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getResp2.m
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getResp2.m
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function [files,fRun,fSes,fSes_echoCat,param] = getResp2(volTs,dsgn,fMask,param,force,verbose)
% see /autofs/space/takoyaki_001/users/proulxs/tools/vasomoTools/getAct.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'); volAnat = []; 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
%% Data files
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
%% Mask files
if isempty(fMask)
if isfield(volTs,'vol2vec')
fMask = volTs.vol2vec;
end
end
if ~all(diff([volTs.tr])<0.01); dbstack; error('runs have different tr'); end
%% Functional design
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;
param.funDsgn.condSeq = ones(size(param.funDsgn.startSeq));
param.funDsgn.label = dsgn.label;
param.funDsgn.trDecon = param.trDecon;
%% Run afni's 3dDeconvolve
[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);
%% Simplify stat outputs
disp('Simplifying stat outputs')
forceThis = force;
cmd = {srcAfni};
for i = 1:numel(fSes)
fIn = fSes(i).fStat;
fOut = replace(fIn,'_stats.nii.gz','_respF.nii.gz');
fSes(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)
fIn = fRun(i).fStat;
fOut = replace(fIn,'_stats.nii.gz','_respF.nii.gz');
fRun(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
if nEcho>1
for i = 1:numel(fSes_echoRms)
fIn = fSes_echoRms(i).fStat;
fOut = replace(fIn,'_stats.nii.gz','_respF.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','_respF.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
end
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
%% Add baseline to estimated responses (for later visualization as movies)
forceThis = force;
% useFittedBaseline = 1;
cmd = {srcAfni};
%%% Each run
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
%%% Whole session
if nRun>1 && ~isempty(fSes) && ~param.skipCat
for E = 1:nEcho+1
%%% Define file names
if E>nEcho
if nEcho==1; continue; end
fResp = fSes_echoRms.fResp;
fBase = replace(fResp,'_resp.nii.gz','_base.nii.gz');
fRespOnBase = replace(fResp,'_resp.nii.gz','_respOnBase.nii.gz');
fSes_echoRms.fBase = fBase;
fSes_echoRms.fRespOnBase = fRespOnBase;
% if useFittedBaseline
% Use fitted baseline
fStat = fSes_echoRms.fStat;
% else
% % Use plain average as baseline
% copyfile(fFunc.fAvCatAvEchoRms,fBase);
% end
else
fResp = fSes(1,E).fResp;
fBase = replace(fResp,'_resp.nii.gz','_base.nii.gz');
fRespOnBase = replace(fResp,'_resp.nii.gz','_respOnBase.nii.gz');
fSes(1,E).fBase = fBase;
fSes(1,E).fRespOnBase = fRespOnBase;
% if useFittedBaseline
% Use fitted baseline
fStat = fSes(1,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) = [];
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
% else
% fSes = fRun;
end
%%% Run command
disp('Adding estimated baseline and responses for visualization as movies')
if forceThis || ~exist(fRespOnBase,'file') || ~exist(fBase,'file')
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
end
disp(' done')
else
disp(' already done, skipping')
end
%%% Make the movies
movieFlag = MRIread(fVolTs{1},1); movieFlag = movieFlag.depth==1;
if movieFlag
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 nRun>1 && ~isempty(fSes) && ~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
fIn = fSes_echoRms.fRespOnBase;
fOut = replace(fIn,'.nii.gz','');
fSes_echoRms.fRespOnBaseMovie = [fOut '.avi'];
fSes_echoRms.fRespOnBaseMovieHighBit = [fOut '.mj2'];
else
fIn = fSes(1,E).fRespOnBase;
fOut = replace(fIn,'.nii.gz','');
fSes(1,E).fRespOnBaseMovie = [fOut '.avi'];
fSes(1,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
end
%% Reconcile output with convention
forceThis = force;
disp('Catenating functional analyses')
cmd = {srcAfni};
fieldListIn = {'fBase' 'fResp' 'fRespOnBase' 'fRespOnBaseMovie' 'fRespOnBaseMovieHighBit' 'fRespStat' 'fFit' 'fResid' 'fStat' 'fMat' };
fieldListOut = {'base' 'resp' 'respOnBase' 'respOnBaseMovie' 'respOnBaseMovieHighBit' 'respF' 'fit' 'resid' 'stat' 'dsgnMat'};
for i = 1:length(fieldListIn)
fieldIn = fieldListIn{i};
fieldOut = fieldListOut{i};
% if strcmp(fieldOut,'respF'); keyboard; end
if isfield(fRun,fieldIn)
files.(fieldOut).f = reshape({fRun.(fieldIn)},size(fRun));
end
if nEcho>1 && isfield(fRun_echoRms,fieldIn)
files.(fieldOut).fEchoRms = reshape({fRun_echoRms.(fieldIn)},size(fRun_echoRms));
end
if nRun>1 && ~isempty(fSes) && isfield(fSes,fieldIn) && ~param.skipCat
files.(fieldOut).fSes = reshape({fSes.(fieldIn)},size(fSes));
end
if nRun>1 && nEcho>1 && isfield(fSes_echoRms,fieldIn) && ~isempty(fSes) && ~param.skipCat
files.(fieldOut).fSesEchoRms = reshape({fSes_echoRms.(fieldIn)},size(fSes_echoRms));
end
%%% catenate echo
if nEcho>1
if any(ismember(fieldOut,{'base' 'respF'}))
if isfield(fRun,fieldIn)
fIn = reshape({fRun.(fieldIn)},size(fRun));
files.(fieldOut).fEchoCat = cell([size(fIn,1) 1]);
for R = 1:size(fIn,1)
fOut = fIn{R,1}; fOut = strsplit(fOut,'_'); fOut{contains(fOut,'echo-')} = 'echo-cat'; fOut = {strjoin(fOut,'_')};
files.(fieldOut).fEchoCat(R,1) = fOut; if ~exist(fileparts(char(fOut)),'dir'); mkdir(fileparts(char(fOut))); end
if forceThis || ~exist(char(fOut),'file')
if any(ismember(fieldOut,{'respF'}))
cmd{end+1} = '3dbucket -overwrite \';
else
cmd{end+1} = '3dTcat -overwrite \';
end
cmd{end+1} = ['-prefix ' char(fOut) ' \'];
cmd{end+1} = strjoin(fIn(R,:));
end
end
end
if ~isempty(fSes) && isfield(fSes,fieldIn) && ~param.skipCat
fIn = {fSes.(fieldIn)};
fOut = fIn{1}; fOut = strsplit(fOut,'_'); fOut{contains(fOut,'echo-')} = 'echo-cat'; fOut = {strjoin(fOut,'_')};
files.(fieldOut).fSesEchoCat = fOut; if ~exist(fileparts(char(fOut)),'dir'); mkdir(fileparts(char(fOut))); end
if forceThis || ~exist(char(fOut),'file')
if any(ismember(fieldOut,{'respF'}))
cmd{end+1} = '3dbucket -overwrite \';
else
cmd{end+1} = '3dTcat -overwrite \';
end
cmd{end+1} = ['-prefix ' char(fOut) ' \'];
cmd{end+1} = strjoin(fIn);
end
end
end
end
%%% catenate runs
if nRun>1
if any(ismember(fieldOut,{'base' 'respF'}))
if isfield(fRun,fieldIn)
fIn = reshape({fRun.(fieldIn)},size(fRun));
files.(fieldOut).fCat = cell([1 size(fIn,2)]);
for E = 1:size(fIn,2)
fOut = fIn{1,E}; fOut = strsplit(fOut,'_'); fOut{contains(fOut,'run-')} = 'run-cat'; fOut = {strjoin(fOut,'_')};
fOut = strsplit(char(fOut),filesep); fOut{end} = ['run-cat_' fOut{end}]; fOut = {strjoin(fOut,filesep)};
files.(fieldOut).fCat(1,E) = fOut; if ~exist(fileparts(char(fOut)),'dir'); mkdir(fileparts(char(fOut))); end
if forceThis || ~exist(char(fOut),'file')
if any(ismember(fieldOut,{'respF'}))
cmd{end+1} = '3dbucket -overwrite \';
else
cmd{end+1} = '3dTcat -overwrite \';
end
cmd{end+1} = ['-prefix ' char(fOut) ' \'];
cmd{end+1} = strjoin(fIn(:,E));
end
end
if nEcho>1
fIn = reshape({fRun_echoRms.(fieldIn)},size(fRun_echoRms));
fOut = fIn{1}; fOut = strsplit(fOut,'_'); fOut{contains(fOut,'run-')} = 'run-cat'; fOut = {strjoin(fOut,'_')};
fOut = strsplit(char(fOut),filesep); fOut{end} = ['run-cat_' fOut{end}]; fOut = {strjoin(fOut,filesep)};
files.(fieldOut).fCatEchoRms = fOut; if ~exist(fileparts(char(fOut)),'dir'); mkdir(fileparts(char(fOut))); end
if forceThis || ~exist(char(fOut),'file')
if any(ismember(fieldOut,{'respF'}))
cmd{end+1} = '3dbucket -overwrite \';
else
cmd{end+1} = '3dTcat -overwrite \';
end
cmd{end+1} = ['-prefix ' char(fOut) ' \'];
cmd{end+1} = strjoin(fIn(:));
end
end
end
end
end
end
%% Produce fdr maps
%clean up the old catenation approach
if param.skipCat
if isfield(files.respF,'fCat')
if exist(char(files.respF.fCat),'file')
delete(char(files.respF.fCat))
end
files.respF = rmfield(files.respF,'fCat');
end
end
fieldList = fields(files.respF);
for i = 1:length(fieldList)
f = files.respF.(fieldList{i});
fOut = replace(f,'_respF.nii.gz','_respFfdr.nii.gz');
for E = 1:size(f,2)
for R = 1:size(f,1)
if force || ~exist(fOut{R,E},'file')
cmd{end+1} = ['df=$(3dAttribute BRICK_STATAUX ' f{R,E} ')'];
cmd{end+1} = 'df1=$(echo $df | awk ''{print $(NF-1)}'')';
cmd{end+1} = 'df2=$(echo $df | awk ''{print $NF}'')';
cmd{end+1} = '3dcalc -overwrite \';
cmd{end+1} = ['-prefix ' fOut{R,E} ' \'];
cmd{end+1} = ['-a ' f{R,E} ' \'];
cmd{end+1} = '-expr "1-stat2cdf(a,4,$df1,$df2,0)" 2> /dev/null';
end
end
end
files.respF_fdr.(fieldList{i}) = fOut;
end
% % if nEcho>1
% %%% for each echo
% allCandidate = {'f' 'fCat' 'fSes'};
% for i = 1:length(allCandidate)
% candidate = allCandidate{i};
% if isfield(files.respF,candidate)
% f = files.respF.(candidate);
% fOut = cell(size(f));
% for E = 1:nEcho
% fOut{E} = replace(f{E},'_respF.nii.gz','_respFfdr.nii.gz');
% if force || ~exist(fOut{E},'file')
% cmd{end+1} = ['df=$(3dAttribute BRICK_STATAUX ' f{E} ')'];
% cmd{end+1} = 'df1=$(echo $df | awk ''{print $(NF-1)}'')';
% cmd{end+1} = 'df2=$(echo $df | awk ''{print $NF}'')';
% cmd{end+1} = '3dcalc -overwrite \';
% cmd{end+1} = ['-prefix ' fOut{E} ' \'];
% cmd{end+1} = ['-a ' f{E} ' \'];
% cmd{end+1} = '-expr "1-stat2cdf(a,4,$df1,$df2,0)" 2> /dev/null';
% end
% end
% files.respF_fdr.(candidate) = fOut;
% end
% end
%
% %%% for echo rms
% candidate = {'fSesEchoRms' 'fEchoRms'};
% candidate = candidate(ismember(candidate,fields(files.respF)));
% if ~isempty(candidate)
% candidate = candidate{1};
% f = files.respF.(candidate);
% fOut = cell(size(f));
% E = 1;
% fOut{E} = replace(f{E},'_respF.nii.gz','_respFfdr.nii.gz');
% if force || ~exist(fOut{E},'file')
% cmd{end+1} = ['df=$(3dAttribute BRICK_STATAUX ' f{E} ')'];
% cmd{end+1} = 'df1=$(echo $df | awk ''{print $(NF-1)}'')';
% cmd{end+1} = 'df2=$(echo $df | awk ''{print $NF}'')';
% cmd{end+1} = '3dcalc -overwrite \';
% cmd{end+1} = ['-prefix ' fOut{E} ' \'];
% cmd{end+1} = ['-a ' f{E} ' \'];
% cmd{end+1} = '-expr "1-stat2cdf(a,4,$df1,$df2,0)" 2> /dev/null';
% end
% files.respF_fdr.(candidate) = fOut;
% end
% % else
% % % dbstack; error('code this');
% % end
files.cmd = strjoin(cmd,newline);
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
% %% Generate visualization commands
% if ~isempty(fAnat) && ~isempty(fAnat{1})
% fT1w = fAnat{contains(fAnat,'_T1w.nii.gz')};
%
% ind = contains(fAnat,'echo-rms_satIndex.nii.gz');
% if any(ind); fSatinIndex_echoRms = fAnat{ind}; else; fSatinIndex_echoRms = []; end
% ind = contains(fAnat,'echo-rms_satIndexNumOnBack.nii.gz');
% if any(ind); fSatinIndexPlus_echoRms = fAnat{ind}; else; fSatinIndexPlus_echoRms = []; end
% ind = contains(fAnat,'echo-rms_satIndexNumAbs.nii.gz');
% if any(ind); fSatinIndexAbs_echoRms = fAnat{ind}; else; fSatinIndexAbs_echoRms = []; end
% ind = contains(fAnat,'echo-cat_satIndex.nii.gz');
% if any(ind); fSatinIndex_echoCat = fAnat{ind}; else; fSatinIndex_echoCat = []; end
% ind = contains(fAnat,'echo-cat_satIndexNumOnBack.nii.gz');
% if any(ind); fSatinIndexPlus_echoCat = fAnat{ind}; else; fSatinIndexPlus_echoCat = []; end
% ind = contains(fAnat,'echo-cat_satIndexNumAbs.nii.gz');
% if any(ind); fSatinIndexAbs_echoCat = fAnat{ind}; else; fSatinIndexAbs_echoCat = []; end
% else
% fT1w = [];
% fSatinIndex_echoRms = [];
% fSatinIndexPlus_echoRms = [];
% fSatinIndexAbs_echoRms = [];
% fSatinIndex_echoCat = [];
% fSatinIndexPlus_echoCat = [];
% fSatinIndexAbs_echoCat = [];
% end
% if ~isempty(fFmap) && ~isempty(fFmap{1})
% ind = contains(fFmap,'rec-FA_TB1SRGE.nii.gz');
% if any(ind); fB1 = fFmap{ind}; else; fB1 = []; end
% % fB1 = fFmap{contains(fFmap,'rec-FA_TB1SRGE.nii.gz')};
% else
% fB1 = [];
% end
%
% %%% individual runs
% for I = 1:size(fRun,1)
% E = 1; % multi-echo visualization not implemented
% fRun(I,E).fUnder = fFunc.fAv{I,E};
%
% cmd = {srcAfni};
% if isfield(param,'layout') && ~isempty(param.layout) && exist(param.layout,'file')
% cmd{end+1} = ['afni -layout ' param.layout ' \'];
% else
% cmd{end+1} = 'afni \';
% end
% cmd{end+1} = ['-tbar run' num2str(I) 'echo ' num2str(E) ' \'];
% cmd{end+1} = [fRun(I,E).fUnder ' \'];
% cmd{end+1} = [fRun(I,E).fStat ' \'];
% cmd{end+1} = [fRun(I,E).fResp ' &'];
% cmd = strjoin(cmd,newline); % disp(cmd)
% fRun(I,E).cmdVisAfni = cmd;
%
% if verbose; disp(cmd); end
% if verbose>1; [status,cmdout] = system(cmd); end
%
% % https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.driver.html
% % https://afni.nimh.nih.gov/pub/dist/doc/program_help/plugout_drive.html
% % afni -yesplugouts
% % plugout_drive -com 'SWITCH_SESSION A.afni' \
% % -com 'OPEN_WINDOW A.axialimage geom=600x600+416+44 \
% % ifrac=0.8 opacity=9' \
% % -com 'OPEN_WINDOW A.sagittalimage geom=+45+430 \
% % ifrac=0.8 opacity=9' \
% % -com 'SWITCH_UNDERLAY anat' \
% % -com 'SWITCH_OVERLAY strip' \
% % -com 'SEE_OVERLAY +' \
% % -com 'SET_DICOM_XYZ 7 12 2' \
% % -com 'OPEN_WINDOW A.axialimage keypress=v' \
% % -quit
% %
% % SET_SUBBRICKS
%
%
%
% % fT1w = dir(fullfile(bidsDir,'anat','*proc-RMS_T1w.nii.gz')); fT1w = fullfile(fT1w.folder,fT1w.name);
% % fB1 = dir(fullfile(bidsDir,'fmap','*rec-FA_TB1SRGE.nii.gz')); fB1 = fullfile(fB1.folder,fB1.name);
% cmd = {srcFs};
% cmd{end+1} = 'freeview \';
% cmd{end+1} = [fRun(I).fUnder ' \'];
% if ~isempty(fT1w)
% cmd{end+1} = [fT1w ':resample=cubic \'];
% end
% if ~isempty(fB1)
% cmd{end+1} = [fB1 ':resample=cubic:visible=0 \'];
% end
% cmd{end+1} = [fRun(I).fResp ':resample=cubic:visible=0 \'];
% if ~isempty(fSatinIndexPlus_echoRms)
% cmd{end+1} = [fSatinIndexPlus_echoRms ':resample=cubic:visible=0 \'];
% end
% thresh = abs(norminv(0.95));
% if ~isempty(fSatinIndex_echoRms)
% cmd{end+1} = [fSatinIndex_echoRms ':colormap=heat:resample=cubic:visible=0 \'];
% end
% cmd{end+1} = [fRun(I).fStat ':colormap=heat:resample=cubic:visible=0 &'];
% cmd = strjoin(cmd,newline);
%
% fRun(I).cmdVisFs = cmd;
% end
%
%
% %%% full session
% if isempty(fSes)
% fSes = fRun;
% end
% if isempty(fSes_echoRms)
% fSes_echoRms = fRun_echoRms;
% end
%
% if nEcho>1
% if isempty(fSes_echoRms)
% fSes_echoRms = fRun_echoRms;
% end
% %%%% Multi echo
% %%%%% catenate echo
% fSes_echoCat = fSes(:,1);
% fSes_echoCat.fResp = {fSes.fResp};
% fSes_echoCat.fBase = {fSes.fBase};
% fSes_echoCat.fRespOnBase = {fSes.fRespOnBase};
% fSes_echoCat.fFit = {fSes.fFit};
% fSes_echoCat.fResid = {fSes.fResid};
%
% fOut = strsplit(fSes(1).fStat,'_'); fOut{contains(fOut,'echo-')} = 'echo-cat';
% fOut = replace(strjoin(fOut,'_'),'_stats.nii.gz','_fullF.nii.gz'); if ~exist(fileparts(fOut),'dir'); mkdir(fileparts(fOut)); end
%
% cmd = {srcAfni};
% cmd{end+1} = '3dbucket -overwrite \';
% cmd{end+1} = ['-prefix ' fOut ' \'];
% cmd{end+1} = [strjoin({fSes.fStat},'[0] ') '[0]'];
% % cmd = {srcAfni};
% % cmd{end+1} = '3dTcat -overwrite \';
% % cmd{end+1} = ['-prefix ' fOut ' \'];
% % cmd{end+1} = [strjoin({fSes.fStat},'[0] ') '[0]'];
% cmd = strjoin(cmd,newline);
% [status,cmdout] = system(cmd); if status || isempty(cmdout); dbstack; error(cmdout); error('x'); end
% fSes_echoCat.cmd = cmd;
% fSes_echoCat.fStat = fOut;
%
% cadidateField = {'fAvCatAvEchoCat' 'fAvEchoCat' 'fAvCatAv' 'fAv'};
% cadidateField = cadidateField(ismember(cadidateField,fields(fFunc)));
% fSes_echoCat.fUnder = fFunc.(cadidateField{1});
%
% %%%%% catenate cross-echo rms
% fSes_echoCat.rms.fResp = fSes_echoRms.fResp;
% fSes_echoCat.rms.fBase = fSes_echoRms.fBase;
% fSes_echoCat.rms.fRespOnBase = fSes_echoRms.fRespOnBase;
% fSes_echoCat.rms.fRespOnBaseMovie = fSes_echoRms.fRespOnBaseMovie;
% fSes_echoCat.rms.fRespOnBaseMovieHighBit = fSes_echoRms.fRespOnBaseMovieHighBit;
% fSes_echoCat.rms.fFit = fSes_echoRms.fFit;
% fSes_echoCat.rms.fResid = fSes_echoRms.fResid;
% fSes_echoCat.rms.fStat = fSes_echoRms.fStat;
%
% cadidateField = {'fAvCatAvEchoRms' 'fAvEchoRms' 'fAvCatAv' 'fAv'};
% cadidateField = cadidateField(ismember(cadidateField,fields(fFunc)));
% fSes_echoCat.rms.fUnder = fFunc.(cadidateField{1});
%
%
%
%
%
% % %%%%% visulaize with afni
% % cmd = {srcAfni};
% % if isfield(param,'layout') && ~isempty(param.layout) && exist(param.layout,'file')
% % cmd{end+1} = ['afni -layout ' param.layout ' \'];
% % else
% % cmd{end+1} = 'afni \';
% % end
% % cmd{end+1} = ['-tbar ' num2str(size(fRun,1)) 'runs \'];
% % cmd{end+1} = [fSes_echoCat.fUnder ' \'];
% % cmd{end+1} = [fSes_echoCat.rms.fUnder ' \'];
% % cmd{end+1} = [fSes_echoCat.fStat ' \'];
% % cmd{end+1} = [fSes_echoCat.rms.fStat ' \'];
% % cmd{end+1} = [strjoin([fSes_echoCat.fResp fSes_echoCat.rms.fResp],' ') ' &'];
% % cmd = strjoin(cmd,newline); % disp(cmd)
% % fSes_echoCat.cmdVisAfni = cmd;
% %
% % if verbose; disp(cmd); end
% % if verbose>1; [status,cmdout] = system(cmd); end
%
% %%%%% visulaize with freeview
% cmd = {srcFs};
% cmd{end+1} = 'freeview \';
% cmd{end+1} = '-timecourse \';
% % cmd{end+1} = '-subtitle \';
% cmd{end+1} = [char(fSes_echoCat.fUnder) ':name=echo-cat_funcAv:visible=0 \'];
% cmd{end+1} = [char(fSes_echoCat.rms.fUnder) ':name=echo-rms_funcAv:visible=1 \'];
% if ~isempty(fT1w)
% cmd{end+1} = [fT1w ':resample=cubic:name=T1w:visible=0 \'];
% end
% if ~isempty(fB1)
% cmd{end+1} = [fB1 ':colormap=turbo:resample=cubic:name=B1map:colorscale=50,130:visible=0 \'];
% end
% for E = 1:length(fSes_echoCat.fResp)
% tmp = strsplit(fSes_echoCat.fResp{E},'_');
% cmd{end+1} = [fSes_echoCat.fResp{E} ':name=' tmp{contains(tmp,'echo-')} '_resp:visible=0 \'];
% cmd{end+1} = [fSes_echoCat.fBase{E} ':name=' tmp{contains(tmp,'echo-')} '_base:visible=0 \'];
% cmd{end+1} = [fSes_echoCat.fRespOnBase{E} ':name=' tmp{contains(tmp,'echo-')} '_respOnBase:visible=0 \'];
% end
% cmd{end+1} = [fSes_echoCat.rms.fResp ':name=echo-rms_resp:visible=0 \'];
% cmd{end+1} = [fSes_echoCat.rms.fBase ':name=echo-rms_base:visible=0 \'];
% cmd{end+1} = [fSes_echoCat.rms.fRespOnBase ':name=echo-rms_respOnBase:visible=0 \'];
% if ~isempty(fSatinIndexPlus_echoRms)
% cmd{end+1} = [fSatinIndexPlus_echoRms ':resample=cubic:name=echo-rms_satIndexNumPlusBack:visible=0 \'];
% end
% if ~isempty(fSatinIndexPlus_echoCat)
% cmd{end+1} = [fSatinIndexPlus_echoCat ':resample=cubic:name=echo-cat_satIndexNumPlusBack:visible=0 \'];
% end
% if ~isempty(fSatinIndexAbs_echoRms)
% cmd{end+1} = [fSatinIndexAbs_echoRms ':resample=cubic:name=echo-rms_satIndexNumAbs:visible=0 \'];
% end
% if ~isempty(fSatinIndexAbs_echoCat)
% cmd{end+1} = [fSatinIndexAbs_echoCat ':resample=cubic:name=echo-cat_satIndexNumAbs:visible=0 \'];
% end
% if ~isempty(fSatinIndex_echoRms)
% cmd{end+1} = [fSatinIndex_echoRms ':colormap=heat:resample=cubic:name=echo-rms_satIndex:visible=0 \'];
% end
% if ~isempty(fSatinIndex_echoCat)
% cmd{end+1} = [fSatinIndex_echoCat ':colormap=heat:resample=cubic:name=echo-cat_satIndex:visible=0 \'];
% end
%
% for E = 1:size(fSes,2)
% cmdTmp = {srcAfni};
% cmdTmp{end+1} = ['fdrval -qinput ' fSes(E).fStat ' 0 0.05'];
% [~,tmp] = system(strjoin(cmdTmp,newline));
% tmp = strsplit(tmp,newline);
% thresh(E) = str2num(tmp{end-1});
%
% cmdTmp = {srcAfni};
% cmdTmp{end+1} = ['3dBrickStat ' fSes(E).fStat];
% [~,tmp] = system(strjoin(cmdTmp,newline));
% tmp = strsplit(tmp,newline);
% maxF(E) = str2num(tmp{end-1});
% if maxF(E)>20; maxF(E) = 20; end
% cmd{end+1} = [fSes(E).fStat ':colormap=heat:heatscale=' num2str(thresh(E)) ',' num2str(maxF(E)) ':name=echo-' num2str(E) '_fullF:visible=0 \'];
% end
% thresh = mean(thresh);
% maxF = min(maxF); if maxF>20; maxF = 20; end
% cmd{end+1} = [fSes_echoCat.fStat ':colormap=heat:heatscale=' num2str(thresh) ',' num2str(maxF) ':name=echo-cat_fullF:visible=0 \'];
%
% cmdTmp = {srcAfni};
% cmdTmp{end+1} = ['fdrval -qinput ' fSes_echoCat.rms.fStat ' 0 0.05'];
% [~,tmp] = system(strjoin(cmdTmp,newline));
% tmp = strsplit(tmp,newline);
% thresh = str2num(tmp{end-1});
%
% cmdTmp = {srcAfni};
% cmdTmp{end+1} = ['3dBrickStat ' fSes_echoCat.rms.fStat];
% [~,tmp] = system(strjoin(cmdTmp,newline));
% tmp = strsplit(tmp,newline);
% maxF = str2num(tmp{end-1});
% maxF = min(maxF); if maxF>20; maxF = 20; end
% cmd{end+1} = [fSes_echoCat.rms.fStat ':colormap=heat:heatscale=' num2str(mean(thresh)) ',' num2str(maxF) ':name=echo-rms_fullF &'];
%
% cmd = strjoin(cmd,newline);
% fSes_echoCat.cmdVisFs = cmd;
% else
% %%%% single-echo
% fSes_echoCat = [];
% E = 1;
%
% % %%%%% visualize with afni
% % fSes(1,E).fUnder = fFunc.fAvCatAv{1,E};
% % cmd = {srcAfni};
% % if isfield(param,'layout') && ~isempty(param.layout) && exist(param.layout,'file')
% % cmd{end+1} = ['afni -layout ' param.layout ' \'];
% % else
% % cmd{end+1} = 'afni \';
% % end
% % cmd{end+1} = ['-tbar ' num2str(size(fRun,1)) 'runs \'];
% % cmd{end+1} = [fSes(1,E).fUnder ' \'];
% % cmd{end+1} = [fSes(1,E).fStat ' \'];
% % cmd{end+1} = [fSes(1,E).fResp ' &'];
% % cmd = strjoin(cmd,newline); %disp(cmd)
% % fSes(1,E).cmdVisAfni = cmd;
% %
% % if verbose; disp(cmd); end
% % if verbose>1; [status,cmdout] = system(cmd); if status || isempty(cmdout); dbstack; error(cmdout); error('x'); end; end
%
% %%%%% visualize with freeview
% cmd = {srcFs};
% cmd{end+1} = 'freeview \';
% cmd{end+1} = [fSes(1,E).fBase ' \'];
% if ~isempty(fT1w)
% cmd{end+1} = [fT1w ':resample=cubic \'];
% end
% if ~isempty(fB1)
% cmd{end+1} = [fB1 ':resample=cubic:visible=0 \'];
% end
% cmd{end+1} = [fSes(1,E).fResp ':resample=cubic:visible=0 \'];
% if ~isempty(fSatinIndexPlus_echoRms)
% cmd{end+1} = [fSatinIndexPlus_echoRms ':resample=cubic:visible=0 \'];
% end
% thresh = abs(norminv(0.95));
% if ~isempty(fSatinIndex_echoRms)
% cmd{end+1} = [fSatinIndex_echoRms ':colormap=heat:resample=cubic:visible=0 \'];
% end
% cmd{end+1} = [fSes(1,E).fStat ':colormap=heat:resample=cubic &'];
% cmd = strjoin(cmd,newline);
%
% fSes(1,E).cmdVisFs = cmd;
% end
function [fRun,fSes,param] = runAfni(fList,param,fMask,force,verbose)
global srcAfni srcFs
if ~exist('fMask','var'); fMask = []; end
if ~exist('force','var'); force = []; end
if ~exist('verbose','var'); verbose = []; end
if isempty(force); force = 0; end
if isempty(verbose); verbose = 0; end
%% %%%%%%%%%%%%%%%%%%
% Functional design %
%%%%%%%%%%%%%%%%%% %%
k = param.funDsgn.k;
trStim = param.funDsgn.trStim;
durSeq = param.funDsgn.durSeq;
condSeq = param.funDsgn.condSeq;
startSeq = param.funDsgn.startSeq;
%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Fixed-effect model on individual runs %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%
trDecon = param.funDsgn.trDecon;
TENTzeroFlag = 1;
cmd = {srcAfni};
for E = 1:size(fList,2)
for I = 1:size(fList,1)
%% Define files
fIn = fList{I,E};
fOut = fIn;
fStat = fullfile(fileparts(replace(fOut,'.nii.gz','')),'cond-visOn_stats.nii.gz');
fMat = fullfile(fileparts(replace(fOut,'.nii.gz','')),'cond-visOn_stats.xmat.1D');
fMatFig = fullfile(fileparts(replace(fOut,'.nii.gz','')),'cond-visOn_stats.xmat.fig');
fStim = fullfile(fileparts(replace(fOut,'.nii.gz','')),'cond-visOn_startTime.1D');
fResp = fullfile(fileparts(replace(fOut,'.nii.gz','')),'cond-visOn_resp.nii.gz');
fFit = fullfile(fileparts(replace(fOut,'.nii.gz','')),'cond-visOn_fit.nii.gz');
fResid = fullfile(fileparts(replace(fOut,'.nii.gz','')),'cond-visOn_resid.nii.gz');
fRun(I,E).fResp = fResp;
fRun(I,E).fFit = fFit;
fRun(I,E).fResid = fResid;
fRun(I,E).fStat = fStat;
fRun(I,E).fMat = fMat;
fRun(I,E).fMatFig = fMatFig;
%% Construct afni command
cmdTmp = {};
if size(fList,2)>1
cmdTmp{end+1} = ['echo '' ''run' num2str(I) '/' num2str(size(fList,1)) ' -- echo' num2str(E) '/' num2str(size(fList,2))];
else
cmdTmp{end+1} = ['echo '' ''run' num2str(I) '/' num2str(size(fList,1))];
end
% if ~exist(fStat,'file') || force
if ~isfield(param.funDsgn,'trDecon')
if isfield(param.funDsgn,'trStim')
param.funDsgn.trDecon = param.funDsgn.trStim;
else
dbstack; error('please specify deconvolution time resolution (param.funDsgn.trDecon)');
end
end
[tmp,n] = afniCmd(fIn,fMask,fStim,param.nDummy,param.tr,startSeq,condSeq,trDecon,param.funDsgn.label,TENTzeroFlag,fResp,fFit,fResid,fMat,fStat,verbose,param.nDummyRemoved);
cmdTmp = [cmdTmp tmp];
cmdTmp{end+1} = ['echo '' ''' fResp];
cmdTmp{end+1} = ['echo '' ''' fStat];
cmdTmp{end+1} = ['echo '' ''' fMat];
cmdTmp{end+1} = 'echo '' ''done';
% else
% cmdTmp{end+1} = ['echo '' ''' fResp];
% cmdTmp{end+1} = ['echo '' ''' fStat];
% cmdTmp{end+1} = ['echo '' ''' fMat];
% cmdTmp{end+1} = 'echo '' ''already done, skipping';
% end
fRun(I,E).cmd = strjoin(cmdTmp,newline);
if exist(fStat,'file') && ~force
cmdTmp(startsWith(cmdTmp,'-') | startsWith(cmdTmp,'3dDeconvolve')) = [];
cmdTmp{ismember(cmdTmp,{'echo '' ''done'})} = 'echo '' ''already done, skipping';
cmdTmp(endsWith(cmdTmp,' ''done')) = [];
end
cmd = [cmd cmdTmp];
% [status,cmdout] = system(strjoin(cmdTmp,newline),'-echo');
end
end
% %% Extract and plot design matrix
% if verbose>1
% mri = MRIread(fIn,1); trMri = mri.tr/1000; nFrame = mri.nframes-(param.nDummy - param.nDummyRemoved); clear mri
% cmdX = cmdTmp;
% cmdX{contains(cmdTmp,'-input ')} = ['-nodata ' num2str(nFrame) ' ' num2str(trMri,'%f') ' \'];
% ind = find(contains(cmdX,' \'),1,'last');
% cmdX = [cmdX(1:ind) {'-x1D_stop \'} cmdX(ind+1:end)];
% % cmdX = [cmdX(1:end-2) {'-x1D_stop \'} cmdX(end-1:end)];
% cmdX{end} = [cmdX{end}];
% % [status,cmdout] = system(strjoin(cmdX,newline));
% [status,cmdout] = system(strjoin(cmdX,newline),'-echo'); if status || isempty(cmdout) || contains(cmdout,'ERROR'); dbstack; error(cmdout); error('x'); end
% cmdX = {srcAfni};
% cmdX{end+1} = ['1dcat ' fMat];
% % [status,cmdout] = system(strjoin(cmdX,newline));
% [status,cmdout] = system(strjoin(cmdX,newline),'-echo'); if status || isempty(cmdout) || contains(cmdout,'ERROR'); dbstack; error(cmdout); error('x'); end
% param.funDsgn.mat = str2num(cmdout);
% figure('WindowStyle','docked');
% pInd = false([1 size(param.funDsgn.mat,2)]);
% if TENTzeroFlag
% pInd(1:(size(param.funDsgn.mat,2) - n + 2)) = true;
% else
% pInd(1:(size(param.funDsgn.mat,2) - n)) = true;
% end
% % imagesc(param.funDsgn.mat(:,pInd:end)); colormap gray
% imagesc(param.funDsgn.mat); colormap gray
% ax = gca;
% ax.XTick = 1:size(param.funDsgn.mat,2);
% ax.XTickLabel(pInd) = cell(1,nnz(pInd));
% ax.XTickLabel(~pInd) = cellstr(num2str(((0:nnz(~pInd)-1)*dt)','%0.3f'));
% clim([-1 1])
% end
%% Run afni command
[status,cmdout] = system(strjoin(cmd,newline),'-echo'); if status || isempty(cmdout) || contains(cmdout,'ERROR'); dbstack; error(cmdout); error('x'); end