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doIt_vsmDriven3.m
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doIt_vsmDriven3.m
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% Branching from doIt_vsmDriven2.m. Here we start doing
% run-condition-specific functional analysis
clear all
close all
[outDir,pipId] = fileparts(mfilename('fullpath'));
outDir = fullfile(outDir,pipId); if ~exist(outDir,'dir'); mkdir(outDir); end
%%%%%%%%%%%%%%%%
%% Preparation %
%%%%%%%%%%%%%%%%
%%% Dependencies
% matlab
addpath(genpath(fullfile(pwd,pipId)))
addpath(genpath('/usr/local/freesurfer/stable7.4.1/matlab/'))
addpath(genpath('/space/takoyaki/1/users/proulxs/tools/chronux'))
addpath(genpath('/space/takoyaki/1/users/proulxs/tools/vasomoTools'))
addpath(genpath('/space/takoyaki/1/users/proulxs/tools/bassReg2'))
addpath(genpath('/space/takoyaki/1/users/proulxs/tools/martinosTools'))
% bash
global srcAfni srcFs
srcFs = 'source /usr/local/freesurfer/fs-stable741-env-autoselect';
srcAfni = 'export PATH=$PATH:/usr/pubsw/packages/AFNI/23.1.05';
info.dataSetLabel = 'vsmDriven'; % 'svfmri_long_short' 'satin' 'mitraShahin' 'feruJingyuan'
%%% Variables and Paths
switch info.dataSetLabel
case 'vsmDriven'
info.preprocDir = outDir;
info.pipId = pipId;
info.bidsDir = fullfile(info.preprocDir,'bids'); if ~exist(info.bidsDir,'dir'); mkdir(info.bidsDir); end
%%% Data location
info.dbDir = '/space/takoyaki/1/users/proulxs/vasomo/source/expDb';
otherwise
dbstack; error('code that')
end
%% %%%%%%%%%%%%%
%% %%%%%%%%%%%%%%
% Preprocessing %
%%%%%%%%%%%%%% %%
if 0
subList = {};
sesList = {};
bidsDirList = {};
sesDbList = {};
sesDbFileList = {};
volTrList = {};
runCondList = {};
volTrList = {};
dummyList = {};
kList = {};
winLengthList = {};
winStepList = {};
onsetsList = {};
ondursList = {};
dtStimList = {};
labelList = {};
extraList = {};
%%% Subject and session
switch info.dataSetLabel
case 'vsmDriven'
K = 5;
winLength = 15;
runCond = {};
fMap = {};
avMap = {};
memprage = {};
sa2rage = {};
pcMRA = {};
b0 = {};
b1 = {};
%%%%%%%%%%%%%%
%%%% vsmDriven
sesDbListTmp{1} = {
'/autofs/space/takoyaki_001/users/proulxs/vasomo/source/expDb/vsmDrivenP1/2024-07-28--bay2--vsmDrivenP1'
'/autofs/space/takoyaki_001/users/proulxs/vasomo/source/expDb/vsmDrivenP1/2024-08-09--bay2--vsmDrivenP1'
};
sesDbListTmp{2} = {
'/autofs/space/takoyaki_001/users/proulxs/vasomo/source/expDb/vsmDrivenP2/2024-07-28--bay2--vsmDrivenP2'
'/autofs/space/takoyaki_001/users/proulxs/vasomo/source/expDb/vsmDrivenP2/2024-08-05--bay2--vsmDrivenP2'
};
for sub = 1:2
for ses = 1:2
subList{end+1,1} = ['vsmDrivenP' num2str(sub)];
sesList{end+1,1} = num2str(ses);
bidsDirList{end+1,1} = fullfile(info.bidsDir,['sub-' subList{end}],['ses-' sesList{end}]);
sesDbList{end+1,1} = sesDbListTmp{sub}{ses};
extraList{end+1,1} = '';
%%%%% anat
%%%%%% avMap
avMap{end+1,1}.fList = dir(fullfile(bidsDirList{end,1},'anat','*acq-avMap*.nii.gz'));
%%%%%% memprage
memprage{end+1,1}.fList = dir(fullfile(bidsDirList{end,1},'anat','*_T1w.nii.gz'));
if ~isempty(memprage{end,1}.fList)
tmp = dir(fullfile(info.dbDir,subList{end},'*','fs',subList{end}));
memprage{end,1}.fsDir = tmp(1).folder; clear tmp
end
%%%%%% pcMRA
pcMRA{end+1,1}.fList = dir(fullfile(bidsDirList{end,1},'anat','*acq-venc*.nii.gz'));
%%%%% fmap
%%%%%% topup
b0{end+1,1}.label = 'topup';
b0{end,1}.fList = dir(fullfile(bidsDirList{end,1},'fmap','*_epi.nii.gz'));
%%%%%% sa2rage
b1{end+1,1}.label = 'B1';
b1{end,1}.fList = dir(fullfile(bidsDirList{end,1},'fmap','*_TB1SRGE.nii.gz'));
%%%%% func
runCond{end+1,1} = {};
dummyList{end+1,1} = {};
%%%%%% vfMRI
dummy = 5;
%%%%%%% 50sPrd5sDur
runCond{end,1}{1,end+1}.sub = subList{end};
runCond{end,1}{1,end}.ses = sesList{end};
runCond{end,1}{1,end}.label = '50sPrd5sDur';
runCond{end,1}{1,end}.labelAcq = 'vfMRI';
runCond{end,1}{1,end}.fList = dir(fullfile(bidsDirList{end,1},'func',['*task-' runCond{end,1}{1,end}.label '*_angio.nii.gz']));
runCond{end,1}{1,end}.fList = fullfile({runCond{end,1}{1,end}.fList.folder},{runCond{end,1}{1,end}.fList.name})';
dsgn.label = runCond{end,1}{1,end}.label;
dsgn.dt = 0.840;
initRest = dsgn.dt*12;
stimPeriod = dsgn.dt*57;
stimDur = dsgn.dt*6;
runDur = dsgn.dt*354;
dsgn.onsetList = initRest:stimPeriod:(runDur-stimPeriod);
dsgn.ondurList = ones(size(dsgn.onsetList)).*(stimDur);
runCond{end,1}{1,end}.dsgn = dsgn;
dummyList{end,1}{1,end+1} = repmat(dummy,size(runCond{end,1}{1,end}.fList));
%%%%%% 50sPrd1sDur
runCond{end,1}{1,end+1}.sub = subList{end};
runCond{end,1}{1,end}.ses = sesList{end};
runCond{end,1}{1,end}.label = '50sPrd1sDur';
runCond{end,1}{1,end}.labelAcq = 'vfMRI';
runCond{end,1}{1,end}.fList = dir(fullfile(bidsDirList{end,1},'func',['*task-' runCond{end,1}{1,end}.label '*_angio.nii.gz']));
runCond{end,1}{1,end}.fList = fullfile({runCond{end,1}{1,end}.fList.folder},{runCond{end,1}{1,end}.fList.name})';
dsgn.label = runCond{end,1}{1,end}.label;
dsgn.dt = 0.840;
initRest = dsgn.dt*12;
stimPeriod = dsgn.dt*57;
stimDur = dsgn.dt*1;
runDur = dsgn.dt*354;
dsgn.onsetList = initRest:stimPeriod:(runDur-stimPeriod);
dsgn.ondurList = ones(size(dsgn.onsetList)).*(stimDur);
runCond{end,1}{1,end}.dsgn = dsgn;
dummyList{end,1}{1,end+1} = repmat(dummy,size(runCond{end,1}{1,end}.fList));
%%%%%% 10sPrd1sDur
runCond{end,1}{1,end+1}.sub = subList{end};
runCond{end,1}{1,end}.ses = sesList{end};
runCond{end,1}{1,end}.label = '10sPrd1sDur';
runCond{end,1}{1,end}.labelAcq = 'vfMRI';
runCond{end,1}{1,end}.fList = dir(fullfile(bidsDirList{end,1},'func',['*task-' runCond{end,1}{1,end}.label '*_angio.nii.gz']));
runCond{end,1}{1,end}.fList = fullfile({runCond{end,1}{1,end}.fList.folder},{runCond{end,1}{1,end}.fList.name})';
dsgn.label = runCond{end,1}{1,end}.label;
dsgn.dt = 0.840;
initRest = dsgn.dt*12;
stimPeriod = dsgn.dt*12;
stimDur = dsgn.dt*1;
runDur = dsgn.dt*354;
dsgn.onsetList = initRest:stimPeriod:(runDur-stimPeriod);
dsgn.nullTrial = false(size(dsgn.onsetList));
dsgn.nullTrial(14) = true;
dsgn.ondurList = ones(size(dsgn.onsetList)).*stimDur;
runCond{end,1}{1,end}.dsgn = dsgn;
dummyList{end,1}{1,end+1} = repmat(dummy,size(runCond{end,1}{1,end}.fList));
%%%%%% 15sPrd1sDur
runCond{end,1}{1,end+1}.sub = subList{end};
runCond{end,1}{1,end}.ses = sesList{end};
runCond{end,1}{1,end}.label = '15sPrd1sDur';
runCond{end,1}{1,end}.labelAcq = 'vfMRI';
runCond{end,1}{1,end}.fList = dir(fullfile(bidsDirList{end,1},'func',['*task-' runCond{end,1}{1,end}.label '*_angio.nii.gz']));
runCond{end,1}{1,end}.fList = fullfile({runCond{end,1}{1,end}.fList.folder},{runCond{end,1}{1,end}.fList.name})';
dsgn.label = runCond{end,1}{1,end}.label;
dsgn.dt = 0.840;
initRest = dsgn.dt*12;
stimPeriod = dsgn.dt*17;
stimDur = dsgn.dt*1;
runDur = dsgn.dt*354;
dsgn.onsetList = initRest:stimPeriod:(runDur-stimPeriod);
dsgn.nullTrial = false(size(dsgn.onsetList));
dsgn.nullTrial(14) = true;
dsgn.ondurList = ones(size(dsgn.onsetList)).*stimDur;
runCond{end,1}{1,end}.dsgn = dsgn;
dummyList{end,1}{1,end+1} = repmat(dummy,size(runCond{end,1}{1,end}.fList));
%%%%%% 20sPrd1sDur
runCond{end,1}{1,end+1}.sub = subList{end};
runCond{end,1}{1,end}.ses = sesList{end};
runCond{end,1}{1,end}.label = '20sPrd1sDur';
runCond{end,1}{1,end}.labelAcq = 'vfMRI';
runCond{end,1}{1,end}.fList = dir(fullfile(bidsDirList{end,1},'func',['*task-' runCond{end,1}{1,end}.label '*_angio.nii.gz']));
runCond{end,1}{1,end}.fList = fullfile({runCond{end,1}{1,end}.fList.folder},{runCond{end,1}{1,end}.fList.name})';
dsgn.label = runCond{end,1}{1,end}.label;
dsgn.dt = 0.840;
initRest = dsgn.dt*12;
stimPeriod = dsgn.dt*24;
stimDur = dsgn.dt*1;
runDur = dsgn.dt*354;
dsgn.onsetList = initRest:stimPeriod:(runDur-stimPeriod);
dsgn.nullTrial = false(size(dsgn.onsetList));
dsgn.nullTrial(7) = true;
dsgn.ondurList = ones(size(dsgn.onsetList)).*stimDur;
runCond{end,1}{1,end}.dsgn = dsgn;
dummyList{end,1}{1,end+1} = repmat(dummy,size(runCond{end,1}{1,end}.fList));
%%%%%% bold
dummy = 5;
%%%%%%% 50sPrd1sDur
runCond{end,1}{1,end+1}.sub = subList{end};
runCond{end,1}{1,end}.ses = sesList{end};
runCond{end,1}{1,end}.label = '50sPrd1sDur';
runCond{end,1}{1,end}.labelAcq = 'bold';
runCond{end,1}{1,end}.fList = dir(fullfile(bidsDirList{end,1},'func',['*task-' runCond{end,1}{1,end}.label '*_bold.nii.gz']));
runCond{end,1}{1,end}.fList = fullfile({runCond{end,1}{1,end}.fList.folder},{runCond{end,1}{1,end}.fList.name})';
dsgn.label = runCond{end,1}{1,end}.label;
dsgn.dt = 0.840;
initRest = dsgn.dt*12;
stimPeriod = dsgn.dt*57;
stimDur = dsgn.dt*1;
runDur = dsgn.dt*354;
dsgn.onsetList = initRest:stimPeriod:(runDur-stimPeriod);
dsgn.ondurList = ones(size(dsgn.onsetList)).*(stimDur);
runCond{end,1}{1,end}.dsgn = dsgn;
dummyList{end,1}{1,end+1} = repmat(dummy,size(runCond{end,1}{1,end}.fList));
end
end
% subList
% runCond{1}{:}
% runCond{2}{:}
% pcMRA{2}.fList.name
% memprage{4}
% avMap{4}
% b0{4}.fList.name
% b1{4}.fList.name
end
%%%%%%%%%%%%%%
% Session loop
runSet = cell(size(runCond));
volAnat = cell(size(runCond));
sesIndList = 1:length(subList);
for s = 1:length(subList(sesIndList))
S = sesIndList(s);
% see doIt_pilotPipeline08c/stepTemplate.m
%% Housekeeping
info.sub = subList{S};
info.ses = sesList{S};
info.sesDb = sesDbList{S};
info.bidsDir = bidsDirList{S};
info.bidsDerivDir = fullfile(info.bidsDir,'derivatives'); if ~exist(info.bidsDerivDir,'dir'); mkdir(info.bidsDerivDir); end
tic; disp(' '); disp(' '); disp(' ');
tmp = {['sub-' info.sub '_ses-' info.ses]};
tmp{end+1} = [num2str(s) '/' num2str(length(sesIndList))];
tmp{end+1} = ['Nses=' num2str(length(subList))];
tmp = strjoin(tmp,'; ');
disp(repmat('+',1,length(tmp))); disp(repmat('+',1,length(tmp))); disp(repmat('+',1,length(tmp))); disp(tmp)
%% Main analysis steps
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Within-run preprocessing %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
do.loadIt = 0;
do.doIt = 1;
do.saveIt = 0;
switch info.dataSetLabel
case 'vsmDriven'
%%% vfMRI
runSet{S}{1,end+1}.sub = subList{S};
runSet{S}{end}.ses = sesList{S};
runSet{S}{end}.label = 'vfMRI';
runSet{S}{end}.wd = outDir;
runSet{S}{end}.bidsDir = bidsDirList{S};
runSet{S}{end}.bidsDerivDir = fullfile(bidsDirList{S},'derivatives',['set-' runSet{S}{end}.label]);
ind = [runCond{S}{:}]; ind = {ind.labelAcq}; ind = ismember(ind,runSet{S}{end}.label);
runSet{S}{end}.fList = [runCond{S}{ind}];
runSet{S}{end}.fList = cat(1,runSet{S}{end}.fList.fList);
runSet{S}{end}.nDummy = cat(1,dummyList{S}{ind});
if ~isempty(runSet{S}{end}.fList)
forceThis = 0;
verboseThis = 1;
runSet{S}{end}.initFiles = initPreproc(runSet{S}{end},[],[],forceThis,verboseThis);
forceThis = 0;
verboseThis = 1;
info.useSynth = 0;
fMask = volAnatPreproc2(do,info,runSet{S}{end},forceThis,verboseThis);
fMask = fMask.func.mask.brainInv.mri.fspec;
forceThis = 0;
verboseThis = 1;
param.baseType = 'first'; % 'first' 'av' 'mcAv'
param.spSmFac = 1;
fBase = [];
runSet{S}{end}.wrMocoFiles = estimMotionWR2(runSet{S}{end}.initFiles,param,fBase,fMask,forceThis,verboseThis);
end
%%% bold
runSet{S}{1,end+1}.sub = subList{S};
runSet{S}{end}.ses = sesList{S};
runSet{S}{end}.label = 'bold';
runSet{S}{end}.wd = outDir;
runSet{S}{end}.bidsDir = bidsDirList{S};
runSet{S}{end}.bidsDerivDir = fullfile(bidsDirList{S},'derivatives',['set-' runSet{S}{end}.label]);
ind = [runCond{S}{:}]; ind = {ind.labelAcq}; ind = ismember(ind,runSet{S}{end}.label);
runSet{S}{end}.fList = [runCond{S}{ind}];
runSet{S}{end}.fList = cat(1,runSet{S}{end}.fList.fList);
runSet{S}{end}.nDummy = cat(1,dummyList{S}{ind});
if ~isempty(runSet{S}{end}.fList)
forceThis = 0;
verboseThis = 1;
runSet{S}{end}.initFiles = initPreproc(runSet{S}{end},[],[],forceThis,verboseThis);
forceThis = 0;
verboseThis = 1;
info.useSynth = 1;
fMask = volAnatPreproc2(do,info,runSet{S}{end},forceThis,verboseThis);
fMask = fMask.func.mask.brainInv.mri.fspec;
forceThis = 0;
verboseThis = 1;
param.baseType = 'first'; % 'first' 'av' 'mcAv'
param.spSmFac = 1;
fBase = [];
runSet{S}{end}.wrMocoFiles = estimMotionWR2(runSet{S}{end}.initFiles,param,fBase,fMask,forceThis,verboseThis);
end
end
%% %%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Between-run preprocessing %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% run or load preprocessing
do.loadIt = 0;
do.doIt = 1;
do.saveIt = 0;
switch info.dataSetLabel
case 'vsmDriven'
for rs = 1:length(runSet{S})
if isempty(runSet{S}{rs}.fList); continue; end
switch runSet{S}{rs}.label
case {'vfMRI' 'bold'}
forceThis = 0;
verboseThis = 1;
param.baseType = 'firstRun_avFrame'; % 'first' 'av' 'mcAv'
param.spSmFac = 1;
fBase = [];
fMask = cellstr(runSet{S}{rs}.wrMocoFiles.fMaskList);
if length(unique(fMask))==1
fMask = fMask{1}; else; dbstack; error('code that');
end
runSet{S}{rs}.brMocoFiles = estimMotionBR(runSet{S}{rs}.wrMocoFiles,fBase,fMask,param,forceThis,verboseThis);
otherwise
dbstack; error('code that');
end
end
otherwise
dbstack; error('code that');
end
%% %%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Between-session preprocessing %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% run or load preprocessing
do.loadIt = 0;
do.doIt = 1;
do.saveIt = 0;
forceThis = 0;
verboseThis = 1;
switch info.dataSetLabel
case 'vsmDriven'
for rs = 1:length(runSet{S})
if isempty(runSet{S}{rs}.fList); continue; end
if S>1
runSetRef = {};
for SS = 1:S-1
for rsrs = 1:length(runSet{SS})
if strcmp(runSet{SS}{rsrs}.sub,runSet{S}{rs}.sub) && ...
str2num(runSet{SS}{rsrs}.ses)<str2num(runSet{S}{rs}.ses) && ...
strcmp(runSet{SS}{rsrs}.label,runSet{S}{rs}.label) && ...
~isempty(runSet{SS}{rsrs}.fList)
runSetRef{end+1} = runSet{SS}{rsrs};
end
end
end
if ~isempty(runSetRef)
runSetRef = runSetRef{1};
param.sourceType = 'avRun_avFrame';
param.spSmFac = 1;
fBase = fullfile(runSetRef.brMocoFiles.wd,'av_cat_mcBR_av_mcWR_setPlumb_volTs.nii.gz');
fMask = cellstr(runSetRef.brMocoFiles.fMask);
if length(unique(fMask))==1
fMask = fMask{1}; else; dbstack; error('code that');
end
runSet{S}{rs}.bsMocoFiles = estimMotionBS2(runSet{S}{rs}.brMocoFiles,fBase,fMask,param,forceThis,verboseThis);
runSet{S}{rs}.bsMocoFiles.fGeomSes1 = runSetRef.initFiles.fGeom;
end
end
%
% switch runSet{S}{rs}.label
% case {'vfMRI' 'bold'}
% forceThis = 0;
% verboseThis = 1;
% param.baseType = 'firstRun_avFrame'; % 'first' 'av' 'mcAv'
% param.spSmFac = 1;
% fBase = [];
% fMask = cellstr(runSet{S}{rs}.wrMocoFiles.fMaskList);
% if length(unique(fMask))==1
% fMask = fMask{1}; else; dbstack; error('code that');
% end
% runSet{S}{rs}.brMocoFiles = estimMotionBR(runSet{S}{rs}.wrMocoFiles,fBase,fMask,param,forceThis,verboseThis);
% otherwise
% dbstack; error('code that');
% end
end
otherwise
dbstack; error('code that');
end
%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Finalize preprocessing (one-step interpolation) %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
do.loadIt = 0;
do.doIt = 1;
do.saveIt = 0;
switch info.dataSetLabel
case 'vsmDriven'
for rs = 1:length(runSet{S})
if isempty(runSet{S}{rs}.fList); continue; end
forceThis = 0;
verboseThis = 1;
initFiles = runSet{S}{rs}.initFiles;
preprocFiles = {runSet{S}{rs}.wrMocoFiles runSet{S}{rs}.brMocoFiles};
if isfield(runSet{S}{rs},'bsMocoFiles')
preprocFiles = [preprocFiles {runSet{S}{rs}.bsMocoFiles}];
else
preprocFiles = [preprocFiles {[]}];
end
runSet{S}{rs}.finalFiles = finalizePreproc2(initFiles,preprocFiles,forceThis,verboseThis);
end
% fList = replace(runSet{S}.wrMocoFiles.fMocoList,'.nii.gz','.param.1D');
% for f = 1:length(fList)
% cmd = {srcAfni};
% cmd{end+1} = '1dplot \';
% cmd{end+1} = '-yaxis "-1.5:1.5:1:1" - \';
% cmd{end+1} = ['-ynames `head -2 ' fList{f} ' | tail -1 | cut -c 3-` - \'];
% cmd{end+1} = fList{f};
% [status,cmdout] = system(strjoin(cmd,newline),'-echo'); if status; dbstack; error(cmdout); error('x'); end
% end
otherwise
dbstack; error('code that')
end
%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% For surface registration %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
forceThis = 0;
%%% fs
volAnat{S}{1,end+1}.sub = subList{S};
volAnat{S}{end}.ses = sesList{S};
volAnat{S}{end}.label = 'fs';
volAnat{S}{end}.dbDir = sesDbList{S};
fsDir = dir(fullfile(volAnat{S}{end}.dbDir,'fs',volAnat{S}{1,end}.sub));
if isempty(memprage{S}.fList) || isempty(fsDir)
volAnat{S}{end}.wd = '';
volAnat{S}{end}.bidsDir = '';
volAnat{S}{end}.bidsDerivDir = '';
volAnat{S}{end}.fsDir = '';
else
disp('fsDir found in dbDir')
volAnat{S}{end}.wd = outDir;
volAnat{S}{end}.bidsDir = bidsDirList{S};
volAnat{S}{end}.bidsDerivDir = fullfile(bidsDirList{S},'derivatives',['set-' volAnat{S}{end}.label]);
volAnat{S}{end}.fsDir = fullfile(volAnat{S}{end}.bidsDerivDir,'fs');
% copy to bids derivDir
fsDir = fsDir(1).folder;
if ~isFS(fsDir); dbstack; error('fsDir in dbDir does not seem to contain fs analysis'); end
if forceThis || ~isFS(volAnat{S}{end}.fsDir)
disp('copying fsDir from dbDir to bidsDerivDir')
copyfile(fsDir,volAnat{S}{end}.fsDir)
else
disp('fsDir already in bidsDerivDir')
end
end
%%% avMap
volAnat{S}{1,end+1}.sub = subList{S};
volAnat{S}{end}.ses = sesList{S};
volAnat{S}{end}.label = 'avMap';
if isempty(avMap{S}.fList)
volAnat{S}{end}.fList = '';
volAnat{S}{end}.dbDir = '';
volAnat{S}{end}.wd = '';
volAnat{S}{end}.bidsDir = '';
volAnat{S}{end}.bidsDerivDir = '';
else
volAnat{S}{end}.fList = avMap{S}.fList;
volAnat{S}{end}.dbDir = sesDbList{S};
volAnat{S}{end}.wd = outDir;
volAnat{S}{end}.bidsDir = bidsDirList{S};
volAnat{S}{end}.bidsDerivDir = fullfile(bidsDirList{S},'derivatives',['set-' volAnat{S}{end}.label]);
end
%% %%%%%%%%%%%%%%%%%%%%%%%%%%
end
%%%%%%%%%%%%%%%%%%%%%%%
%% avMap registration %
%%%%%%%%%%%%%%%%%%%%%%%
forceThis = 0;
subList2 = unique(subList);
avMap = cell(size(subList2));
fs = cell(size(subList2));
vfMRI = cell(size(subList2));
%%% get relevant data struct for each subject
for S = 1:length(subList2)
volAnat2 = volAnat(ismember(subList,subList2{S}));
runSet2 = runSet(ismember(subList,subList2{S}));
for s = 1:length(volAnat2)
for ar = 1:length(volAnat2{s})
%%% get avMap
if strcmp(volAnat2{s}{ar}.label,'avMap') && ~isempty(volAnat2{s}{ar}.fList)
avMap{S}{end+1} = volAnat2{s}{ar};
end
%%% get fs
if strcmp(volAnat2{s}{ar}.label,'fs') && ~isempty(volAnat2{s}{ar}.fsDir)
fs{S}{end+1} = volAnat2{s}{ar};
end
end
for ar = 1:length(runSet2{s})
%%% get vfMRI
if strcmp(runSet2{s}{ar}.label,'vfMRI') && isfield(runSet2{s}{ar},'finalFiles') && strcmp(runSet2{s}{ar}.ses,'1')
vfMRI{S}{end+1} = runSet2{s}{ar}.finalFiles;
end
end
end
%%% make sure data struct make sense
if length(fs{S})~=1; dbstack; error(['expecting a single data struct for fs of ' subList2{S}]); end
fs{S} = fs{S}{1};
if length(avMap{S})~=1; dbstack; error(['expecting a single data struct for avMap of ' subList2{S}]); end
avMap{S} = avMap{S}{1};
if length(vfMRI{S})~=1; dbstack; error(['expecting a single data struct for vfMRI of ' subList2{S}]); end
vfMRI{S} = vfMRI{S}{1};
end
%%% write avMap into functional space without resampling
for S = 1:length(avMap)
fList = fullfile({avMap{S}.fList.folder},{avMap{S}.fList.name})';
ref = fullfile(vfMRI{S}.bidsDerivDir,'sesAvCat_av_cat_av_preproc_volTs.nii.gz');
fAvMap = fullfile(avMap{S}.bidsDerivDir,replace(avMap{S}.fList(1).name,'.nii.gz',''));
fAvMap = replace(fAvMap,'echo-1','echo-cat'); if ~exist(fAvMap,'dir'); mkdir(fAvMap); end
fAvMap = fullfile(fAvMap,'in-vfMRI.nii.gz');
if forceThis || ~exist(fAvMap,'file')
mriRef = MRIread(ref,1);
for i = 1:length(fList)
mri = MRIread(fList{i});
if i==1
mriRef.vol = mri.vol;
mriRef.volres = mri.volres;
mriRef.xsize = mri.xsize;
mriRef.ysize = mri.ysize;
mriRef.zsize = mri.zsize;
mriRef.tr = mri.tr;
mriRef.te = mri.te;
else
mriRef.vol = cat(4,mriRef.vol,mri.vol);
end
end
MRIwrite(mriRef,fAvMap);
end
avMap{S}.fList_invfMRI = cellstr(fAvMap);
for i = 1:length(volAnat2{S})
if ~strcmp(volAnat2{S}{i}.label,'avMap'); continue; end
volAnat2{S}{i}.fList_invfMRI = cellstr(fAvMap);
end
end
% disp(strjoin([fullfile(vfMRI{S}.bidsDerivDir,'sesAvCat_av_cat_av_preproc_volTs.nii.gz')
% fullfile({avMap{S}.fList.folder},{avMap{S}.fList.name})'
% avMap{S}.fList_invfMRI],[' \\' newline]))
% %%% Surface registration not working for avMap for a lack of WM to GM
% %%% contrast. May be able to make it work somehow but too much work
% [SUBJECTS_DIR,SUBJECT,~] = fileparts(fs{S}.fsDir);
% MOV = {avMap{S}.fList.name}'; MOV = avMap{S}.fList(contains(MOV,'echo-1')); MOV = fullfile(MOV.folder,MOV.name);
% [~,curOutDir,~] = fileparts(replace(MOV,'.nii.gz','')); curOutDir = fullfile(avMap{S}.bidsDerivDir,curOutDir);
% surfReg(SUBJECTS_DIR,SUBJECT,MOV,curOutDir)
for s = 1:length(runSet)
for ar = 1:length(runSet{s})
if ~strcmp(runSet{s}{ar}.label,'vfMRI'); continue; end
sub = runSet{s}{ar}.sub;
for S = 1:length(avMap)
if ~strcmp(avMap{S}.sub,sub); continue; end
runSet{s}{ar}.avMap.f = avMap{S}.fList_invfMRI;
end
end
end
%% %%%%%%%%%%%%%%%%%%%%%%
%% %%%%%%%%%%%%%%%%%%%%%%%%%%
% Refactor from set to cond %
%%%%%%%%%%%%%%%%%%%%%%%%%% %%
[runCond,subList,runCondAcqList,runCondStimList] = set2cond2(runSet,runCond);
save(mfilename,'runCond','subList','runCondAcqList','runCondStimList')
else
load(mfilename,'runCond','subList','runCondAcqList','runCondStimList')
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Anatomical processing (masks and rois) %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
do.loadIt = 0;
do.doIt = 1;
do.saveIt = 0;
forceThis = 0;
forceRoi = 0;
verboseThis = 1;
for S = 1:size(runCond,1)
info.sub = subList{S};
for rca = 1:length(runCondAcqList)
if ~isfield(runCond{S},runCondAcqList{rca}); continue; end
out = volAnatPreproc3(do,info,runCond{S}.(runCondAcqList{rca}),forceThis,forceRoi);
for rcs = 1:length(runCondStimList)
if ~isfield(runCond{S}.(runCondAcqList{rca}),runCondStimList{rcs}); continue; end
runCond{S}.(runCondAcqList{rca}).(runCondStimList{rcs}).volAnatSub = out;
end
end
end
%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%
% Subject loop
volTsAll = cell(size(subList));
volPsdAll = cell(size(subList));
allCmd = cell(size(subList));
sesIndList = 1:length(subList);
for s = 1:length(subList(sesIndList))
S = sesIndList(s);
% see doIt_pilotPipeline08c/stepTemplate.m
%% Housekeeping
info.sub = subList{S};
% info.ses = sesList{S};
% info.sesDb = sesDbList{S};
% info.bidsDir = bidsDirList{S};
% info.bidsDerivDir = fullfile(info.bidsDir,'derivatives'); if ~exist(info.bidsDerivDir,'dir'); mkdir(info.bidsDerivDir); end
tic; disp(' '); disp(' '); disp(' ');
tmp = {['sub-' info.sub]};
tmp{end+1} = [num2str(s) '/' num2str(length(sesIndList))];
tmp{end+1} = ['Nses=' num2str(length(subList))];
tmp = strjoin(tmp,'; ');
disp(repmat('+',1,length(tmp))); disp(repmat('+',1,length(tmp))); disp(repmat('+',1,length(tmp))); disp(tmp)
%%
%% Main analysis steps
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Load data (and write the cross-run mean) %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
forceThis = 0;
copyFieldList = {'sub' 'ses' 'label' 'labelAcq' 'dsgn' 'wd' 'bidsDir' 'bidsDerivDir' 'ppLabelList' 'dataType' 'fOrigList' 'fPreprocList' 'fTransList' 'fTransCatList' 'bidsList' 'acqTime' 'nDummy' 'volAnat' 'volAnatSes' 'volAnatSub'};
disp('loading volTs')
switch info.dataSetLabel
case 'vsmDriven'
ar = 1;
acqRunCond = 'vfMRI'; runCondAcqList{ar};
for sr = 1:length(runCondStimList)
stimRunCond = runCondStimList{sr};
if ~isfield(runCond{S}.(acqRunCond),stimRunCond); continue; end
nr = length(runCond{S}.(acqRunCond).(stimRunCond).fPreprocList);
volTs = [];
[nrPerSes, sesList] = groupcounts(cellstr(runCond{S}.(acqRunCond).(stimRunCond).ses));
volTsSes = cell(size(sesList));
volTsSub = [];
fOrigList = runCond{S}.(acqRunCond).(stimRunCond).fOrigList;
fPreprocList = runCond{S}.(acqRunCond).(stimRunCond).fPreprocList;
for rr = 1:nr
disp([' ' info.sub '; ' acqRunCond '; ' stimRunCond ' ' num2str(sr) '/' num2str(length(runCondStimList)) '; file ' num2str(rr) '/' num2str(nr) ' (' fPreprocList{rr} ')'])
volTs(rr,1).mri = MRIread(fPreprocList{rr});
for i = 1:length(copyFieldList)
if isfield(runCond{S}.(acqRunCond).(stimRunCond),copyFieldList{i})
if size(runCond{S}.(acqRunCond).(stimRunCond).(copyFieldList{i}),1)==1
volTs(rr,1).mri.(copyFieldList{i}) = runCond{S}.(acqRunCond).(stimRunCond).(copyFieldList{i});
else
volTs(rr,1).mri.(copyFieldList{i}) = runCond{S}.(acqRunCond).(stimRunCond).(copyFieldList{i})(rr);
end
end
end
nFrameOrig = MRIread(fOrigList{rr},1); nFrameOrig = nFrameOrig.nframes;
nFrame = runCond{S}.(acqRunCond).(stimRunCond).nFrame(rr);
volTs(rr,1).mri.nDummyRemoved = nFrameOrig-nFrame;
if rr==1
volTsSub.mri = volTs(rr).mri;
else
volTsSub.mri.vol = volTsSub.mri.vol...
+ volTs(rr).mri.vol;
end
% if rr==1
% runCond{S}.(acqRunCond).(stimRunCond).volTsSub.mri = runCond{S}.(acqRunCond).(stimRunCond).volTs(rr).mri;
% else
% runCond{S}.(acqRunCond).(stimRunCond).volTsSub.mri.vol = runCond{S}.(acqRunCond).(stimRunCond).volTsSub.mri.vol...
% + runCond{S}.(acqRunCond).(stimRunCond).volTs(rr).mri.vol;
% end
sesInd = ismember(sesList,runCond{S}.(acqRunCond).(stimRunCond).ses(rr));
if isempty(volTsSes{sesInd})
volTsSes{sesInd}.mri = volTs(rr).mri;
else
volTsSes{sesInd}.mri.vol = volTsSes{sesInd}.mri.vol...
+ volTs(rr).mri.vol;
end
end
%divide by number of runs
volTsSub.mri.vol = volTsSub.mri.vol ./ nr;
% runCond{S}.(acqRunCond).(stimRunCond).volTsSub.mri.vol = runCond{S}.(acqRunCond).(stimRunCond).volTsSub.mri.vol ./ nr;
volTsSes = cat(1,volTsSes{:});
for ses = 1:size(volTsSes,1)
volTsSes(ses).mri.vol = volTsSes(ses).mri.vol ./ nrPerSes(ses);
end
%write averages
for ses = 1:size(volTsSes,1)
mri = volTsSes(ses).mri;
f = mri.fspec; f = strsplit(f,filesep); f{end-1} = strsplit(f{end-1},'_'); f{end-1}{contains(f{end-1},'run-')} = 'run-av'; f{end-1} = strjoin(f{end-1},'_'); if ~exist(strjoin(f(1:end-1),filesep),'dir'); mkdir(strjoin(f(1:end-1),filesep)); end; f = strjoin(f,filesep);
if forceThis || ~exist(f,'file')
disp([' writing ses-' sesList{ses} ' cross-run average (' f ')'])
MRIwrite(mri,f);
else
disp([' ses-' sesList{ses} ' cross-run average already done, skipping (' f ')'])
end
mri.fspec = f;
volTsSes(ses).mri = mri; clear mri
end
mri = volTsSub.mri;
f = mri.fspec; f = strsplit(f,filesep); f{end-1} = strsplit(f{end-1},'_'); f{end-1}{contains(f{end-1},'run-')} = 'run-av'; f{end-1}{contains(f{end-1},'ses-')} = 'ses-av'; f{end-1} = strjoin(f{end-1},'_'); if ~exist(strjoin(f(1:end-1),filesep),'dir'); mkdir(strjoin(f(1:end-1),filesep)); end; f = strjoin(f,filesep);
f = strsplit(f,filesep); fTmp = f(1:end-2); fTmp{contains(fTmp,'ses-')} = 'ses-av'; f(1:end-2) = fTmp; if ~exist(strjoin(f(1:end-1),filesep),'dir'); mkdir(strjoin(f(1:end-1),filesep)); end; f = strjoin(f,filesep);
if forceThis || ~exist(f,'file')
disp([' writing cross-session cross-run average (' f ')'])
MRIwrite(mri,f);
else
disp([' cross-session cross-run average already done, skipping (' f ')'])
end
mri.fspec = f;
volTsSub.mri = mri; clear mri
%compile
runCond{S}.(acqRunCond).(stimRunCond).volTs = volTs; clear volTs
runCond{S}.(acqRunCond).(stimRunCond).volTsSes = volTsSes; clear volTsSes
runCond{S}.(acqRunCond).(stimRunCond).volTsSub = volTsSub; clear volTsSub
end
otherwise
dbstack; error('code that');
end
%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Event-related response %
%%%%%%%%%%%%%%%%%%%%%%%%%%%
do.loadIt = 0;
do.doIt = 1;
do.saveIt = 0;
do.writeIt = 1;
forceThis = 0;
verboseThis = 1;
switch info.dataSetLabel
case 'vsmDriven'
ar = 1;
acqRunCond = 'vfMRI'; runCondAcqList{ar};
for sr = 1:length(runCondStimList)
stimRunCond = runCondStimList{sr};
if ~isfield(runCond{S}.(acqRunCond),stimRunCond); continue; end
volAnat = runCond{S}.(acqRunCond).(stimRunCond).volAnatSub;
%individual runs
[volResp, ~, info] = volTsGetResp2(do,info,runCond{S}.(acqRunCond).(stimRunCond).volTs,[],volAnat,forceThis,verboseThis);
for rr = 1:size(volResp,1)
runCond{S}.(acqRunCond).(stimRunCond).volTs(rr,1).volResp = volResp(rr,1);
end
clear volResp
%within session average across runs
for ses = 1:size(runCond{S}.(acqRunCond).(stimRunCond).volTsSes,1)
[runCond{S}.(acqRunCond).(stimRunCond).volTsSes(ses).volResp, ~, info] = volTsGetResp2(do,info,runCond{S}.(acqRunCond).(stimRunCond).volTsSes(ses),[],volAnat,forceThis,verboseThis);
end
%cross-session and cross-run average
[runCond{S}.(acqRunCond).(stimRunCond).volTsSub.volResp, ~, info] = volTsGetResp2(do,info,runCond{S}.(acqRunCond).(stimRunCond).volTsSub,[],volAnat,forceThis,verboseThis);
clear volAnat
end
otherwise
dbstack; error('code that')
end
%% %%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Visualize Event-related response %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if 0
% condLabel = 'task_10sPrd1sDur';
% condLabel = 'task_15sPrd1sDur';
% condLabel = 'task_50sPrd1sDur';
% condLabel = 'task_50sPrd5sDur';
% condLabel = 'task_20sPrd1sDur';
S = 2;
acqCondLabel = 'vfMRI'; fields(runCond{S});
stimCondLabel = ''; fields(runCond{S}.(acqCondLabel));
cmd = fsCommand2(runCond{S}.(acqCondLabel),stimCondLabel);
stimCondLabel = 'task_20sPrd1sDur';
cmd = fsCommand2(runCond{S}.(acqCondLabel),stimCondLabel);
S = 2;
acqCondLabel = 'vfMRI'; fields(runCond{S});
stimCondLabel = ''; fields(runCond{S}.(acqCondLabel));
cmd = fsCommand2(runCond{S},acqCondLabel,stimCondLabel);
stimCondLabel = 'task_20sPrd1sDur';
cmd = fsCommand(runCond{S},acqCondLabel,stimCondLabel);
runCond{S}.(acqCondLabel).(stimCondLabel).volTs
% mri = [runCond{S}.(acqCondLabel).(stimCondLabel).volTs.mri];
% tmp = [runCond{S}.(acqCondLabel).(stimCondLabel).volTs.volResp];
% tmp(1).ts.fspec
% {mri.fspec}'
%
% tmp = MRIread(char(fRespFav));
% figure('WindowStyle','docked');
% imagesc(tmp.vol(:,:,:,1)); colorbar
% tmp = MRIread(char(fRespF));
% figure('WindowStyle','docked');
% imagesc(tmp.vol(:,:,:,1)); colorbar
%
% tmp = MRIread(char(fRespAv));
% figure('WindowStyle','docked');
% imagesc(tmp.vol(:,:,:,3)); colorbar
end
%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Full (space-time-spectral) multitaper analysis %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%
do.loadIt = 0;
do.doIt = 1;
do.saveIt = 0;
do.writeIt = 1;
switch info.dataSetLabel
case 'vsmDriven'
% info.K = kList{S};
ar = 1;
acqRunCond = 'vfMRI'; runCondAcqList{ar};
for sr = 1:length(runCondStimList)
stimRunCond = runCondStimList{sr};
if ~isfield(runCond{S}.(acqRunCond),stimRunCond) || ~isfield(runCond{S}.(acqRunCond).(stimRunCond),'volTsSes') || isempty(runCond{S}.(acqRunCond).(stimRunCond).volTsSes)
continue; end
volAnat = runCond{S}.(acqRunCond).(stimRunCond).volAnatSub;
roiLabelList = [volAnat.roi{:}]; roiLabelList = {roiLabelList.label}';
for ses = 1:size(runCond{S}.(acqRunCond).(stimRunCond).volTsSes,1)
volTs = rmfield(runCond{S}.(acqRunCond).(stimRunCond).volTsSes(ses,1),'volResp');
info.ses = volTs.mri.ses;
if ~isfield(volTs,'dsgn'); volTs.dsgn = runCond{S}.(acqRunCond).(stimRunCond).dsgn; end
switch stimRunCond
case {'task_10sPrd1sDur'
'task_15sPrd1sDur'}
info.win = inf;
info.K = 10;
case {'task_20sPrd1sDur'}
info.win = round(9 / (volTs.mri.tr/1000)); %info.win.*(volTs.mri.tr/1000)
info.win(2) = 1;
info.K = 3;