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ps_LST_long.m
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function varargout = ps_LST_longX(varargin)
%ps_LST_long Longitudinal lesion segmentation.
% Part of the LST toolbox, www.statistical-modeling.de/lst.html
%
% ps_LST_long quantifies the change in lesion structure between different
% lesion probability maps. The pipeline proceeds by comparing all
% consecutive time points in an iterative manner. It decides if changes
% in lesion structure are significant or due to natural variations of the
% FLAIR signal. Non-significant changes are labeled as lesions in both
% probability maps, thus, probability lesion maps are corrected within
% this procedure and may differ from the ones that served as input. As a
% final result, lesion change labels are produced for all consecutive
% time points. In these images the three possible cases decrease, no
% change and increase are labeled by the numbers 1, 2, and 3,
% repsectively.
%
% The longitudinal pipeline works through the following steps:
% 1) Filling of
% (a) T1 images for all time points if LGA was used.
% (b) FLAIR images for all time points if LGA was used without
% reference images.
% (c) reference images for all time points if LGA was used with
% reference images.
% 2) Coregistration of the filled image for time point t + 1 to time
% point t, for t = 1, ..., m - 1. The estimated coregistrations
% are then applied to (FLAIR(t+1)) and (ples(t+1)).
% 3) Analyzation of relative change in FLAIR intensity
% (FLAIR(t) - FLAIR(t+1)) / ((FLAIR(t) + FLAIR(t+1)) / 2) in
% healthy WM in order to obtain the amount of normal/random deviation.
% 4) Information of 3) is used to threshold relative change in FLAIR
% intensity along observed lesions.
%
% As a result this pipeline produces the following output:
% lples_[].nii ... probability lesion map for all time points after
% including all information in the segmentation process.
% Here, [] is either lga_[kappa]_FLAIR(t) for LGA or l
% pa_namFLAIR(t+1) for LPA. All lesion maps are in the
% same space as the image for t = 1. The 'l' indicates
% 'longitudinal'.
% LCL_[].nii ... lesion change label, i.e. an image in the same space
% as the first image that indicates if lesions
% disapeared (1), remain constant (2), or appeared new
% (3). Here, [] is something like
% [LGA/LPA]_FLAIR(t)_FLAIR(t+1)
% report_LST_long_[] ... A HTML report of the segmentation if sepcified
% by the user.
% LST_long_[] ... a folder that contains a report (HTML) along with some
% images.
%
% ps_LST_long(m) asks the user for the lesion probability (lesion
% probability maps computed by LGA or LPA, but not both) maps of the m
% time points.
% ps_LST_long(m, html) same as above but with the possibility to
% deactivate the creation of the HTML report.
%
% ps_LST_long(job) Same as above but with job being a harvested job data
% structure (see matlabbatch help).
%
% Welcome text
fprintf('\n')
fprintf(repmat('-', 1, 72));
fprintf('\n')
%fprintf('\nThis is LST')
strout = 'This is LST';
fprintf(strout)
tt = 'www.statistical-modeling.de/lst.html\n';
strout = [repmat(' ', 1, 72 - numel(tt) - numel(strout) + 2), tt];
fprintf(strout)
strout = 'Algorithm:';
fprintf(strout)
tt = 'Longitudinal segmentation\n';
strout = [repmat(' ', 1, 72 - numel(tt) - numel(strout) + 2), tt];
fprintf(strout)
% Create log file
pthor = cd;
nameLog = ['LST_log_', ps_create_timestamp, '.txt'];
fileID = fopen(nameLog, 'wt');
strout = 'If anything goes wrong:';
fprintf(strout)
tt = [nameLog, '\n'];
strout = [repmat(' ', 1, 72 - numel(tt) - numel(strout) + 2), tt];
fprintf(strout)
% Check input
if ~isempty(varargin) && isfield(varargin{1}, 'data_long_tmp')
viajob = 1;
else
viajob = 0;
end
if ~viajob
if nargin == 0
fprintf('I need at least the number of time points!\n');
fclose(fileID);
spm_unlink(nameLog);
return;
end
if nargin > 2
fprintf('Wrong number of input parameters!\n');
fclose(fileID);
spm_unlink(nameLog);
return;
else
% If function is called without a harvested job data structure input
% must be a scalar that gives the number of time points.
if isnumeric(varargin{1})
fprintf(fileID, 'Select files by function ... ');
m = varargin{1};
Vles = cell(m, 1);
for j = 1:m
Vles{j} = spm_select(Inf, 'image', ['Select lesion probability maps for t = ', num2str(j)]);
end
fprintf(fileID, 'ok.\n');
else
if iscell(varargin{1})
Vles = varargin{1};
m = numel(Vles);
else
fprintf(['Input for this function must either be a harvested job ', ...
'data structure, a numeric value, or a cell with cells of ', ...
'image names.\n']);
fclose(fileID);
spm_unlink(nameLog);
return;
end
end
if nargin > 1
html_report = varargin{2};
else
html_report = 1;
end
end
else
job = varargin{1};
Vles = job.data_long_tmp;
html_report = job.html_report;
m = numel(Vles);
end
fprintf(fileID, 'Load volume header ... ');
Vles = spm_vol(Vles);
fprintf(fileID, 'ok.\n');
%Vles{1}
%numel(Vles{1})
%arrayfun(@(x) numel(Vles{x}), (1:m))
% Check if all time points have the same number of images
if ~all(cellfun(@numel, Vles) == numel(Vles{1}))
fprintf('Number of images for all time points must match.\n');
fclose(fileID);
spm_unlink(nameLog);
return;
end
if numel(Vles{1}) == 0
fprintf('No images selected.\n');
fclose(fileID);
spm_unlink(nameLog);
return;
end
fprintf(fileID, 'Longitudinal segmentation\n');
% Summarize input
fprintf(fileID, 'Input summary:\n');
fprintf(fileID, ['Jobs: ', num2str(numel(Vles{1})), '\n']);
strout = 'Number of jobs to process:';
fprintf(strout)
tt = [num2str(numel(Vles{1})), '\n'];
strout = [repmat(' ', 1, 72 - numel(tt) - numel(strout) + 2), tt];
fprintf(strout)
fprintf(fileID, ['Time points: ', num2str(m), '\n']);
strout = 'Number of time points:';
fprintf(strout)
tt = [num2str(m), '\n'];
strout = [repmat(' ', 1, 72 - numel(tt) - numel(strout) + 2), tt];
fprintf(strout)
% Loop over all subjects
for i = 1:numel(Vles{1})
fprintf(fileID, '\n******************************\n');
fprintf(fileID, ['Job ', num2str(i), ' of ', num2str(numel(Vles{1})), '\n']);
fprintf(fileID, '*******************************\n');
% Which subject?
strout = '\nWorking on job';
fprintf(strout)
tt = [num2str(i), ' out of ', num2str(numel(Vles{1})), ' (', num2str(i/numel(Vles{1})*100), '%%)\n'];
strout = [repmat(' ', 1, 72 - numel(tt) - numel(strout) + 5), tt];
fprintf(strout)
% Extract names of the ith subject
Vles_tmp = cell(m, 1);
pthles = Vles_tmp; namles = pthles; extles = pthles;
for j = 1:m
if viajob
Vles_tmp{j} = Vles{j}{i};
else
Vles_tmp{j} = Vles{j}(i);
end
[pthles{j}, namles{j}, extles{j}] = fileparts(Vles_tmp{j}.fname);
end
% ---------------------------------------------------------------------
% Preprocessing
% ---------------------------------------------------------------------
% Check weather lga or lpa was used for lesion segmentation.
ch_lga = cellfun(@(x) ~isempty(regexp(x, '_lga_') > 0), namles);
if ~all(ch_lga == ch_lga(1))
fprintf('Images are not from the same lesion segmentation algorithm.\n');
fclose(fileID);
spm_unlink(nameLog);
return;
end
% Get some information about the lesion segmentation
if ch_lga(1)
% get FLAIR names
alg_text = 'LGA';
us_pos = cellfun(@(x) regexp(x, '_'), namles, 'UniformOutput', false);
namf2 = arrayfun(@(x) namles{x}((us_pos{x}(3)+1):end), 1:m, 'UniformOutput', false);
% lga.mat files
lst = cell(m, 1);
for j = 1:m
cd(pthles{j})
load(['LST_lga_', namf2{j}, '.mat'])
lst{j} = lga;
end
cd(pthles{1})
% name of images that need to be filled/coregistered
namcoreg = cellfun(@(x) x.Vt1.fname, lst, 'UniformOutput', false);
%for j = 1:numel(lst)
% namcoreg{j} = [ps_fileparts(namcoreg{j}, 1:2), '_', num2str(j), ps_fileparts(namcoreg{j}, 3)];
%end
% Create folder for report and stuff
nameFolder = ['LST_long_lga_', num2str(m), '_', ps_create_timestamp];
mkdir(nameFolder)
% write p0 for t = 2 , ..., t = m
for j = 1:m
p0 = zeros(lst{j}.Vt1.dim); p0(lst{j}.indx_brain) = lst{j}.p0_vec;
Vp0 = lst{j}.Vt1; Vp0.fname = fullfile(nameFolder, ['p0_', num2str(j), '.nii']);
spm_write_vol(Vp0, p0);
end
else
% get FLAIR names
alg_text = 'LPA';
us_pos = cellfun(@(x) regexp(x, '_'), namles, 'UniformOutput', false);
namf2 = arrayfun(@(x) namles{x}((us_pos{x}(2)+1):end), 1:m, 'UniformOutput', false);
% lpa.mt files
lst = cell(m, 1);
for j = 1:m
cd(pthles{j})
load(['LST_lpa_', namf2{j}, '.mat'])
lst{j} = lpa;
end
cd(pthles{1})
% name of images that need to be filled/coregistered
if isfield(lst{1}, 'Vref')
namcoreg = cellfun(@(x) x.Vref.fname, lst, 'UniformOutput', false);
else
namcoreg = cellfun(@(x) x.Vf2.fname, lst, 'UniformOutput', false);
end
%for j = 1:numel(lst)
% namcoreg{j} = [ps_fileparts(namcoreg{j}, 1:2), '_', num2str(j), ps_fileparts(namcoreg{j}, 3)];
%end
% Create folder for report and stuff
nameFolder = ['LST_long_lpa_', num2str(m), '_', ps_create_timestamp];
mkdir(nameFolder)
% write p0 for t = 2, ..., t = m
for j = 1:m
p0 = zeros(lst{j}.Vf2.dim); p0(lst{j}.indx_brain) = lst{j}.I;
Vp0 = lst{j}.Vf2; Vp0.fname = fullfile(nameFolder, ['p0_', num2str(j), '.nii']);
spm_write_vol(Vp0, p0);
end
end
or = lst{1}.or;
fl = lst{1}.fl;
% ---------------------------------------------------------------------
% Filling
% ---------------------------------------------------------------------
% original name of coreg images
or_namcoreg = namcoreg;
fprintf(fileID, 'Filling ...');
strout = 'Fill images ';
fprintf(strout)
tic
% Copy images to temporary folder
%cellfun(@(x) copyfile(x, fullfile(nameFolder, '.')), namcoreg);
for j = 1:m
copyfile(namcoreg{j}, fullfile(nameFolder, [ps_fileparts(namcoreg{j}, 2), '_', num2str(j), ps_fileparts(namcoreg{j}, 3)]));
namcoreg{j} = [ps_fileparts(namcoreg{j}, 1:2), '_', num2str(j), ps_fileparts(namcoreg{j}, 3)];
end
for j = 1:m
if strcmp(ps_fileparts(namcoreg{j}, 3), '.img')
copyfile([ps_fileparts(namcoreg{j}, 1:2), '.hdr'], fullfile(nameFolder, '.'))
end
end
namcoreg = cellfun(@(x) fullfile(pthles{1}, nameFolder, ps_fileparts(x, 2:3)), namcoreg, 'UniformOutput', false);
% fill images
nam_del = cell(m, 1);
for j = 1:m
nam_del{j} = namcoreg{j};
namcoreg{j} = fullfile(pthles{1}, nameFolder, ps_LST_lesfill(namcoreg{j}, Vles_tmp{j}.fname, 1, 0));
spm_unlink(nam_del{j});
end
tt = toc; tt = [num2str(round(tt)), 's'];
strout = [repmat(' ', 1, 72 - numel(tt) - numel(strout)), tt, '\n'];
fprintf(strout)
fprintf(fileID, ' ok.\n');
% ---------------------------------------------------------------------
% Coregistration
% ---------------------------------------------------------------------
if 0
% Simple non-symmetric registration
[~, job2] = ps_LST_lpa_preproc_default;
fprintf(fileID, 'Coregistration ...');
strout = 'Coregistration ';
fprintf(strout)
tic
job2.roptions.prefix = 'rl';
for j= 2:m
cd(pthles{1})
copyfile(fullfile(pthles{j}, [namf2{j}, '.nii']), fullfile(nameFolder, [namf2{j}, '_', num2str(j), '.nii']))
copyfile(Vles_tmp{j}.fname, fullfile(nameFolder, [ps_fileparts(Vles_tmp{j}.fname, 2), '_', num2str(j), '.nii']))
job2.ref = {namcoreg{1}};
job2.source = {namcoreg{j}};
%job2.other = {fullfile(pthles{j}, [namf2{j}, '.nii']), ...
% Vles_tmp{j}.fname, ...
% fullfile(nameFolder, ['p0_', num2str(j), '.nii'])};
job2.other = {fullfile(nameFolder, [namf2{j}, '_', num2str(j), '.nii']), ...
fullfile(nameFolder, [namles{j}, '_', num2str(j), '.nii']), ...
fullfile(nameFolder, ['p0_', num2str(j), '.nii'])};
ps_LST_spm_run_coreg(job2);
spm_unlink(namcoreg{j})
spm_unlink(fullfile(nameFolder, ['p0_', num2str(j), '.nii']))
copyfile(fullfile(nameFolder, ['rl', namf2{j}, '_', num2str(j), '.nii']), pthles{j})
copyfile(fullfile(nameFolder, ['rl', namles{j}, '_', num2str(j), '.nii']), pthles{j})
end
copyfile(fullfile(pthles{1}, [namles{1}, extles{1}]), fullfile(pthles{1}, ['rl', namles{1}, '_1', extles{1}]));
copyfile(fullfile(pthles{1}, [namf2{1}, '.nii']), fullfile(pthles{1}, ['rl', namf2{1}, '_1', '.nii']));
copyfile(fullfile(pthles{1}, nameFolder, 'p0_1.nii'), fullfile(pthles{1}, nameFolder, 'rlp0_1.nii'));
spm_unlink(fullfile(pthles{1}, nameFolder, 'p0_1.nii'));
else
% longitudinal registration pipeline
fprintf(fileID, 'Longitudinal coregistration ...');
strout = 'Longitudinal rigid registration by CAT12\n';
fprintf(strout)
job = ps_LST_cat12long_default(namcoreg);
spm_jobman('run', job);
%cellfun(@(x) spm_unlink(x), namc3oreg)
cellfun(@(x) movefile(fullfile(ps_fileparts(x, 1), ['r' ps_fileparts(x, 2:3)]), ...
fullfile(ps_fileparts(x, 1), ['rl' ps_fileparts(x, 2:3)])), namcoreg)
namcoreg = cellfun(@(x) fullfile(ps_fileparts(x, 1), ['rl' ps_fileparts(x, 2:3)]), ...
namcoreg, 'UniformOutput', false);
fprintf(fileID, ' ok.\n');
[~, job2] = ps_LST_lpa_preproc_default;
fprintf(fileID, 'Coregistration ...');
strout = 'Coregistration ';
fprintf(strout)
tic
job2.roptions.prefix = 'rl';
for j= 1:m
cd(pthles{1})
copyfile(fullfile(pthles{j}, [namf2{j}, '.nii']), ...
fullfile(nameFolder, [namf2{j}, '_', num2str(j), '.nii']))
copyfile(Vles_tmp{j}.fname, ...
fullfile(nameFolder, [ps_fileparts(Vles_tmp{j}.fname, 2), '_', num2str(j), '.nii']))
if 0
if j == 1
copyfile('rtmplSpace_flairmask-T2.nii', ...
fullfile(nameFolder, ['rtmplSpace_flairmask-T2', '_', num2str(j), '.nii']))
else
copyfile(fullfile(pthles{2}, 'rtmplSpace_flairmask-T2.nii'), ...
fullfile(nameFolder, ['rtmplSpace_flairmask-T2', '_', num2str(j), '.nii']))
copyfile(fullfile(pthles{2}, 'rtmplSpace_flairmask-T2Enl.nii'), ...
fullfile(nameFolder, ['rtmplSpace_flairmask-T2Enl.nii']))
copyfile(fullfile(pthles{2}, 'rtmplSpace_flairmask-T2New.nii'), ...
fullfile(nameFolder, ['rtmplSpace_flairmask-T2New.nii']))
end
end
job2.ref = {namcoreg{j}};
job2.source = {fullfile(nameFolder, [namf2{j}, '_', num2str(j), '.nii'])};
job2.other = {fullfile(nameFolder, [namles{j}, '_', num2str(j), '.nii']), ...
fullfile(nameFolder, ['p0_', num2str(j), '.nii'])};
if 0
if j == 1
job2.other = {fullfile(nameFolder, 'rtmplSpace_flairmask-T2_1.nii'), ...
fullfile(nameFolder, [namles{j}, '_', num2str(j), '.nii']), ...
fullfile(nameFolder, ['p0_', num2str(j), '.nii'])};
else
job2.other = {fullfile(nameFolder, 'rtmplSpace_flairmask-T2_2.nii'), ...
fullfile(nameFolder, 'rtmplSpace_flairmask-T2Enl.nii'), ...
fullfile(nameFolder, 'rtmplSpace_flairmask-T2New.nii'), ...
fullfile(nameFolder, [namles{j}, '_', num2str(j), '.nii']), ...
fullfile(nameFolder, ['p0_', num2str(j), '.nii'])};
end
end
job2.roptions.interp = 0;
ps_LST_spm_run_coreg(job2);
job2.ref = {namcoreg{j}};
job2.source = {fullfile(nameFolder, [namf2{j}, '_', num2str(j), '.nii'])};
%job2.other = {fullfile(pthles{j}, [namf2{j}, '.nii']), ...
% Vles_tmp{j}.fname, ...
% fullfile(nameFolder, ['p0_', num2str(j), '.nii'])};
job2.other = {or_namcoreg{j}};
job2.roptions.interp = 4;
ps_LST_spm_run_coreg(job2);
%spm_unlink(namcoreg{j})
%spm_unlink(fullfile(nameFolder, ['p0_', num2str(j), '.nii']))
%copyfile(namcoreg{j}, pthles{j})
copyfile(fullfile(nameFolder, ['rl', namf2{j}, '_', num2str(j), '.nii']), pthles{j})
copyfile(fullfile(nameFolder, ['rl', namles{j}, '_', num2str(j), '.nii']), pthles{j})
%copyfile(fullfile(nameFolder, ['rl', ps_fileparts(or_namcoreg{j}, 2:3)]), pthles{j})
Vles_tmp{j} = spm_vol(fullfile(ps_fileparts(Vles_tmp{j}.fname, 1), ['rl', namles{j}, '_', num2str(j), '.nii']));
end
end
tt = toc; tt = [num2str(round(tt)), 's'];
strout = [repmat(' ', 1, 72 - numel(tt) - numel(strout)), tt, '\n'];
fprintf(strout)
fprintf(fileID, ' ok.\n');
% ---------------------------------------------------------------------
% Longitudinal
% ---------------------------------------------------------------------
thrs = 0.1;
for t = 1:numel(thrs)
for j = 1:numel(namf2)
copyfile(fullfile(nameFolder, ['rl', namf2{j}, '_', num2str(j), '.nii']), pthles{j})
copyfile(fullfile(nameFolder, ['rl', namles{j}, '_', num2str(j), '.nii']), pthles{j})
end
fprintf(fileID, 'Load data ...');
strout = 'Compare time points ';
fprintf(strout)
tic
changes = zeros([Vles_tmp{1}.dim m - 1]);
counter = 0;
ch = zeros(1, m - 1);
while any(ch == 0) && counter < 30
counter = counter + 1;
fprintf(fileID, '\n***********************\n');
fprintf(fileID, ['Iteration ', num2str(counter), '\n']);
fprintf(fileID, '***********************');
for j = 1:(m-1)
fprintf(fileID, ['\n*** Compare time point ', num2str(j), ' with time point ', num2str(j+1), '\n']);
fprintf(fileID, 'Load images ...');
if counter == 1
les_01 = spm_read_vols(spm_vol(fullfile(pthles{j}, ['rl', namles{j}, '_', num2str(j), '.nii'])));
les_02 = spm_read_vols(spm_vol(fullfile(pthles{j+1}, ['rl', namles{j+1}, '_', num2str(j+1), '.nii'])));
else
les_01 = spm_read_vols(spm_vol(fullfile(pthles{j}, ['l', namles{j}, '_', num2str(j), '.nii'])));
les_02 = spm_read_vols(spm_vol(fullfile(pthles{j+1}, ['l', namles{j+1}, '_', num2str(j+1), '.nii'])));
end
les_01 = 1 .* (les_01 > 0.5);
les_02 = 1 .* (les_02 > 0.5);
les_0102 = les_02 - les_01;
joint = 1 .* (les_01 > 0 | les_02 > 0);
Vf2 = spm_vol(fullfile(pthles{j}, ['rl', namf2{j}, '_', num2str(j), '.nii']));
f2_01 = spm_read_vols(Vf2);
f2_02 = spm_read_vols(spm_vol(fullfile(pthles{j+1}, ['rl', namf2{j+1}, '_', num2str(j+1), '.nii'])));
p0_01 = spm_read_vols(spm_vol(fullfile(nameFolder, ['rlp0_', num2str(j), '.nii'])));
p0_02 = spm_read_vols(spm_vol(fullfile(nameFolder, ['rlp0_', num2str(j+1), '.nii'])));
p0_01(isnan(f2_01) | isnan(f2_02)) = 0;
p0_02(isnan(f2_01) | isnan(f2_02)) = 0;
fprintf(fileID, ' ok.\n');
fprintf(fileID, 'Normalize FLAIR images ...');
% Normalize FLAIR
tmp = f2_01((p0_01 > 1.5 & p0_01 < 2.5) | (p0_02 > 1.5 & p0_02 < 2.5) & joint < 1);
f2_01 = f2_01 ./ mean(tmp(~isnan(tmp)));
tmp = f2_02((p0_01 > 1.5 & p0_01 < 2.5) | (p0_02 > 1.5 & p0_02 < 2.5) & joint < 1);
f2_02 = f2_02 ./ mean(tmp(~isnan(tmp)));
fprintf(fileID, ' ok.\n');
fprintf(fileID, 'Relative change ...');
% relative change
f2_relchange = (f2_02 - f2_01) ./ ((f2_01 + f2_02) ./ 2);
f2_relchange(isinf(f2_relchange)) = NaN;
f2_relchange(p0_01 == 0) = 0; f2_relchange(p0_02 == 0) = 0;
fprintf(fileID, ' ok.\n');
fprintf(fileID, 'Healthy WM ...');
% Healthy WM
tmp = f2_relchange(p0_01 > 2.9 & p0_01 < 3.1 & (p0_02 > 2.9 & p0_02 < 3.1) & joint == 0);
%tmp = f2_relchange(p0_01 == 3 & (p0_02 > 2.9 & p0_02 < 3.1) & joint == 0);
tmp(isnan(tmp)) = [];
m3 = mean(tmp);
sd3 = std(tmp);
fprintf(fileID, [' ok, mean = ', num2str(m3), ', sd = ', num2str(sd3), '.\n']);
% Use the smoothed relchange for thresholding
fprintf(fileID, 'Smoothing and thresholding ...');
sf2_relchange_les = joint .* f2_relchange;
spm_smooth(sf2_relchange_les, sf2_relchange_les, [1, 1, 1] .* 2);
%thr1 = norminv(.1, m3, sd3);
thr1 = ps_qnorm(thrs(t), m3, sd3);
%thr2 = norminv(.9, m3, sd3);
thr2 = ps_qnorm(1-thrs(t), m3, sd3);
%change = les_0102 .* (sf2_relchange_les < thr1 | sf2_relchange_les > thr2);
change = 2 .* (sf2_relchange_les > thr1 & sf2_relchange_les < thr2 & joint > 0);
change(sf2_relchange_les < thr1) = 1;
change(sf2_relchange_les > thr2) = 3;
change(les_01 > 0 & les_02 > 0) = 2;
fprintf(fileID, [' ok, thr1 = ', num2str(thr1), ', thr2 = ', num2str(thr2), '.\n']);
% delete all change voxels that lie directly on CSF
indx_tmp = find(change ~= 0);
csf = 1 .* (p0_01 < 1.5 | p0_02 < 1.5);
csf = ps_set_border_zero(csf);
nh = getNeighborhood2(csf, indx_tmp, 1);
change(indx_tmp(sum(nh > 0) > 0)) = 0;
% Process all voxels that were identified as change
fprintf(fileID, 'Postprocessing ...');
st = 0;
while ~st
indx_les_02 = find(les_02 > 0 & les_01 == 0 & change == 0);
nh = getNeighborhood2(change, indx_les_02, 1);
indx_tmp = indx_les_02(sum(nh > 0) > 0 & ...
abs(sf2_relchange_les(indx_les_02))' > thr2 * .75 & ...
joint(indx_les_02)' > 0);
if isempty(indx_tmp)
st = 1;
else
%change(indx_tmp) = 1;
change(indx_tmp) = 3;
end
end
fprintf(fileID, ' ok ... ');
st = 0;
while ~st
indx_les_01 = find(les_01 > 0 & les_02 == 0 & change == 0);
nh = getNeighborhood2(change, indx_les_01, 1);
indx_tmp = indx_les_01(sum(nh < 0) > 0 & ...
abs(sf2_relchange_les(indx_les_01))' > thr1 * .75 & ...
joint(indx_les_01)' > 0);
if isempty(indx_tmp)
st = 1;
else
%change(indx_tmp) = -1;
change(indx_tmp) = 1;
end
end
fprintf(fileID, ' ok.\n');
% Process all voxels that were identified as change
fprintf(fileID, 'Postprocessing ...');
st = 0;
while ~st
indx_les_02 = find(les_02 > 0 & les_01 == 0 & change == 2);
nh = getNeighborhood2(1 .* (change > 2), indx_les_02, 1);
indx_tmp = indx_les_02(sum(nh > 0) > 0 & ...
abs(sf2_relchange_les(indx_les_02))' > thr2 * .75 & ...
joint(indx_les_02)' > 0);
if isempty(indx_tmp)
st = 1;
else
change(indx_tmp) = 3;
end
end
fprintf(fileID, ' ok ... ');
st = 0;
while ~st
indx_les_01 = find(les_01 > 0 & les_02 == 0 & change == 2);
nh = getNeighborhood2(1 .* (change == 1), indx_les_01, 1);
indx_tmp = indx_les_01(sum(nh > 0) > 0 & ...
abs(sf2_relchange_les(indx_les_01))' > thr1 * .75 & ...
joint(indx_les_01)' > 0);
if isempty(indx_tmp)
st = 1;
else
change(indx_tmp) = 1;
end
end
fprintf(fileID, ' ok.\n');
% Delete all lesions that are smaller than 0.01 ml
fprintf(fileID, 'Delete lesions that are smaller than 0.01 ml ...');
volfactor = abs(det(Vf2.mat(1:3,1:3))) / 1000;
if 0
for k = [-1,1]
%b = bwconncomp(1 .* (change == k), 6);
%change(cell2mat(b.PixelIdxList(cellfun(@numel, b.PixelIdxList) .* volfactor < 0.01)')) = 0;
if sum(change(:) == k) > 0
b = ps_bwlabeln(1 .* (change == k));
if max(b(:)) > 0
c_tmp = ps_count(b(b > 0));
for kk = 1:size(c_tmp, 2)
if (c_tmp(2,kk) * volfactor) < 0.01
change(b == c_tmp(1,kk)) = 0;
end
end
end
end
end
end
clear change2;
fprintf(fileID, ' ok.\n');
fprintf(fileID, 'Create new lesion maps ...');
if 0
les_01_new = 0.*les_01;
les_02_new = 0.*les_02;
les_01_new(change < 0 | (les_01 > 0 & les_02 > 0)) = 1;
les_02_new(change > 0 | (les_01 > 0 & les_02 > 0)) = 1;
change = 0 .* les_01;
change(les_01_new > 0 & les_02_new == 0) = 1;
change(les_01_new > 0 & les_02_new > 0) = 2;
change(les_01_new == 0 & les_02_new > 0) = 3;
change2 = 2 .* (sf2_relchange_les > thr1 & sf2_relchange_les < thr2 & joint > 0);
change2(sf2_relchange_les < thr1) = 1;
change2(sf2_relchange_les > thr2) = 3;
les_01_new = 1 .* (change2 > 0 & change2 < 3);
les_02_new = 1 .* (change2 > 1);
change = change2;
end
tmp = changes(:,:,:,j) - change;
if m > 2
ch(j) = numel(tmp(tmp ~= 0)) < 3;
else
ch(j) = 1;
end
%ch(j) = isequal(changes(:,:,:,j), change);
changes(:,:,:,j) = change;
% Adjust old lesion maps
if counter == 1
les_01_or = spm_read_vols(spm_vol(fullfile(pthles{j}, ['rl', namles{j}, '_', num2str(j), '.nii'])));
Vles_tmp{j+1} = spm_vol(fullfile(pthles{j+1}, ['rl', namles{j+1}, '_', num2str(j+1), '.nii']));
les_02_or = spm_read_vols(Vles_tmp{j+1});
else
les_01_or = spm_read_vols(spm_vol(fullfile(pthles{j}, ['l', namles{j}, '_', num2str(j), '.nii'])));
les_02_or = spm_read_vols(spm_vol(fullfile(pthles{j+1}, ['l', namles{j+1}, '_', num2str(j+1), '.nii'])));
end
les_02_or(les_02_or > 1) = 1;
les_or = [les_01_or(:), les_02_or(:)];
les_01_or(change == 2) = max(les_or(change == 2,:), [], 2);
les_02_or(change == 2) = max(les_or(change == 2,:), [], 2);
les_01_or(change == 3) = 0;
les_02_or(change == 1) = 0;
les_01_or(change == 0) = 0;
les_02_or(change == 0) = 0;
les_01_or = 1 .* (change > 0 & change < 3);
les_02_or = 1 .* (change > 1);
Vles_tmp{j}.fname = fullfile(pthles{j}, ['l', namles{j}, '_', num2str(j), extles{j}]);
Vles_tmp{j}.descrip = 'Probability lesion map obtained by longitudinal pipeline within LST toolbox';
spm_write_vol(Vles_tmp{j}, les_01_or);
Vles_tmp{j+1}.fname = fullfile(pthles{j+1}, ['l', namles{j+1}, '_', num2str(j+1), extles{j+1}]);
Vles_tmp{j+1}.descrip = 'Probability lesion map obtained by longitudinal pipeline within LST toolbox';
spm_write_vol(Vles_tmp{j+1}, les_02_or);
end
end
% save lesion change label
for j = 1:(m-1)
Vles_tmp{j}.fname = fullfile(pthles{j}, ['LCL_', namles{j}, '_', namles{j+1}, '.nii']);
Vles_tmp{j}.descrip = ['Lesion change label for timepoint ', num2str(j), ' and ', num2str(j+1)];
spm_write_vol(Vles_tmp{j}, changes(:,:,:,j));
end
% Change name of images
if 1
for j = 1:m
movefile(fullfile(pthles{j}, ['l', namles{j}, '_', num2str(j), extles{j}]), ...
fullfile(pthles{j}, ['l', namles{j}, extles{j}]))
movefile(fullfile(pthles{j}, ['rl', namf2{j}, '_', num2str(j), '.nii']), ...
fullfile(pthles{j}, ['l', namf2{j}, '.nii']))
end
end
tt = toc; tt = ['finished after ', num2str(counter) ' iterations, ', num2str(round(tt)), 's'];
strout = [repmat(' ', 1, 72 - numel(tt) - numel(strout)), tt, '\n'];
fprintf(strout)
fprintf(fileID, ' ok.\n\n');
end
if html_report
% -----------------------------------------------------------------
% Create HTML report
% -----------------------------------------------------------------
stroutHTML = 'Create HTML report';
fprintf(stroutHTML);
fprintf(fileID, 'Create main HTML file ...');
% Main HTML file
copyfile(fullfile(spm('dir'), 'toolbox', 'LST', 'LST_main_html.html'), ['report_', nameFolder, '.html'])
HTMLid = fopen(['report_', nameFolder, '.html'], 'at');
strout = [' <script src=\"', ps_fullfile(spm('dir'), 'toolbox', 'LST', 'js', 'raphael.js'), '\"></script>\n', ...
' <script src=\"', ps_fullfile(spm('dir'), 'toolbox', 'LST', 'js', 'jquery.min.js'), '\"></script>\n', ...
' <link href=\"', ps_fullfile(spm('dir'), 'toolbox', 'LST', 'js', 'jquery-ui.css'), '\" rel=\"stylesheet\"></script>\n', ...
' <script src=\"', ps_fullfile(spm('dir'), 'toolbox', 'LST', 'js', 'jquery-ui.js'), '\"></script>\n', ...
' </head>\n <body>\n'];
fprintf(HTMLid, strout);
fprintf(fileID, ' ok.\n');
strout = '';
%strout = '';
fprintf(fileID, 'Create PNGs ...');
for j = 1:(m-1)
if 0
if j == 1
Vimg1 = fullfile(pthles{j}, [namf2{j}, '.nii']);
else
Vimg1 = fullfile(pthles{j}, ['l', namf2{j}, '.nii']);
end
else
Vimg1 = fullfile(pthles{j}, ['l', namf2{j}, '.nii']);
end
Vimg2 = fullfile(pthles{j+1}, ['l', namf2{j+1}, '.nii']);
if numel(Vimg1) < numel(Vimg2)
Vimg1 = [Vimg1, repmat(' ', 1, numel(Vimg2) - numel(Vimg1))];
else
Vimg2 = [Vimg2, repmat(' ', 1, numel(Vimg1) - numel(Vimg2))];
end
Vimg = [Vimg1; Vimg2];
p0_01 = spm_read_vols(spm_vol(fullfile(nameFolder, ['rlp0_', num2str(j), '.nii'])));
p0_02 = spm_read_vols(spm_vol(fullfile(nameFolder, ['rlp0_', num2str(j+1), '.nii'])));
c_tmp = indx2coord(find(p0_01 > .9 & p0_02 > .9), size(p0_01, 1), size(p0_01, 2));
r = [min(c_tmp(:,3)),max(c_tmp(:,3))];
pngFailed = '';
try
[~, r] = ps_LST_create_gif(Vimg, fullfile(pthles{j}, ['LCL_', namles{j}, '_', namles{j+1}, '.nii']), fullfile(pthles{1}, nameFolder, ['overlay_', num2str(j), '_', num2str(j+1)]), r, [or, fl]);
catch ME
fprintf(fileID, ' failed!.\n');
pngFailed = ME.message;
end
fprintf(fileID, 'Create glass brains ...');
change = changes(:,:,:,j);
if 1
% Create images for glass brains
ps_LST_create_glass_brain(1 .* (change == 1), ...
1 .* (p0_01 > 0.5 & p0_02 > 0.5), ...
fullfile(nameFolder, ['gb_decreased_', num2str(j), '_', num2str(j+1)]), [or, fl]);
ps_LST_create_glass_brain(1 .* (change == 2), ...
1 .* (p0_01 > 0.5 & p0_02 > 0.5), ...
fullfile(nameFolder, ['gb_unchanged_', num2str(j), '_', num2str(j+1)]), [or, fl]);
ps_LST_create_glass_brain(1 .* (change == 3), ...
1 .* (p0_01 > 0.5 & p0_02 > 0.5), ...
fullfile(nameFolder, ['gb_increased_', num2str(j), '_', num2str(j+1)]), [or, fl]);
end
fprintf(fileID, ' ok.\n');
fprintf(fileID, 'Create subject specific HTML file ...');
les_01_or = spm_read_vols(spm_vol(fullfile(pthles{j}, ['l', namles{j}, '.nii'])));
les_02_or = spm_read_vols(spm_vol(fullfile(pthles{j+1}, ['l', namles{j+1}, '.nii'])));
if any(les_01_or(:) > .5)
b = ps_bwlabeln(1*(les_01_or > 0.5));
if any(b(:) > 0)
for k = 1:max(b(:))
if (sum(b(:) == k) * volfactor) <= 0.015
b(find(b) == k) = 0;
end
end
end
else
b = 0 .* les_01_or;
end
les_01_or = les_01_or .* (b > 0);
if any(les_02_or(:) > .5)
b = ps_bwlabeln(1*(les_02_or > 0.5));
if any(b(:) > 0)
for k = 1:max(b(:))
if (sum(b(:) == k) * volfactor) <= 0.015
b(find(b) == k) = 0;
end
end
end
else
b = 0 .* les_02_or;
end
les_02_or = les_02_or .* (b > 0);
%tlv1 = sum(les_01_or(:) > .5) * volfactor;
%tlv2 = sum(les_02_or(:) > .5) * volfactor;
joint = 0 .* les_01_or;
joint(:) = max([les_01_or(:), les_02_or(:)], [], 2);
tlv_joint = sum(joint(:) > .5) * volfactor;
tlv_unch = sum(joint(change(:) == 2) > .5) * volfactor;
tlv_decr = sum(joint(change(:) == 1) > .5) * volfactor;
tlv_incr = sum(joint(change(:) == 3) > .5) * volfactor;
if any(joint(:) > .5)
b = ps_bwlabeln(1 .* (joint > .5) .* (change > 0));
b_count = ps_count(b(:));
b_count(:,find(b_count(1,:) == 0)) = [];
b_count = b_count(:,find((b_count(2,:) .* volfactor) > 0.015));
tlv_joint = sum(b_count(2,:) .* volfactor);
else
tlv_joint = 0;
end
if any(joint(change(:) == 2) > .5)
b = ps_bwlabeln(1 .* (joint > .5) .* (change == 2));
b_count = ps_count(b(:));
b_count(:,find(b_count(1,:) == 0)) = [];
b_count = b_count(:,find((b_count(2,:) .* volfactor) > 0.015));
tlv_unch = sum(b_count(2,:) .* volfactor);
else
tlv_unch = 0;
end
if any(joint(change(:) == 1) > .5)
b = ps_bwlabeln(1 .* (joint > .5) .* (change == 1));
b_count = ps_count(b(:));
b_count(:,find(b_count(1,:) == 0)) = [];
%b_count = b_count(:,find((b_count(2,:) .* volfactor) > 0.015));
tlv_decr = sum(b_count(2,:) .* volfactor);
else
tlv_decr = 0;
end
if any(joint(change(:) == 3) > .5)
b = ps_bwlabeln(1 .* (joint > .5) .* (change == 3));
b_count = ps_count(b(:));
b_count(:,find(b_count(1,:) == 0)) = [];
%b_count = b_count(:,find((b_count(2,:) .* volfactor) > 0.015));
tlv_incr = sum(b_count(2,:) .* volfactor);
else
tlv_incr = 0;
end
if any(les_01_or(:) > .5)
b = ps_bwlabeln(1 .* (les_01_or > .5));
b_count = ps_count(b(:));
b_count(:,find(b_count(1,:) == 0)) = [];
b_count = b_count(:,find((b_count(2,:) .* volfactor) > 0.015));
numles_01 = size(b_count, 2);
tlv1 = sum(b_count(2,:) .* volfactor);
else
numles_01 = 0;
tlv1 = 0;
end
if any(les_02_or(:) > .5)
b = ps_bwlabeln(1 .* (les_02_or > .5));
b_count = ps_count(b(:));
b_count(:,find(b_count(1,:) == 0)) = [];
b_count = b_count(:,find((b_count(2,:) .* volfactor) > 0.015));
numles_02 = size(b_count, 2);
tlv2 = sum(b_count(2,:) .* volfactor);
else
numles_02 = 0;
tlv2 = 0;
end
% Save data to file
if j > 1
fileIDData = fopen('longdata_LST.csv', 'a');
if viajob
fprintf(fileIDData, [ps_fullfile(ps_fileparts(Vles{j+1}{i}.fname, 1)), ',', num2str(j+1), ',', num2str(numles_02), ',', num2str(tlv2), ',', num2str(tlv_decr), ',', num2str(tlv_unch), ',', num2str(tlv_incr), '\n']);
else
fprintf(fileIDData, [ps_fullfile(ps_fileparts(Vles{j+1}(i).fname, 1)), ',', num2str(j+1), ',', num2str(numles_02), ',', num2str(tlv2), ',', num2str(tlv_decr), ',', num2str(tlv_unch), ',', num2str(tlv_incr), '\n']);
end
fclose(fileIDData);
else
fileIDData = fopen('longdata_LST.csv', 'wt');
fprintf(fileIDData, 'Subject,TimePoint,LesionNr,Vol,VolDecr,VolUnch,VolIncr\n');
if viajob
fprintf(fileIDData, [ps_fullfile(ps_fileparts(Vles{1}{i}.fname, 1)), ',', num2str(j), ',', num2str(numles_01), ',', num2str(tlv1), ',,,\n']);
fprintf(fileIDData, [ps_fullfile(ps_fileparts(Vles{2}{i}.fname, 1)), ',', num2str(j+1), ',', num2str(numles_02), ',', num2str(tlv2), ',', num2str(tlv_decr), ',', num2str(tlv_unch), ',', num2str(tlv_incr), '\n']);
else
fprintf(fileIDData, [ps_fullfile(ps_fileparts(Vles{1}(i).fname, 1)), ',', num2str(j), ',', num2str(numles_01), ',', num2str(tlv1), ',,,\n']);
fprintf(fileIDData, [ps_fullfile(ps_fileparts(Vles{2}(i).fname, 1)), ',', num2str(j+1), ',', num2str(numles_02), ',', num2str(tlv2), ',', num2str(tlv_decr), ',', num2str(tlv_unch), ',', num2str(tlv_incr), '\n']);
end
fclose(fileIDData);
end
jsid = [nameFolder, '_', num2str(j), num2str(j+1)];
jsid(regexp(jsid, '\.')) = [];
strout = [strout, ...
'\n<div class=\"container\">\n', ...
' <h1>Longitudinal lesion segmentation by LST</h1>\n', ...
' <div class=\"column-01\">\n', ...
' <h2>Input summary</h2>\n', ...
' <table style=\"min-width: 500px;\">\n', ...
' <tr>\n', ...
' <td>Date of analysis</td>\n', ...
' <td class=\"ta_right\">', datestr(clock()), '</td>\n', ...
' </tr>\n', ...
' <tr>\n', ...
' <td>Directory for t = ' num2str(j), '</td>\n', ...
' <td class=\"ta_right\">', ps_shorten_string(ps_fullfile(pthles{j}), 28), '</td>\n', ...
' </tr>\n', ...
' <tr>\n', ...
' <td>Directory for t = ' num2str(j+1), '</td>\n', ...
' <td class=\"ta_right\">', ps_shorten_string(ps_fullfile(pthles{j+1}), 28), '</td>\n', ...
' </tr>\n', ...
' <tr>\n', ...
' <td>Lesion map for t = ' num2str(j), '</td>\n', ...
' <td class=\"ta_right\">', namles{j}, extles{j}, '</td>\n', ...
' </tr>\n', ...
' <tr>\n', ...
' <td>Lesion map for t = ' num2str(j+1), '</td>\n', ...
' <td class=\"ta_right\">', namles{j+1}, extles{j+1}, '</td>\n', ...
' </tr>\n', ...
' <tr>\n', ...
' <td>Algorithm used for segmentation</td>\n', ...
' <td class=\"ta_right\">', alg_text, '</td>\n', ...
' </tr>\n', ...
' </table>\n', ...
' </div>\n', ...
' <div class=\"column-02\">\n', ...
' <h2>Results</h2>\n', ...
' <table style=\"width: 500px\">\n', ...
' <tr>\n', ...
' <td>Lesion volume for t = ' num2str(j), '</td>\n', ...
' <td class=\"ta_right\">', num2str(tlv1), ' ml</td>\n', ...
' </tr>\n', ...
' <tr>\n', ...
' <td>Number of lesions for t = ' num2str(j), '</td>\n', ...
' <td class=\"ta_right\">', num2str(numles_01), '</td>\n', ...
' </tr>\n', ...
' <tr>\n', ...
' <td>Lesion volume for t = ' num2str(j+1), '</td>\n', ...
' <td class=\"ta_right\">', num2str(tlv2), ' ml</td>\n', ...
' </tr>\n', ...
' <tr>\n', ...
' <td>Number of lesions for t = ' num2str(j+1), '</td>\n', ...
' <td class=\"ta_right\">', num2str(numles_02), '</td>\n', ...
' </tr>\n', ...
' <tr>\n', ...
' <td>Joint lesion volume</td>\n', ...
' <td class=\"ta_right\">', num2str(tlv_joint), ' ml</td>\n', ...
' </tr>\n', ...
' <tr>\n', ...
' <td>Unchanged lesion volume</td>\n', ...
' <td class=\"ta_right\">', num2str(tlv_unch), ' ml</td>\n', ...
' </tr>\n', ...
' <tr>\n', ...
' <td>Decreased lesion volume</td>\n', ...
' <td class=\"ta_right\">', num2str(tlv_decr), ' ml (', num2str(tlv_decr / tlv1 * 100, 3), '%%)</td>\n', ...
' </tr>\n', ...
' <tr>\n', ...
' <td>Increased lesion volume</td>\n', ...
' <td class=\"ta_right\">', num2str(tlv_incr), ' ml (', num2str(tlv_incr / tlv1 * 100, 3), '%%)</td>\n', ...
' </tr>\n', ...
' <tr>\n', ...
' <td>Lesion volume change</td>\n', ...
' <td class=\"ta_right\">', num2str(-tlv_decr + tlv_incr), ' ml (', (num2str((-tlv_decr + tlv_incr) / tlv1 * 100, 3)), '%%)</td>\n', ...
' </tr>\n', ...
' </table>\n', ...
' </div>\n', ...
' <div style=\"clear:both\"></div>\n', ...
' <div class=\"column-01\">\n', ...
' <h2>Lesion change plot (LCP)</h2>\n', ... %' <script src=\"', fullfile(cd, nameFolder, ['lcp_', num2str(id), '.js']), '\" type=\"text/javascript\"></script>\n', ...
' <script src=\"', ps_fullfile(cd, nameFolder, ['lcp_', num2str(j), num2str(j+1), '.js']), '\" type=\"text/javascript\"></script>\n', ...
' <div id=\"canvas_', nameFolder, '_', num2str(j), num2str(j+1), '\" class=\"canvas\"></div>\n', ...
' </div>\n', ...
' <div class=\"column-02\" style=\"vertical-align: top;\">\n', ...
' <h2>Overlay</h2>\n'];
if strcmp(pngFailed, '')
strout = [strout, ...
' <img width=\"450px\" id=\"overlay', jsid, '\" src=\"', ps_fullfile(cd, nameFolder, ['overlay_', num2str(j), '_', num2str(j+1), '_', num2str(round(mean(r))), '.png']), '\" />\n', ...
' <div id=\"slider_', jsid, '\" style=\"width: 450px; text-align: center;\"></div>\n', ...