);
Y_sd(:,:,i) = std(real(real_Y_tmp(:,:,idxs)),[],3); % real part chosen to mitigate noise problems
Y_mn(:,:,i) = mean(real(real_Y_tmp(:,:,idxs)),3);
end
[~,min_index] = min(Y_sd,[],3); % !! min_index is a 2D array. Size given by resolution along read and phase directions
for x_nr = 1:V_SE(1).dim(1)
for y_nr = 1:V_SE(1).dim(2)
% Y_mn_out is the relative flip angle value averaged over the
% Nonominalvalues flip angles (determined by minimising the SD,
% i.e. keeping the most uniform relative flip angle values)
Y_mn_out(x_nr,y_nr,p) = Y_mn(x_nr,y_nr, min_index(x_nr,y_nr));
% Y_sd_out is the corresponding standard deviation between the
% relative flip angle values
Y_sd_out(x_nr,y_nr,p) = Y_sd(x_nr,y_nr, min_index(x_nr,y_nr));
end
end
spm_progress_bar('Set',p);
end
%-Save everything in OUTPUT dir
%-----------------------------------------------------------------------
% define generic output header
input_files = b1map_params.b1input;
Output_hdr = init_b1_output_metadata(input_files, b1map_params);
Output_hdr.history.procstep.descrip = [Output_hdr.history.procstep.descrip ' (EPI SE/STE protocol)'];
% save B1 map (still distorted and not smoothed)
Output_hdr.history.output.imtype = 'SE/STE B1 mapping - Distorted B1+ map';
Output_hdr.history.output.units = 'p.u.';
V_save = struct('fname',V_SE(1).fname,'dim',V_SE(1).dim,'mat',V_SE(1).mat,'dt',V_SE(1).dt,'descrip','B1 map [%]');
[~,outname,e] = fileparts(V_save.fname);
V_save.fname = fullfile(outpath,['B1map_' outname e]);
V_save = spm_write_vol(V_save,Y_mn_out*100);
set_metadata(V_save.fname,Output_hdr,json);
% save SD map (still distorted and not smoothed)
Output_hdr.history.output.imtype = 'SE/STE B1 mapping - Distorted SD (error) map';
Output_hdr.history.output.units = 'p.u.';
W_save = struct('fname',V_SE(1).fname,'dim',V_SE(1).dim,'mat',V_SE(1).mat,'dt',V_SE(1).dt,'descrip','SD [%]');
W_save.fname = fullfile(outpath,['SDmap_' outname e]);
W_save = spm_write_vol(W_save,Y_sd_out*100);
set_metadata(W_save.fname,Output_hdr,json);
% save SD map (still distorted and not smoothed)
Output_hdr.history.output.imtype = 'SE/STE B1 mapping - SSQ image';
Output_hdr.history.output.units = 'a.u.';
X_save = struct('fname',V_SE(1).fname,'dim',V_SE(1).dim,'mat',V_SE(1).mat,'dt',V_SE(1).dt,'descrip','SE SSQ matrix');
X_save.fname = fullfile(outpath,['SumOfSq' outname e]);
X_save = spm_write_vol(X_save,Ssq_matrix); %#ok<*NASGU>
set_metadata(X_save.fname,Output_hdr,json);
%-B0 undistortion
%-----------------------------------------------------------------------
% since B0 data will be coregistered and resliced with the B1 data, we copy
% them into the calcpath directory to avoid altering the the raw data:
Qtmp = cell(size(b0input,1),1);
for i=1:size(b0input,1)
Qtmp{i} = fullfile(outpath, spm_file(b0input(i,:), 'filename'));
copyfile(deblank(b0input(i,:)), Qtmp{i});
try copyfile([spm_str_manip(deblank(b0input(i,:)),'r') '.json'],[spm_str_manip(Qtmp{i},'r') '.json']); end %#ok<*TRYNC>
end
b0input = char(Qtmp);
% magnitude image
% NOTE: must strip the ',1' (at the end of the file extension '.nii,1')!!
magfnam = spm_file(b0input(1,:),'number','');
% phase image
phasefnam = spm_file(b0input(3,:),'number','');
% both fieldmap images
fmfnam = char(phasefnam,magfnam);
% image to be corrected ("anatomical" reference = SSQ image)
anatfnam = X_save.fname;
% other images to be corrected (distorted B1 and SD maps)
otherfnam{1} = V_save.fname;
otherfnam{2} = W_save.fname;
% unwarp
[fmap_img,unwarp_img] = hmri_create_B1Map_unwarp(fmfnam, anatfnam, otherfnam, b1map_params);
uanat_img{1} = unwarp_img{1}.fname;
ub1_img{1} = unwarp_img{2}.fname;
ustd_img{1} = unwarp_img{3}.fname;
% set metadata for unwrapped output images
% define generic header for B0-unwarp process
scphasefnam = fullfile(b1map_params.outpath, spm_file(spm_file(fmfnam(2,:),'prefix','sc'),'filename'));
% relate outputs to inputs remaining visible after cleanup! i.e. original
% B1 and B0 mapping images (not to the intermediate images created
% during B1 calculation):
% input_files = cat(1,{anatfnam},{fmfnam(1,:)},{fmfnam(2,:)},otherfnam{1},otherfnam{2});
input_files = char(b1map_params.b1input,b1map_params.b0input);
Output_hdr = init_b1_output_metadata(input_files, b1map_params);
Output_hdr.history.procstep.descrip = [Output_hdr.history.procstep.descrip ' (EPI SE/STE protocol)'];
% set metadata for unwarped B1 image
Output_hdr.history.output.imtype = 'SE/STE B1 mapping - Unwarped B1 map';
Output_hdr.history.output.units = 'p.u.';
set_metadata(ub1_img{1},Output_hdr,json);
% set metadata for unwarped SD map
Output_hdr.history.output.imtype = 'SE/STE B1 mapping - Unwarped SD (error) map';
Output_hdr.history.output.units = 'p.u.';
set_metadata(ustd_img{1},Output_hdr,json);
% set metadata for unwarped SSQ map
Output_hdr.history.output.imtype = 'SE/STE B1 mapping - Unwarped SSQ image for anatomical reference';
Output_hdr.history.output.units = 'a.u.';
set_metadata(uanat_img{1},Output_hdr,json);
% set metadata for phase-unwrapped regularised field map (Hz) (fpm_* file)
Output_hdr.history.output.imtype = 'SE/STE B1 mapping - Phase-unwrapped regularised field map';
Output_hdr.history.output.units = 'Hz';
set_metadata(fmap_img{1}.fname,Output_hdr,json);
% set metadata for Voxel Displacement Map (vdm5_* file)
Output_hdr.history.output.imtype = 'SE/STE B1 mapping - Voxel displacement map';
Output_hdr.history.output.units = 'Vx';
set_metadata(fmap_img{2}.fname,Output_hdr,json);
% set metadata for phase map scaled between +/-pi (sc* file)
Output_hdr.history.output.imtype = 'SE/STE B1 mapping - Phase map rescaled between [-pi, pi]';
Output_hdr.history.output.units = 'Radians';
set_metadata(scphasefnam,Output_hdr,json);
%-B1 map processing (masking, padding, smoothing, ...)
%--------------------------------------------------------------------------
fpm_img{1} = fmap_img{1};
vdm_img{1} = fmap_img{2};
[allub1_img] = hmri_create_B1Map_process(ub1_img,ustd_img,vdm_img,fpm_img,b1map_params);
% set metadata for processing B1 images
% define generic header for B1 process
% relate outputs to inputs remaining visible after cleanup! i.e. original
% B1 and B0 mapping images (not to the intermediate images created
% during B1 calculation):
% input_files = cat(1,ub1_img,ustd_img,vdm_img{1}.fname,fpm_img{1}.fname);
input_files = char(b1map_params.b1input,b1map_params.b0input);
Output_hdr = init_b1_output_metadata(input_files, b1map_params);
Output_hdr.history.procstep.descrip = [Output_hdr.history.procstep.descrip ' (EPI SE/STE protocol)'];
% set metadata for each output
for i=1:length(allub1_img)
Output_hdr.history.output.imtype = ['SE/STE B1 mapping - ' allub1_img{i}.descrip];
Output_hdr.history.output.units = 'p.u.';
set_metadata(allub1_img{i}.fname,Output_hdr,json);
end
% set correct output for the current subfunction (unwrapped "anatomical"
% image (SSQ) for coregistration and final B1 map). For coherence among B1
% protocol, rename these files *_B1ref (for anatomical reference) and
% *_B1map (for B1+ bias map in p.u.):
B1map = fullfile(outpath,[outname '_B1map.nii']);
copyfile(allub1_img{2}.fname, B1map);
try copyfile([spm_str_manip(allub1_img{2}.fname,'r') '.json'],[spm_str_manip(B1map,'r') '.json']); end
B1ref = fullfile(outpath,[outname '_B1ref.nii']);
copyfile(uanat_img{1}, B1ref);
try copyfile([spm_str_manip(uanat_img{1},'r') '.json'],[spm_str_manip(B1ref,'r') '.json']); end
P_trans = char(B1ref, B1map);
end
%% =======================================================================%
% B1 map scaling
% Written by Tobias Leutritz; adapted by Luke Edwards
%=========================================================================%
function P_trans = calc_scaled_b1map(jobsubj, b1map_params, offset, scaling, descrip)
json = hmri_get_defaults('json');
P = b1map_params.b1input(2,:); % scaled FA map
Q = b1map_params.b1input(1,:); % anatomical image
% read header information and volumes
V1 = spm_vol(P); % image volume information
V2 = spm_vol(Q);
input_files = cat(1,{V2.fname},{V1.fname}); % for metadata
Vol1 = spm_read_vols(V1);
% determine output directory path
outpath = jobsubj.path.b1path;
b1map_params.outpath = outpath;
% copy anatomical image to outpath to prevent modification of original data
anat_fname = fullfile(outpath, [spm_file(V2.fname, 'basename') '_B1ref.nii']);
copyfile(V2.fname, anat_fname);
try copyfile([spm_str_manip(V2.fname,'r') '.json'],[spm_str_manip(anat_fname,'r') '.json']); end %#ok<*TRYNC>
V2 = spm_vol(anat_fname);
% generating the map
B1map_norm = (abs(Vol1)+offset)*scaling;
% masking; mask is written out to folder of the anatomical image
% (this should be outpath due to copying the anatomical file above)
mask = mask_for_B1(V2,b1map_params.b1mask);
% smoothed map
smB1map_norm = smoothB1(V1,B1map_norm,b1map_params.b1proc.B1FWHM,mask);
% Save B1map in OUTPUT dir
%-----------------------------------------------------------------------
sname = spm_file(V1.fname,'basename');
VB1 = V1;
VB1.pinfo(1) = max(smB1map_norm(:))/spm_type(VB1.dt(1),'maxval');
VB1.fname = fullfile(outpath, [sname '_B1map.nii']);
VB1.descrip = ['B1+ map - smoothed ( ' sprintf('%d ',b1map_params.b1proc.B1FWHM) 'mm ) and normalised (p.u.) - ' descrip];
spm_write_vol(VB1,smB1map_norm);
% set and write metadata
Output_hdr = init_b1_output_metadata(input_files, b1map_params);
Output_hdr.history.procstep.descrip = [Output_hdr.history.procstep.descrip ' (' descrip ')'];
set_metadata(VB1.fname,Output_hdr,json);
% requires anatomical image + map
P_trans = char(char(anat_fname),char(VB1.fname));
end
%% =======================================================================%
% Determine whether b1 data are available and whether any processing should
% be applied. If so, all the required parameters for b1map calculation are
% retrieved, including b1map and b0map acquisition parameters and
% processing parameters, if applicable. Check whether input data are
% coherent with the processing type selected. Missing parameters will be
% retrieved from the hmri_get_defaults.
%=========================================================================%
function b1map_params = get_b1map_params(jobsubj)
% retrieve b1 protocol from job
% (can be different - a variation of - the b1 type)
f = fieldnames(jobsubj.b1_type);
b1_protocol = f{1};
% pre-set filename of defaults file
deffnam = '';
custom_def = false;
% load customized defaults parameters from customized defaults file if any
% (the customized defaults file must be run to overwrite the standard
% defaults parameters)
if isfield(jobsubj.b1_type.(b1_protocol),'b1parameters')
% first reinitialise processing parameters to standard defaults:
hmri_b1_standard_defaults;
deffnam = fullfile(fileparts(mfilename('fullpath')),'config','hmri_b1_standard_defaults.m');
custom_def = false;
% then, if customized defaults file available, run it to overwrite
% standard defaults parameters.
if isfield(jobsubj.b1_type.(b1_protocol).b1parameters,'b1defaults')
deffnam = jobsubj.b1_type.(b1_protocol).b1parameters.b1defaults;
spm('Run',deffnam);
custom_def = true;
end
end
% load all B1 bias correction defaults parameters & add default file
b1map_params = hmri_get_defaults(['b1map.' b1_protocol]);
b1map_params.defaults_file = deffnam;
b1map_params.custom_defaults = custom_def;
% flags for logging information and warnings
b1map_params.defflags = jobsubj.log.flags; % default flags
b1map_params.nopuflags = jobsubj.log.flags; % force no Pop-Up
b1map_params.nopuflags.PopUp = false;
hmri_log(sprintf('\t------------ B1 MAP CALCULATION (%s) %s ------------',b1_protocol, datetime('now')),b1map_params.nopuflags);
% save SPM version (slight differences may appear in the results depending
% on the SPM version!)
[v,r] = spm('Ver');
b1map_params.SPMver = sprintf('%s (%s)', v, r);
% load B1 input images if any
% (NB: if a 'b1input' field is present, it should NOT be empty)
if isfield(jobsubj.b1_type.(b1_protocol),'b1input')
b1map_params.b1input = char(spm_file(jobsubj.b1_type.(b1_protocol).b1input,'number',''));
if isempty(b1map_params.b1input)
hmri_log(sprintf(['WARNING: expected B1 input images missing. Switching to "no \n' ...
'\tB1 correction" mode. If you meant to apply B1 bias correction, \n' ...
'\tcheck your data and re-run the batch.']),b1map_params.defflags);
b1_protocol = 'no_B1_correction';
b1map_params = hmri_get_defaults('b1map.no_B1_correction');
end
end
% load B0 input images if any
% (NB: if a 'b0input' field is present, it may be empty)
if isfield(jobsubj.b1_type.(b1_protocol),'b0input')
b1map_params.b0input = char(spm_file(jobsubj.b1_type.(b1_protocol).b0input,'number',''));
if isempty(b1map_params.b0input)
% hmri_log(sprintf(['WARNING: expected B0 fieldmap not available for EPI undistortion.\n' ...
% '\tNo fieldmap correction will be applied.']),b1map_params.defflags);
% b1map_params.b0avail = false;
hmri_log(sprintf(['WARNING: expected B0 fieldmap not available for EPI undistortion.\n' ...
'\tThe current implementation does not allow you to apply EPI-based B1 bias \n' ...
'\tcorrection without phase unwrapping. Switching to "no B1 correction" mode.\n' ...
'\tIf you meant to apply B1 bias correction, check your data and re-run the batch.']),b1map_params.defflags);
b1_protocol = 'no_B1_correction';
b1map_params = hmri_get_defaults('b1map.no_B1_correction');
end
end
% process job inputs according to B1 type
switch b1_protocol
case 'UNICORT'
hmri_log(sprintf('No B1 map available. UNICORT will be applied.'),b1map_params.nopuflags);
case 'no_B1_correction'
hmri_log(sprintf('No B1 map available. No B1 correction applied (semi-quantitative maps only)'),b1map_params.nopuflags);
case 'pre_processed_B1'
b1map_params.scafac = jobsubj.b1_type.(b1_protocol).scafac;
if ~isempty(b1map_params.b1input)
if b1map_params.scafac == 1
hmri_log(sprintf('Preprocessed B1 map available. \nAssuming it is in percent units of the nominal flip angle. \nNo calculation required.'),b1map_params.defflags);
else
hmri_log(sprintf('Preprocessed B1 map available. \nScaling factor provided: %f. Assuming B1 map will be expressed \nin p.u. of the nominal flip angle after rescaling.', b1map_params.scafac),b1map_params.defflags);
end
end
case 'i3D_EPI'
if ~isempty(b1map_params.b1input)
hmri_log(sprintf('SE/STE EPI protocol selected ...'),b1map_params.nopuflags);
b1hdrFile = b1map_params.b1input(1,:);
V = spm_vol(b1map_params.b1input);
assert(rem(length(V),2)==0, ...
['B1 mapping image volumes must be a set of SE, STE pairs ' ...
'thus the number of input volumes (currently %d) must be even.'], length(V));
% splitting images into SE and STE volumes
% assumes conventional hMRI toolbox order as default but checks this order
% when echo times are defined and b1validation.checkTEs is true
% Echo times for input validation
tmp = get_metadata_val(b1hdrFile,'EchoTime');
b1map_params.b1acq.EchoTimes=[];
if b1map_params.b1validation.checkTEs
if isempty(tmp)
hmri_log(sprintf('WARNING: no echo times found for SE/STE input;\ninput validation based on echo time will not be performed'),b1map_params.defflags);
b1map_params.b1validation.checkTEs = false;
else
b1map_params.b1acq.EchoTimes=zeros(1,size(b1map_params.b1input,1));
for n=1:size(b1map_params.b1input,1)
b1map_params.b1acq.EchoTimes(n) = get_metadata_val(b1map_params.b1input(n,:),'EchoTime');
end
end
end
EchoTimes=b1map_params.b1acq.EchoTimes;
if b1map_params.b1validation.checkTEs && ~isempty(EchoTimes) % check echo times defined
uEchoTimes=unique(EchoTimes);
switch length(uEchoTimes)
case 2
% shorter TE assumed to be SE, longer STE.
% flip angle pairs are assumed to be in the order given in
% b1map_params.b1acq.beta
V_SE = V(b1map_params.b1acq.EchoTimes == min(uEchoTimes));
V_STE = V(b1map_params.b1acq.EchoTimes == max(uEchoTimes));
case 1 % assume conventional hMRI toolbox order but warn
hmri_log(sprintf(...
['WARNING: expected 2 different echo times (corresponding to\n' ...
'spin echo and stimulated echo) in 3D EPI input data, but\n' ...
'all data have the same echo time. Standard input order will\n' ...
'be assumed, but it is recommended to check this is correct.']),...
b1map_params.defflags);
V_SE = V(1:2:end);
V_STE = V(2:2:end);
otherwise % assume conventional hMRI toolbox order but warn
hmri_log(sprintf(...
['WARNING: expected 2 different echo times (corresponding to\n' ...
'spin echo and stimulated echo) in 3D EPI input data, but\n' ...
'there are %i different echo times. Standard input order will\n' ...
'be assumed, but it is recommended to check this is correct.'],...
length(uEchoTimes)),b1map_params.defflags);
V_SE = V(1:2:end);
V_STE = V(2:2:end);
end
else
% assume conventional hMRI toolbox order as default in absence of other
% information or when TE check is disabled
V_SE = V(1:2:end);
V_STE = V(2:2:end);
end
assert(length(V_SE) == length(V_STE), ...
['Number of spin echo volumes (%d) does not match the number of' ...
'stimulated echo volumes (%d)!'], length(V_SE), length(V_STE));
if b1map_params.b1validation.useBidsFlipAngleField
tmp = get_metadata_val(b1hdrFile,'FlipAngle');
FA_SE = zeros(1,length(V_SE));
FA_STE = FA_SE;
if ~isempty(tmp)&&tmp~=0
for n = 1:length(V_SE)
FA_SE(n) = get_metadata_val(V_SE(n).fname, 'FlipAngle');
FA_STE(n) = get_metadata_val(V_STE(n).fname, 'FlipAngle');
end
else
hmri_log('WARNING: "useBidsFlipAngleField" is true but FlipAngle is empty or zero', ...
b1map_params.defflags);
end
assert(all(sort(FA_SE)==sort(FA_STE)),'the set of SE and STE flip angles must be identical!')
if any([FA_SE(:),FA_STE(:)]==0)
hmri_log('WARNING: zero flip angles detected in SE/STE metadata. This is probably not correct.', ...
b1map_params.defflags);
end
% make sure that SE and STE volumes are in the correct
% order. Note that calc_SESTE_b1map expects fa in
% decreasing order
[b1map_params.b1acq.beta, fa_order] = sort(FA_SE, 'descend');
V_SE = V_SE(fa_order);
[~, fa_order] = sort(FA_STE, 'descend');
V_STE = V_STE(fa_order);
else
tmp = get_metadata_val(b1hdrFile,'B1mapNominalFAValues');
if isempty(tmp)
hmri_log(sprintf('WARNING: using defaults value for nominal SE/STE flip angle values \n(%s) instead of metadata', ...
sprintf('%d ',b1map_params.b1acq.beta)),b1map_params.defflags);
else
b1map_params.b1acq.beta = tmp;
end
end
assert(length(V_SE) == numel(b1map_params.b1acq.beta), ...
['Number of B1 mapping image pairs (%d) does not match ' ...
'the number of nominal flip angles (%d)!'], ...
length(V_SE), numel(b1map_params.b1acq.beta));
b1map_params.SEinput = char({V_SE.fname}');
b1map_params.STEinput = char({V_STE.fname}');
tmp = get_metadata_val(b1hdrFile,'B1mapMixingTime');
if isempty(tmp)
hmri_log(sprintf('WARNING: using defaults value for mixing time \n(%d ms) instead of metadata', ...
b1map_params.b1acq.TM),b1map_params.defflags);
else
b1map_params.b1acq.TM = tmp;
end
tmp = get_metadata_val(b1hdrFile,'epiReadoutDuration'); % must take into account PAT but not PF acceleration
if isempty(tmp)
hmri_log(sprintf('WARNING: using defaults value for EPI readout duration\n(%d ms) instead of metadata', ...
b1map_params.b1acq.tert),b1map_params.defflags);
else
b1map_params.b1acq.tert = tmp;
end
tmp = get_metadata_val(b1hdrFile,'PhaseEncodingDirectionSign');
if isempty(tmp)
hmri_log(sprintf('WARNING: using defaults value for PE direction\n(%d) instead of metadata', ...
b1map_params.b1acq.blipDIR),b1map_params.defflags);
else
b1map_params.b1acq.blipDIR = tmp;
end
% consistency check for T1 value and field strength:
tmp = get_metadata_val(b1hdrFile,'MagneticFieldStrength');
supportedB0 = false;
matchT1fieldstrength = false;
if ~isempty(tmp)
switch round(tmp)
case 3
supportedB0 = true;
expectedT1 = 1192;
case 7
supportedB0 = true;
expectedT1 = 1633;
otherwise
supportedB0 = false;
expectedT1 = NaN;
end
if b1map_params.b1proc.T1 == expectedT1
matchT1fieldstrength = true;
end
if ~supportedB0
hmri_log(sprintf(['WARNING: field strength (B0 = %.0fT) not supported. The reference T1' ...
'\nvalue for B1 map calculation for that field strength is not currently ' ...
'\nimplemented in the hMRI-toolbox. Please make sure the assumed ' ...
'\nvalue (T1 = %.0f ms) is correct, otherwise set it via a customised ' ...
'\nB1 default file (config/local/hmri_b1_local_defaults.m).' ...
'\nIf the value is already properly set, just ignore this message.'], ...
tmp, b1map_params.b1proc.T1),b1map_params.defflags);
else
if ~matchT1fieldstrength && custom_def
hmri_log(sprintf(['WARNING: the assumed T1 value for B1 map calculation does not ' ...
'\nmatch the expected value for the used field strength: ' ...
'\n B0 = %.0fT, T1 = %d/%d (expected/actual) ms.' ...
'\n\nPlease check T1 value is properly set in your local settings ' ...
'\n(see hmri_def.b1map.i3D_EPI.b1proc.T1 in your customised ' ...
'\n%s config file).' ...
'\n\nRecommended values are: ' ...
'\n - @3T: T1 = 1192 ms' ...
'\n - @7T: T1 = 1633 ms' ...
'\n\nIf the value was set differently on purpose, just ignore this message.'], ...
tmp, expectedT1, b1map_params.b1proc.T1, char(spm_file(deffnam,'filename'))), b1map_params.defflags);
elseif ~matchT1fieldstrength && ~custom_def
hmri_log(sprintf(['WARNING: the assumed T1 value for B1 map calculation ' ...
'\nhas been set to match the used field strength: ' ...
'\n B0 = %.0fT, T1 = %d ms.' ...
'\n\nPlease consider properly setting the T1 value uing a local ' ...
'\ndefaults file (see config/local/hmri_b1_local_defaults.m ' ...
'\nand parameter hmri_def.b1map.i3D_EPI.b1proc.T1 therein).' ...
'\n\nRecommended values are: ' ...
'\n - @3T: T1 = 1192 ms' ...
'\n - @7T: T1 = 1633 ms'], ...
tmp, expectedT1),b1map_params.defflags);
b1map_params.b1proc.T1 = expectedT1;
end
end
b1map_params.b1proc.matchT1fieldstrength = matchT1fieldstrength;
b1map_params.b1proc.expectedT1 = expectedT1;
end
if ~isempty(b1map_params.b0input)
% note that the current implementation assumes that
% b0 input images = 2 magnitude images (1st and 2nd
% echoes) and 1 presubtracted phase image.
tmp = get_metadata_val(b1map_params.b0input(1,:),'EchoTime');
if isempty(tmp)
hmri_log(sprintf('WARNING: using defaults value for B0 mapping TEs\n(short TE=%.2fms) instead of metadata', ...
b1map_params.b0acq.shortTE),b1map_params.defflags);
else
b1map_params.b0acq.shortTE = tmp;
end
tmp = get_metadata_val(b1map_params.b0input(2,:),'EchoTime');
if isempty(tmp)
hmri_log(sprintf('WARNING: using defaults value for B0 mapping TEs\n(long TE=%.2fms) instead of metadata', ...
b1map_params.b0acq.longTE),b1map_params.defflags);
else
b1map_params.b0acq.longTE = tmp;
end
b1map_params.b0acq.iformat = 'PM';
end
end
case 'i3D_AFI'
if ~isempty(b1map_params.b1input)
hmri_log(sprintf('AFI protocol selected ...'),b1map_params.nopuflags);
b1hdrFile{1} = b1map_params.b1input(1,:);
b1hdrFile{2} = b1map_params.b1input(2,:);
try
tr1 = get_metadata_val(b1hdrFile{1},'RepetitionTime');
tr2 = get_metadata_val(b1hdrFile{2},'RepetitionTime');
if ~isempty(tr1) && ~isempty(tr2) && tr1~=tr2 % BIDS-like data
b1map_params.b1acq.TR2TR1ratio = tr2/tr1;
else % Use Siemens-style metadata or b1-defaults file value
hmri_log('WARNING: the two repetition times in the AFI B1-mapping metadata are missing or equal. Trying the RepetitionTimes (alTR) field...',b1map_params.defflags);
trList = get_metadata_val(b1hdrFile{1},'RepetitionTimes');
if isempty(trList) % Use b1-defaults file value
assert(b1map_params.b1acq.TR2TR1ratio~=1,'The TR2TR1ratio is not allowed to be 1 in an AFI B1-mapping acquisition! Check the input configuration file.')
hmri_log(sprintf('WARNING: using defaults values for\n(TR ratio = %.1f) instead of metadata', ...
b1map_params.b1acq.TR2TR1ratio),b1map_params.defflags);
else % Use Siemens-style metadata
assert(trList(2)~=trList(1),'The two repetition times (TRs) are not allowed to be equal in an AFI B1-mapping acquisition! Check the input data.')
b1map_params.b1acq.TR2TR1ratio = trList(2)/trList(1);
end
end
tmp = get_metadata_val(b1hdrFile{1},'FlipAngle');
if isempty(tmp)
hmri_log(sprintf('WARNING: using defaults value for flip angle \n(%d deg) instead of metadata', ...
b1map_params.b1acq.alphanom), b1map_params.defflags);
else
b1map_params.b1acq.alphanom = tmp;
end
catch
hmri_log(sprintf(['WARNING: possibly no metadata associated with the input images. \n' ...
'Default acquisition and processing parameters will be used.']),b1map_params.defflags);
end
end
case 'DAM'
if ~isempty(b1map_params.b1input)
hmri_log(sprintf('DAM protocol selected ...'),b1map_params.nopuflags);
try
fa1 = get_metadata_val(b1map_params.b1input(2,:),'FlipAngle');
fa1=fa1{1};
if isempty(fa1)
hmri_log(sprintf('WARNING: using defaults values for flip angle\n(FA = %d deg) instead of metadata', ...
b1map_params.b1acq.alphanom),b1map_params.defflags);
else
b1map_params.b1acq.alphanom = fa1;
% Check whether flip angles match
fa2 = get_metadata_val(b1map_params.b1input(1,:),'FlipAngle');
fa2=fa2{1};
if ~isempty(fa2)
if fa2~=(2*fa1)
hmri_log(sprintf([...
'WARNING: detected flip angle from the metadata of the \n' ...
'first DAM B1 volume (%d deg) is not 2x the detected \n' ...
'flip angle for the second DAM B1 volume (%d deg).\n'...
'Please check the input data carefully.'],fa2,fa1),...
b1map_params.defflags);
end
end
end
catch
hmri_log(sprintf(['WARNING: possibly no metadata associated to the input images. \n' ...
'Default acquisition and processing parameters will be used.']),b1map_params.defflags);
end
end
case 'tfl_b1_map'
if ~isempty(b1map_params.b1input)
hmri_log(sprintf('SIEMENS tfl_b1map protocol selected ...'),b1map_params.nopuflags);
end
case 'rf_map'
if ~isempty(b1map_params.b1input)
hmri_log(sprintf('SIEMENS rf_map protocol selected ...'),b1map_params.nopuflags);
end
otherwise