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getAct3.m
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function [fRun,fSes,fSes_echoCat,param] = getAct3(volTs,dsgn,fMask,param,force,verbose)
% see /autofs/space/takoyaki_001/users/proulxs/tools/vasomoTools/getResp2.m
fSes_echoCat = [];
% global srcAfni srcFs
if ~exist('force','var'); force = []; end
if ~exist('verbose','var'); verbose = []; end
if ~exist('dsgn','var'); dsgn = []; end
if ~exist('fMask','var'); fMask = []; end
if isempty(force); force = 0; end
if isempty(verbose); verbose = 0; end
if isempty(dsgn)
if isfield(volTs,'dsgn') && isequal(dsgn)
dsgn = dsgn;
else
error('badly specified dsgn')
end
end
if ~isfield(param,'skipMov'); param.skipMov = []; end
if ~isfield(param,'skipCat'); param.skipCat = []; end
if ~isfield(param,'skipRun'); param.skipRun = []; end
if ~isfield(param,'dryRun'); param.dryRun = []; end
if isempty(param.skipMov); param.skipMov = 0; end
if isempty(param.skipCat); param.skipCat = 0; end
if isempty(param.skipRun); param.skipRun = 0; end
if isempty(param.dryRun); param.dryRun = 0; end
%% Data files
if ~isempty(volTs)
fVolTs = {volTs.fspec}';
for i = 1:length(fVolTs)
if ~exist(fVolTs{i},'file'); dbstack; error('write file to disk aka code lazy bum'); end
end
else
fVolTs = [];
end
%% Mask files
if isempty(fMask)
dbstack; error('double-check that')
if isfield(volTs,'vol2vec')
fMask = volTs.vol2vec;
end
else
fMask;
end
if ~all(diff([volTs.tr])<0.01); dbstack; error('runs have different tr'); end
%% Functional design
if ~isa(dsgn,'runDsgn')
dbstack; error('old version, reconciliate')
end
if ~isempty(dsgn.cond)
k = sort(unique(dsgn.cond)); if any(diff(k)-1); dbstack; error('cond indices are not monotonically increasing'); end
dsgn.condLabel = repmat({'stim'},size(k));
dsgn.condLabel{k==0} = 'catch';
dsgn.condK = length(k);
else
dbstack; error('double-check')
param.funDsgn.condSeq = ones(size(param.funDsgn.startSeq));
param.funDsgn.condLabel = {'stim'};
if isfield(dsgn,'nullTrial') && ~isempty(dsgn.nullTrial)
param.funDsgn.condSeq(dsgn.nullTrial) = 2;
param.funDsgn.condLabel{end+1} = 'catch';
param.funDsgn.k = 2;
end
end
param.tr = [volTs.tr]./1000;
param.dsgn = dsgn;
% param.tr = volTs(1).tr/1000;
% param.funDsgn.trStim = dsgn.dt;
% param.funDsgn.k = 1;
% param.funDsgn.startSeq = dsgn.onsetList;
% param.funDsgn.durSeq = dsgn.ondurList;
% if isa(dsgn,'runDsgn') && ~isempty(dsgn.cond)
% k = unique(dsgn.cond); if any(diff(k)-1); dbstack; error('cond indices are not monotonically increasing'); end
% dsgn.condLabel = repmat({'stim'},size(k));
% dsgn.condLabel{k==0} = 'catch';
% dsgn.condK = length(k);
% else
% param.funDsgn.condSeq = ones(size(param.funDsgn.startSeq));
% param.funDsgn.condLabel = {'stim'};
% if isfield(dsgn,'nullTrial') && ~isempty(dsgn.nullTrial)
% param.funDsgn.condSeq(dsgn.nullTrial) = 2;
% param.funDsgn.condLabel{end+1} = 'catch';
% param.funDsgn.k = 2;
% end
% end
% param.funDsgn.label = dsgn.task;
% param.funDsgn.trDecon = dsgn.trDecon;
% %% Run afni's 3dDeconvolve for response timecourse estimation
% [fRun,fSes,param] = runAfni(fVolTs,param,fMask,force,verbose); % analysis performed on each echoe within that function
% nEcho = size(fRun,2);
% nRun = size(fRun,1);
%% Run afni's 3dDeconvolve for double-gamma response amplitude (and delay) fit
% 'SPMG1' = 1 parameter SPM gamma variate basis function
% exp(-t)*(A1*t^P1-A2*t^P2) where
% A1 = 0.0083333333 P1 = 5 (main positive lobe)
% A2 = 1.274527e-13 P2 = 15 (undershoot part)
% This function is NOT normalized to have peak=1!
% 'SPMG2' = 2 parameter SPM: gamma variate + d/dt derivative
% [For backward compatibility: 'SPMG' == 'SPMG2']
% 'SPMG3' = 3 parameter SPM basis function set
% ==> ** The SPMGx functions now can take an optional
% (duration) argument, specifying that the primal
% SPM basis functions should be convolved with
% a square wave 'duration' seconds long and then
% be normalized to have peak absolute value = 1;
% e.g., 'SPMG3(20)' for a 20 second duration with
% three basis function. [28 Apr 2009]
% ** Note that 'SPMG1(0)' will produce the usual
% 'SPMG1' wavefunction shape, but normalized to
% have peak value = 1 (for example).
if ~isfield(param,'model') || isempty(param.model); param.model = 'SPMG2'; end
[fRun,fSes,param] = runAfni(fVolTs,param,fMask,force,verbose); % analysis performed on each echoe within that function
%% Get model
verboseThis = verbose;
if ~isempty(fRun)
for R = 1:size(fRun,1)
paramCur = param; paramCur.nFrame = paramCur.nFrame(R); paramCur.tr = paramCur.tr(R);
fRun(R,1) = plotDsgnMat(fRun(R,1),paramCur,fVolTs(R,1),volTs(R,1),verboseThis);
end
end
if ~isempty(fSes)
dbstack; error('double-check that')
fSes = plotDsgnMat(fSes,param,fVolTs,volTs,verboseThis);
end
%% Refactor
if ~isempty(fRun)
for R = 1:size(fRun,1)
tmp(R,1).afni = fRun(R,1);
if isfield(fRun,'fResp')
% tmp(R,1).afni = rmfield(fRun(R,1),'fResp');
tmp(R,1).fs.fRespTs = fRun(R,1).fResp;
end
if isfield(fRun,'fRespStd')
tmp(R,1).fs.fRespTsTrialSd = fRun(R,1).fRespStd;
end
tmp(R,1).fs.fMask = fRun(R,1).fMask;
end
fRun = tmp; clear tmp
end
if ~isempty(fSes)
dbstack; error('double-check that')
if isfield(fSes,'fResp')
tmp.afni = rmfield(fSes,'fResp');
tmp.fs.fRespTs = fSes.fResp;
else
tmp.afni = fSes;
end
tmp.fs.fMask = fMask;
fSes = tmp; clear tmp
end
nEcho = size(fVolTs,2);
nRun = size(fVolTs,1);
if ~isempty(fRun)
f = fRun;
else
f = [];
end
if ~isempty(fSes)
dbstack; error('double-check that')
f = [f; fSes];
end
% if ~isempty(fRun) && ~isempty(fSes)
% f = [fRun; fSes];
% else
% f = [];
% dbstack; error('X');
% end
%
%
%
% if ~isempty(fSes)
% fSes = plotDsgnMat(fSes,param,fVolTs,volTs,verboseThis);
% if isfield(fSes,'fResp')
% tmp.afni = rmfield(fSes,'fResp');
% if ~isempty(fSes.fResp)
% tmp.fs.fRespTs = fSes.fResp;
% end
% fSes = tmp; clear tmp
% else
% tmp = fSes; clear fSes
% fSes.afni = tmp;
% end
% fSes.fs.fMask = fMask;
% end
% nEcho = size(fVolTs,2);
% nRun = size(fVolTs,1);
%% Simplify stat outputs
disp('Simplifying stat outputs')
forceThis = force;
if ~isempty(f)
cmd = {};
if exist('srcAfni','var') && ~isempty(srcAfni); cmd{end+1} = srcAfni; end
for i = 1:numel(f)
for k = 0:param.dsgn.condK % 0 for the full model and following integer for each event conditions
fIn = f(i).afni.fStat;
%%% Fstat
fOut = replace(fIn,'_stats.nii.gz','_fVal.nii.gz');
if k==0 % full-model
else % individual conditions of the model
fOut = replace(fOut,'cond-FULL',['cond-' param.dsgn.condLabel{k}]);
end
f(i).fs.fCondF{k+1,1} = fOut;
if forceThis || ~exist(fOut,'file')
cmd{end+1} = '3dbucket -overwrite \';
cmd{end+1} = ['-prefix ' fOut ' \'];
if k==0 % full-model
cmd{end+1} = [fIn '[Full_Fstat]'];
else % individual conditions of the model
cmd{end+1} = [fIn '[' param.dsgn.task '_' param.dsgn.condLabel{k} '_Fstat]'];
end
end
fIn = fOut;
%%%% also get p-val
fOut = replace(fIn,'_fVal.nii.gz','_fValP.nii.gz');
f(i).fs.fCondF_pVal = fOut;
if force || ~exist(fOut,'file')
cmd{end+1} = ['df=$(3dAttribute BRICK_STATAUX ' fIn ')'];
cmd{end+1} = 'df1=$(echo $df | awk ''{print $(NF-1)}'')';
cmd{end+1} = 'df2=$(echo $df | awk ''{print $NF}'')';
cmd{end+1} = '3dcalc -overwrite \';
cmd{end+1} = ['-prefix ' fOut ' \'];
cmd{end+1} = ['-a ' fIn ' \'];
cmd{end+1} = '-expr "1-stat2cdf(a,4,$df1,$df2,0)" 2> /dev/null';
end
%%%%% also get q-val (fdr)
fOut = replace(fIn,'_fVal.nii.gz','_fValQ.nii.gz');
fMask = f(i).afni.fMask;
f(i).fs.fCondF_qVal = fOut;
if force || ~exist(fOut,'file')
cmd{end+1} = '3dFDR -overwrite -qval \';
cmd{end+1} = ['-prefix ' fOut ' \'];
cmd{end+1} = ['-input ' fIn ' \'];
cmd{end+1} = ['-mask ' fMask];
% cmd{end+1} = '3dbucket -overwrite \';
% cmd{end+1} = ['-prefix ' fOut ' \'];
% cmd{end+1} = [fOut '[FDRq:' param.dsgn.task '_' param.dsgn.condLabel{k} '_Fstat]'];
end
end
%%% Coef
switch param.model
case {'SPMG2'}
dbstack; error('code that')
fIn = f(i).afni.fStat;
fOut = replace(fIn,'_stats.nii.gz','_coef.nii.gz');
f(i).fs.fCoef = fOut;
if forceThis || ~exist(fOut,'file')
cmd{end+1} = '3dbucket -overwrite \';
cmd{end+1} = ['-prefix ' fOut ' \'];
cmd{end+1} = [fIn '[' param.funDsgn.label '#0_Coef,' param.funDsgn.label '#1_Coef]'];
end
case {'SPMG3'}
dbstack; error('code that')
case {'TENT' 'TENTzero'}
otherwise
dbstack; error('code that');
end
end
%%% Baseline (simple temporal average)
fOut = cell(size(f));
fOutExist = false(size(f));
for i = 1:numel(f)
% average within run
fOutR = cell(size(f(i).afni.fIn));
for R = 1:size(f(i).afni.fIn,1)
fIn = f(i).afni.fIn{R};
fOutR{R} = replace(fIn,'preproc_volTs.nii.gz','av_preproc_volTs.nii.gz');
if force || ~exist(fOutR{R},'file')
cmd{end+1} = '3dTstat -overwrite \';
cmd{end+1} = ['-prefix ' fOutR{R} ' \'];
cmd{end+1} = fIn;
end
end
if size(f(i).afni.fIn,1)==1
f(i).fs.fBaseAv = char(fOutR);
else
% catenate runs
fIn = fOutR;
fOut{i} = fIn{1}; fOut{i} = strsplit(fOut{i},'_run-'); fOut{i}{2} = strsplit(fOut{i}{2},'_'); fOut{i}{2}{1} = 'cat'; fOut{i}{2} = strjoin(fOut{i}{2},'_'); fOut{i} = strjoin(fOut{i},'_run-');
if force || ~exist(fOut{i},'file')
cmd{end+1} = '3dTcat -overwrite \';
cmd{end+1} = ['-prefix ' fOut{i} ' \'];
cmd{end+1} = strjoin(fIn,' ');
end
% average across runs
fIn = fOut{i};
fOut{i} = replace(fOut{i},'_run-cat','_run-avCat');
if force || ~exist(fOut{i},'file')
cmd{end+1} = '3dTstat -overwrite \';
cmd{end+1} = ['-prefix ' fOut{i} ' \'];
cmd{end+1} = fIn;
end
f(i).fs.fBaseAv = fOut{i};
end
end
% if any(~fOutExist)
% nFrame = [];
% tsAv = [];
% for R = 1:size(f,1)
% fIn = f(R,1).afni.fIn;
% if length(fIn)>1 && R==size(f,1)
% mri.vol = tsAv./nFrame;
% MRIwrite(mri,fOut{R,1});
% elseif length(fIn)==1
% mri = MRIload3(char(fIn),[],[],0);
% mri.vol = sum(mri.vol,4);
% if R==1
% tsAv = mri.vol;
% nFrame = mri.nframes;
% else
% tsAv = tsAv + mri.vol;
% nFrame = nFrame + mri.nframes;
% end
% mri.vol = mri.vol./mri.nframes;
% MRIwrite(mri,fOut{R,1});
% else
% dbstack; error('X');
% end
% end
% end
end
% if ~isempty(fRun) && ~isempty(fSes)
% fRun = f(1:end-1,:);
% fSes = f(end,:);
% f = [];
% else
% dbstack; error('X');
% end
% if nEcho>1
% dbstack; error('code that');
% switch param.model
% case {'SPMG2' 'SPMG3'}
% dbstack; error('code that');
% case {'TENT' 'TENTzero'}
% for i = 1:numel(fSes_echoRms)
% fIn = fSes_echoRms(i).fStat;
% fOut = replace(fIn,'_stats.nii.gz','_respFval.nii.gz');
% fSes_echoRms(i).fRespStat = fOut;
% if forceThis || ~exist(fOut,'file')
% cmd{end+1} = '3dbucket -overwrite \';
% cmd{end+1} = ['-prefix ' fOut ' \'];
% cmd{end+1} = [fIn '[Full_Fstat]'];
% end
% end
% for i = 1:numel(fRun_echoRms)
% fIn = fRun_echoRms(i).fStat;
% fOut = replace(fIn,'_stats.nii.gz','_respFval.nii.gz');
% fRun_echoRms(i).fRespStat = fOut;
% if forceThis || ~exist(fOut,'file')
% cmd{end+1} = '3dbucket -overwrite \';
% cmd{end+1} = ['-prefix ' fOut ' \'];
% cmd{end+1} = [fIn '[Full_Fstat]'];
% end
% end
% otherwise
% dbstack; error('code that');
% end
% end
%%% Run system commands
if length(cmd)>1
if verbose
[status,cmdout] = system(strjoin(cmd,newline),'-echo'); if status || isempty(cmdout); dbstack; error(cmdout); error('x'); end
else
[status,cmdout] = system(strjoin(cmd,newline)); if status || isempty(cmdout); dbstack; error(cmdout); error('x'); end
% [status,cmdout] = system(strjoin(cmd(1:4),newline)); if status || isempty(cmdout); dbstack; error(cmdout); error('x'); end
end
disp(' done')
else
disp(' already done, skipping')
end
%%% Convert SPMG2 cartesian responses coefficient (gamma + first derivative) to polar (amplitude + delay) coefficient
switch param.model
case {'SPMG2'}
% dbstack; error('double-check that')
disp('convert hrf+derivative cartesian coefficients to polar coefficients')
for i = 1:size(f,1)
fIn = f(i).fs.fCoef;
fOut = replace(fIn,'_coef.nii.gz','_coefPol.nii.gz');
fOutFig = replace(fIn,'_coef.nii.gz','_coefPol.fig');
fFDR = f(i).fs.fFullQ;
f(i).fs.fCoefPol = fOut;
verboseThis = verbose;
forceThis = force;
if forceThis || ~exist(fOut,'file') || ~exist(fOutFig,'file')
% hMat = figure('WindowStyle','docked');
hMat = figure('Visible','off');
coef = MRIread(fIn);
fdr = MRIread(fFDR);
mask = MRIread(fMask);
mask = mask.vol & fdr.vol<0.05;
coef.vol = complex(coef.vol(:,:,:,1),coef.vol(:,:,:,2));
scatter(real(coef.vol(mask)),imag(coef.vol(mask)));
ax = gca; ax.DataAspectRatio = [1 1 1];
grid on
axis([-1 1 -1 1].*max(abs(axis)))
xline(0,'k'); yline(0,'k');
xlabel('SPM canon (coef)')
ylabel('SPM canon derivative (coef)')
%get principal vector
slp = real(coef.vol(mask))\imag(coef.vol(mask));
hRef = refline(slp,0); hRef.Color = 'r';
v = complex(1,slp); v = v./abs(v);
title([num2str(angle(v)/pi*180,'%0.1f°') ' deviation from expected HR delay'])
% subtract that vector orientation from data
coefPol = coef;
coefPol.vol(:,:,:,1) = abs(coef.vol);
coefPol.vol(:,:,:,2) = wrapToPi( angle(coef.vol) - angle(v) );
MRIwrite(coefPol,fOut);
if verboseThis>1
hMat.Visible = 'on';
hMat.WindowStyle = 'docked';
savefig(hMat,fOutFig,'compact')
else
set(hMat, 'CreateFcn', 'set(gcbo,''Visible'',''on'')');
savefig(hMat,fOutFig,'compact')
close(hMat)
end
disp(' done')
else
disp(' already done, skipping')
end
end
% fIn = fSes(i).fs.fCoef;
% fOut = replace(fIn,'_coef.nii.gz','_coefPol.nii.gz');
% fOutFig = replace(fIn,'_coef.nii.gz','_coefPol.fig');
% fSes(i).fs.fCoefPol = fOut;
%
%
% verboseThis = verbose;
% forceThis = 1;
% if forceThis || ~exist(fOut,'file') || ~exist(fOutFig,'file')
% % hMat = figure('WindowStyle','docked');
% hMat = figure('Visible','off');
%
%
% coef = MRIread(fIn);
% fdr = MRIread(fSes(i).fs.fFullQ);
% mask = MRIread(fMask);
% mask = mask.vol & fdr.vol<0.05;
%
% coef.vol = complex(coef.vol(:,:,:,1),coef.vol(:,:,:,2));
% scatter(real(coef.vol(mask)),imag(coef.vol(mask)));
% ax = gca; ax.DataAspectRatio = [1 1 1];
% grid on
% axis([-1 1 -1 1].*max(abs(axis)))
% xline(0,'k'); yline(0,'k');
% xlabel('SPM canon (coef)')
% ylabel('SPM canon derivative (coef)')
%
% %get principal vector
% slp = real(coef.vol(mask))\imag(coef.vol(mask));
% hRef = refline(slp,0); hRef.Color = 'r';
% v = complex(1,slp); v = v./abs(v);
% title([num2str(angle(v)/pi*180,'%0.1f°') ' deviation from expected HR delay'])
%
% % subtract that vector orientation from data
% coefPol = coef;
% coefPol.vol(:,:,:,1) = abs(coef.vol);
% coefPol.vol(:,:,:,2) = wrapToPi( angle(coef.vol) - angle(v) );
% MRIwrite(coefPol,fOut);
%
% if verboseThis>1
% hMat.Visible = 'on';
% hMat.WindowStyle = 'docked';
% else
% close(hMat)
% end
%
% disp(' done')
% else
% disp(' already done, skipping')
% end
case {'SPMG3'}
dbstack; error('code that')
case {'TENT' 'TENTzero'}
otherwise
dbstack; error('code that');
end
%%%%%%%%%%%%%%%%%%%%%%%%%
%% Manipulate baselines %
%%%%%%%%%%%%%%%%%%%%%%%%%
forceThis = force;
cmd = {srcAfni};
if ~isempty(f)
for i = 1:numel(f)
% Extract fitted baseline
fIn = f(i).afni.fStat;
fOut = replace(f(i).fs.fFullF,'_fullFval.nii.gz','_fitBase.nii.gz');
f(i).fs.fBaseFit = fOut;
if force || ~exist(fOut,'file')
buck = num2str(1:size(f(i).afni.fIn,1),'Run#%iPol#0_Coef,'); buck(end) = [];
cmd{end+1} = '3dcalc -overwrite -TR 999 \';
cmd{end+1} = ['-prefix ' fOut ' \'];
cmd{end+1} = ['-a ' fIn '[' buck '] \'];
cmd{end+1} = '-expr a';
end
% Average fitted baseline across runs
fIn = fOut;
fOut = replace(fOut,'run-cat','run-avCat');
if ~exist(fileparts(fOut),'dir'); mkdir(fileparts(fOut)); end
f(i).fs.fBaseFitAv = fOut;
cmd{end+1} = '3dTstat -overwrite \';
cmd{end+1} = ['-prefix ' fOut ' \'];
cmd{end+1} = fIn;
if ~ismember(param.model,{'TENT' 'TENTzero'}); continue; end
% Add this fitted baseline to response fits
fIn = f(i).fs.fRespTs;
fOut = replace(fIn,'_resp.nii.gz','_respOnBaseFit.nii.gz');
fBase = f(i).fs.fBaseFitAv;
f(i).fs.fRespTsOnBaseFit = fOut;
if force || ~exist(fOut,'file')
cmd{end+1} = '3dcalc -overwrite \';
cmd{end+1} = ['-prefix ' fOut ' \'];
cmd{end+1} = ['-a ' fIn ' \'];
cmd{end+1} = ['-b ' fBase ' \'];
cmd{end+1} = '-expr ''a+b''';
end
% Add ts average baseline to response fits
fIn = f(i).fs.fRespTs;
fOut = replace(fIn,'_resp.nii.gz','_respOnBaseAv.nii.gz');
fBase = f(i).fs.fBaseAv;
f(i).fs.fRespTsOnBaseAv = fOut;
if force || ~exist(fOut,'file')
cmd{end+1} = '3dcalc -overwrite \';
cmd{end+1} = ['-prefix ' fOut ' \'];
cmd{end+1} = ['-a ' fIn ' \'];
cmd{end+1} = ['-b ' fBase ' \'];
cmd{end+1} = '-expr ''a+b''';
end
end
end
if param.skipRun && ~param.skipCat
fRun = [];
fSes = f;
elseif ~param.skipRun && ~param.skipCat
fRun = f(1:end-1);
fSes = f(end);
clear f
else
dbstack; error('fix that mess')
if ~isempty(fRun) && ~isempty(fSes)
fRun = f(1:end-1,:);
fSes = f(end,:);
f = [];
else
dbstack; error('X');
end
end
%
% % Fitted baseline
% forceThis = force;
% cmd = {srcAfni};
% %%% Run by run
% if ~isempty(fRun)
% for i = 1:numel(fRun)
% fIn = fRun(i).afni.fStat;
% fOut = replace(fRun(i).fs.fFullF,'_fullFval.nii.gz','_fitBase.nii.gz');
% fRun(i).fs.fBaseFit = fOut;
% if force || ~exist(fOut,'file')
% buck = num2str(1,'Run#%iPol#0_Coef,'); buck(end) = [];
%
% cmd{end+1} = '3dcalc -overwrite \';
% cmd{end+1} = ['-prefix ' fOut ' \'];
% cmd{end+1} = ['-a ' fIn '[' buck '] \'];
% cmd{end+1} = '-expr a';
% end
% end
% end
% %%% Whole session
% if ~isempty(fSes)
% for i = 1:numel(fSes)
% % Fitted baseline
% fIn = fSes(i).afni.fStat;
% fOut = replace(fSes(i).fs.fFullF,'_fullFval.nii.gz','_fitBase.nii.gz');
% fSes(i).fs.fBaseFit = fOut;
% if force || ~exist(fOut,'file')
% buck = num2str(1:nRun,'Run#%iPol#0_Coef,'); buck(end) = [];
%
% cmd{end+1} = '3dcalc -overwrite \';
% cmd{end+1} = ['-prefix ' fOut ' \'];
% cmd{end+1} = ['-a ' fIn '[' buck '] \'];
% cmd{end+1} = '-expr a';
%
% % %add the mean cross-run mean as the first frame
% % fTmp = replace(fOut,'.nii.gz','TMP.nii.gz');
% % cmd{end+1} = '3dTstat -overwrite \';
% % cmd{end+1} = '-mean \';
% % cmd{end+1} = ['-prefix ' fTmp ' \'];
% % cmd{end+1} = [fIn '[' buck ']'];
% % cmd{end+1} = '3dTcat -overwrite \';
% % cmd{end+1} = ['-prefix ' fOut ' \'];
% % cmd{end+1} = [fTmp ' ' fOut];
% end
% end
%
% % Add baseline to response
% switch param.model
% case {'SPMG2' 'SPMG3'}
% case {'TENT' 'TENTzero'}
% fIn = fSes(i).fs.fRespTs;
%
% fOut = replace(fIn,'_resp.nii.gz','_respOnBaseAv.nii.gz');
% fBase = fSes(i).fs.fBaseAv;
% fSes(i).fs.fRespTsOnBaseAv = fOut;
% if force || ~exist(fOut,'file')
% cmd{end+1} = '3dcalc -overwrite \';
% cmd{end+1} = ['-prefix ' fOut ' \'];
% cmd{end+1} = ['-a ' fIn ' \'];
% cmd{end+1} = ['-b ' fBase '[0] \'];
% cmd{end+1} = '-expr ''a+b''';
% end
% fOut = replace(fIn,'_resp.nii.gz','_respOnBaseFit.nii.gz');
% fBase = fSes(i).fs.fBaseFit;
% fSes(i).fs.fRespTsOnBaseFit = fOut;
% if force || ~exist(fOut,'file')
% cmd{end+1} = '3dcalc -overwrite \';
% cmd{end+1} = ['-prefix ' fOut ' \'];
% cmd{end+1} = ['-a ' fIn ' \'];
% cmd{end+1} = ['-b ' fBase '[0] \'];
% cmd{end+1} = '-expr ''a+b''';
% end
% otherwise
% dbstack; error('X');
% end
%
% end
%
%
%
%
% %%% Each run
% if ~isempty(fRun)
% dbstack; error('code that')
% for R = 1:nRun
% for E = 1:nEcho+1
% %%%% Define file names
% if E>nEcho
% if nEcho==1; continue; end
% fResp = fRun_echoRms(R,1).fResp;
% fBase = replace(fResp,'_resp.nii.gz','_base.nii.gz');
% fRespOnBase = replace(fResp,'_resp.nii.gz','_respOnBase.nii.gz');
% fRun_echoRms(R,1).fBase = fBase;
% fRun_echoRms(R,1).fRespOnBase = fRespOnBase;
% % if useFittedBaseline
% % Use fitted baseline
% fStat = fRun_echoRms(R,1).fStat;
% % else
% % % Use plain average as baseline
% % copyfile(fFunc.fAvCatAvEchoRms,fBase);
% % end
% else
% fResp = fRun(R,E).fResp;
% fBase = replace(fResp,'_resp.nii.gz','_base.nii.gz');
% fRespOnBase = replace(fResp,'_resp.nii.gz','_respOnBase.nii.gz');
% fRun(R,E).fBase = fBase;
% fRun(R,E).fRespOnBase = fRespOnBase;
% % if useFittedBaseline
% % Use fitted baseline
% fStat = fRun(R,E).fStat;
% % else
% % % Use plain average as baseline
% % copyfile(fFunc.fAvCatAv{E},fBase);
% % end
% end
%
% % if useFittedBaseline
% %%% Average fitted baselines across runs
% cmd{end+1} = '3dTstat -overwrite \';
% cmd{end+1} = '-mean \';
% cmd{end+1} = ['-prefix ' fBase ' \'];
% % buck = num2str(1:size(fRun,1),'Run#%iPol#0_Coef,'); buck(end) = [];
% buck = 'Run#1Pol#0_Coef';
% cmd{end+1} = [fStat '[' buck ']'];
% % end
%
% %%% Add baseline to response
% cmd{end+1} = '3dcalc -overwrite \';
% cmd{end+1} = ['-prefix ' fRespOnBase ' \'];
% cmd{end+1} = ['-a ' fBase ' \'];
% cmd{end+1} = ['-b ' fResp ' \'];
% cmd{end+1} = '-expr ''a+b''';
% end
% end
% end
%
% %%% Whole session
% if ~isempty(fSes)
% for i = 1:numel(fSes)
% % Simple temporal average as a baseline
% fOut = replace(fSes(i).fs.fFullF,'_fullFval.nii.gz','_tsAv.nii.gz');
% fSes(i).fs.fBaseAv = fOut;
% if force || ~exist(fOut,'file')
% tsAv = volTs(1);
% tsAv.vol = zeros([tsAv.volsize size(volTs,1)]);
% nframes = zeros([1 1 1 size(volTs) ]);
% for r = 1:size(volTs,1)
% if ~isempty(volTs(r).vol)
% tmp = volTs(r);
% else
% tmp = MRIload3(volTs(r),[],[],0);
% end
% tsAv.vol(:,:,:,r) = mean(tmp.vol,4);
% nframes( 1,1,1,r) = tmp.nframes;
% end
% % add the mean cross-run mean as the first frame
% tsAv.vol = cat(4,sum(tsAv.vol.*nframes,4)./sum(nframes),tsAv.vol);
% MRIwrite(tsAv,fOut);
% end
%
% % Fitted baseline
% fIn = fSes(i).afni.fStat;
% fOut = replace(fSes(i).fs.fFullF,'_fullFval.nii.gz','_fitBase.nii.gz');
% fSes(i).fs.fBaseFit = fOut;
% if force || ~exist(fOut,'file')
% buck = num2str(1:nRun,'Run#%iPol#0_Coef,'); buck(end) = [];
%
% cmd{end+1} = '3dcalc -overwrite \';
% cmd{end+1} = ['-prefix ' fOut ' \'];
% cmd{end+1} = ['-a ' fIn '[' buck '] \'];
% cmd{end+1} = '-expr a';
%
% %add the mean cross-run mean as the first frame
% fTmp = replace(fOut,'.nii.gz','TMP.nii.gz');
% cmd{end+1} = '3dTstat -overwrite \';
% cmd{end+1} = '-mean \';
% cmd{end+1} = ['-prefix ' fTmp ' \'];
% cmd{end+1} = [fIn '[' buck ']'];
% cmd{end+1} = '3dTcat -overwrite \';
% cmd{end+1} = ['-prefix ' fOut ' \'];
% cmd{end+1} = [fTmp ' ' fOut];
% end
% end
%
% % Add baseline to response
% switch param.model
% case {'SPMG2' 'SPMG3'}
% case {'TENT' 'TENTzero'}
% fIn = fSes(i).fs.fRespTs;
%
% fOut = replace(fIn,'_resp.nii.gz','_respOnBaseAv.nii.gz');
% fBase = fSes(i).fs.fBaseAv;
% fSes(i).fs.fRespTsOnBaseAv = fOut;
% if force || ~exist(fOut,'file')
% cmd{end+1} = '3dcalc -overwrite \';
% cmd{end+1} = ['-prefix ' fOut ' \'];
% cmd{end+1} = ['-a ' fIn ' \'];
% cmd{end+1} = ['-b ' fBase '[0] \'];
% cmd{end+1} = '-expr ''a+b''';
% end
% fOut = replace(fIn,'_resp.nii.gz','_respOnBaseFit.nii.gz');
% fBase = fSes(i).fs.fBaseFit;
% fSes(i).fs.fRespTsOnBaseFit = fOut;
% if force || ~exist(fOut,'file')
% cmd{end+1} = '3dcalc -overwrite \';
% cmd{end+1} = ['-prefix ' fOut ' \'];
% cmd{end+1} = ['-a ' fIn ' \'];
% cmd{end+1} = ['-b ' fBase '[0] \'];
% cmd{end+1} = '-expr ''a+b''';
% end
% otherwise
% dbstack; error('X');
% end
%
% end
%%% Run command
disp('Writing baselines')
if length(cmd)>1
if verbose
[status,cmdout] = system(strjoin(cmd,newline),'-echo'); if status || isempty(cmdout) || contains(cmdout,'error','IgnoreCase',true); dbstack; error(cmdout); error('x'); end
else
[status,cmdout] = system(strjoin(cmd,newline)); if status || isempty(cmdout) || contains(cmdout,'error','IgnoreCase',true); dbstack; error(cmdout); error('x'); end
end
disp(' done')
else
disp(' already done, skipping')
end
%% %%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%
%% Make videos %%
%%%%%%%%%%%%%%%%%
switch param.model
case {'SPMG2' 'SPMG3'}
case {'TENT' 'TENTzero'}
%%%% Individual runs
if ~param.skipRun
for i = 1:numel(fRun)
fIn = fRun(i).fs.fRespTsOnBaseAv;
fOut = replace(fIn,'.nii.gz','');
% fRun(i).mov.fRespOnBaseAvMovie = [fOut '.avi'];
% fRun(i).mov.fRespOnBaseAvMovieHighBit = [fOut '.mj2'];
fRun(i).mov.fRespOnBaseAvMovie = [];
fRun(i).mov.fRespOnBaseAvMovieHighBit = [];
end
end
%%%% Whole session
if ~param.skipCat
for i = 1:numel(fSes)
fIn = fSes(i).fs.fRespTsOnBaseAv;
fOut = replace(fIn,'.nii.gz','');
fSes(i).mov.fRespOnBaseAvMovie = [fOut '.avi'];
fSes(i).mov.fRespOnBaseAvMovieHighBit = [fOut '.mj2'];
end
end
if ~param.skipMov && volTs(1).depth==1
forceThis = force;
disp('Making movies')
nLoop = 4;
if ~isempty(fMask)
mask = MRIread(fMask); mask = logical(mask.vol);
else
mask = true(volTs.height,volTs.width,volTs.depth);
end
% %%%% Individual runs
% for R = 1:nRun
% for E = 1:nEcho+1
% if E>nEcho && nEcho==1; break; end
% disp([' run' num2str(R) '/' num2str(nRun)])
% disp([' file' num2str(E) '/' num2str(size(fSes,2)+1)])
% if E>nEcho
% fIn = fRun_echoRms(R).fRespOnBase;
% fOut = replace(fIn,'.nii.gz','');
% fRun_echoRms(R).fRespOnBaseMovie = [fOut '.avi'];
% fRun_echoRms(R).fRespOnBaseMovieHighBit = [fOut '.mj2'];
% else
% fIn = fRun(R,E).fRespOnBase;
% fOut = replace(fIn,'.nii.gz','');
% fRun(R,E).fRespOnBaseMovie = [fOut '.avi'];
% fRun(R,E).fRespOnBaseMovieHighBit = [fOut '.mj2'];
% end
% if forceThis || ~exist([fOut '.avi'],'file')
% vOut = VideoWriter(fOut,'Uncompressed AVI');
% end
% if forceThis || ~exist([fOut '.mj2'],'file')
% vOutHighBit = VideoWriter(fOut,'Archival');
% end
%
% if forceThis || ~exist([fOut '.avi'],'file') || ~exist([fOut '.mj2'],'file')
% resp = MRIread(fIn);
% % Scale
% mask = repmat(mask,[1 1 resp.depth resp.nframes]);
% resp.vol(mask) = resp.vol(mask) - min(resp.vol(mask));
% resp.vol(mask) = resp.vol(mask) ./ max(resp.vol(mask));
% mask = mask(:,:,1,1);
% % Crop
% resp.vol(all(~mask,2),:,:,:) = [];
% resp.vol(:,all(~mask,1),:,:) = [];
% % Upsample
% resp.vol = imresize(resp.vol,3,'nearest');
% % Set frame rate to 1cycle/sec
% vOutHighBit.FrameRate = resp.nframes;
% vOut.FrameRate = resp.nframes;
%
% % Write
% open(vOut)
% open(vOutHighBit)
% for L = 1:nLoop
% for f = 1:resp.nframes
% writeVideo(vOut,resp.vol(:,:,1,f));
% writeVideo(vOutHighBit,uint16(resp.vol(:,:,1,f)*(2^16-1)));
% end
% end
% close(vOut)
% close(vOutHighBit)
%
% disp(' done')
% else
% disp(' already done,skipping')
% end
% end
% end
if ~param.skipCat
%%%% Whole session
disp(' runCat')
for E = 1:nEcho+1
if E>nEcho && nEcho==1; break; end
disp([' file' num2str(E) '/' num2str(size(fSes,2)+1)])
if E>nEcho && nEcho>1
dbstack; error('code that');
fIn = fSes_echoRms.fRespOnBase;
fOut = replace(fIn,'.nii.gz','');
fSes_echoRms.fRespOnBaseMovie = [fOut '.avi'];
fSes_echoRms.fRespOnBaseMovieHighBit = [fOut '.mj2'];
else
fIn = fSes(1,E).fs.fRespTsOnBaseAv;
fOut = replace(fIn,'.nii.gz','');
% fSes(1,E).mov.fRespOnBaseAvMovie = [fOut '.avi'];
% fSes(1,E).mov.fRespOnBaseAvMovieHighBit = [fOut '.mj2'];
end
if forceThis || ~exist([fOut '.avi'],'file')
vOut = VideoWriter(fOut,'Uncompressed AVI');
end
if forceThis || ~exist([fOut '.mj2'],'file')
vOutHighBit = VideoWriter(fOut,'Archival');
end
if forceThis || ~exist([fOut '.avi'],'file') || ~exist([fOut '.mj2'],'file')
resp = MRIread(fIn);
mask = repmat(mask,[1 1 resp.depth resp.nframes]);
resp.vol(~mask) = 0;
% Scale
resp.vol(mask) = resp.vol(mask) - min(resp.vol(mask));
resp.vol(mask) = resp.vol(mask) ./ max(resp.vol(mask));
mask = mask(:,:,1,1);
% Crop
resp.vol(all(~mask,2),:,:,:) = [];
resp.vol(:,all(~mask,1),:,:) = [];
% Upsample
resp.vol = imresize(resp.vol,3,'nearest');
% Set frame rate to 1cycle/sec
vOutHighBit.FrameRate = resp.nframes;
vOut.FrameRate = resp.nframes;
% Write
open(vOut)
open(vOutHighBit)
for L = 1:nLoop
for f = 1:resp.nframes
writeVideo(vOut,resp.vol(:,:,1,f));
writeVideo(vOutHighBit,uint16(resp.vol(:,:,1,f)*(2^16-1)));
end
end
close(vOut)
close(vOutHighBit)
disp(' done')
else
disp(' already done,skipping')
end
end
end
end
otherwise
dbstack; error('X');
end