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UPDATE: export_toBIDS - multi-run and multi-model (partially)
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@tiborauer
tiborauer committed Jan 4, 2019
1 parent 9544ef7 commit bcc9dca
Showing 1 changed file with 65 additions and 25 deletions.
90 changes: 65 additions & 25 deletions aa_toolbox/aa_export_toBIDS.m
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Expand Up @@ -4,7 +4,7 @@ function aa_export_toBIDS(varargin)
%
% This function can run standalone or be included at the end of a userscript.
%
% usage: aa_export_toBIDS([aap,] dest[, 'anatt1', <stagetag[|streamname]>][, 'anatt2', <stagetag[|streamname]>])
% usage: aa_export_toBIDS([aap,] dest[, 'anatt1', <stagetag[|streamname]>][, 'anatt2', <stagetag[|streamname]>][, 'model', <stageindex>|'session'])
%
% also uses: aap.directory_conventions.BIDSfiles
%
Expand All @@ -13,7 +13,8 @@ function aa_export_toBIDS(varargin)
% 1) aa_export_toBIDS('/put/results/here');
% 2) aa_export_toBIDS(aap,'/put/results/here');
% 3) aa_export_toBIDS('put/results/here','anatt1','aamod_freesurfer_deface_00001|defaced_structural')
% 4) aa_export_toBIDS(aap,'put/results/here','anatt1','aamod_freesurfer_deface_00001|defaced_structural')
% 4) aa_export_toBIDS('put/results/here','model',1)
% 5) aa_export_toBIDS('put/results/here','model','session')
%
% notes
%
Expand All @@ -23,15 +24,19 @@ function aa_export_toBIDS(varargin)
% reason you would ever pass in aap, assuming you first cd to the directory
% where aap_parameters.mat lives
%
% b) example usage #3 and #4 shows how to override the default structural
% b) example usage #3 shows how to override the default structural
% (i.e. t1) file to copy (in this example a defaced structural is used, which
% is probably required if you're going to upload results to a public
% repository like openfMRI. The syntax goes: stage|streamname. If you don't
% supply an explict stream for t1 (or, optionally, t2), the first appearance
% of t1 [t2] in the analysis tasklist will be used, which is probably the
% output from dicom covert (which is not defaced).
%
% c) BIDS requires three files to appear in the top level directory:
% c) eample usage #4 and #5 show how to select model to extract events. aa
% uses the first model by default. A number here can specify a certain
% model, while 'session' tells aa that every session has its own specific model.
%
% d) BIDS requires three files to appear in the top level directory:
%
% README - a plaintext (ASCII or UTF-8) description of the data
% CHANGES- a plaintext (ASCII or UTF-8) list of version changes
Expand All @@ -49,12 +54,10 @@ function aa_export_toBIDS(varargin)
%
% This function is a work in progress. TODO:
%
% - multi-model
% - multi-session
% - multi-run
% - covariates
% - parametric
% - multi-model


if isstruct(varargin{1})
aap = varargin{1};
Expand All @@ -67,6 +70,7 @@ function aa_export_toBIDS(varargin)
varargin(1) = [];
end
args = vargParser(varargin);
if ~isfield(args,'model'), args.model = 1; end % default model

% identify source stages present from the tasklist

Expand Down Expand Up @@ -152,6 +156,7 @@ function aa_export_toBIDS(varargin)
aas_log(aap,false,'WARNING: No header is available!')
else
loaded = load(fhdr); hdr = loaded.dcmhdr;
if iscell(hdr), hdr = hdr{1}; end; hdr = hdr(1);
json = struct(...
'RepetitionTime',hdr.volumeTR,...
'EchoTime',hdr.volumeTE,...
Expand Down Expand Up @@ -207,18 +212,35 @@ function aa_export_toBIDS(varargin)

aap = aas_setcurrenttask(aap,stage_func);
for sess = 1:numel(aap.acq_details.sessions)
aas_log(aap,false,['\tINFO: Exporting fMRI session: ' aas_getsessname(aap,sess)])
src = aas_getfiles_bystream(aap,'session',[subj sess],'epi','output');
fhdr = aas_getfiles_bystream(aap,'session',[subj sess],'epi_dicom_header','output');
taskname = aas_getsessname(aap,sess);
aas_log(aap,false,['\tINFO: Exporting fMRI session: ' taskname])
src_main = aas_getfiles_bystream(aap,'session',[subj sess],'epi','output');

% image
if isempty(src)
if isempty(src_main)
aas_log(aap,false,'WARNING: No image is available!')
continue;
end

if any(strcmp(aas_getstreams(aap,'output'),'dummyscans'))
src = spm_file(tempname,'ext','nii');
src_dummy = aas_getfiles_bystream(aap,'session',[subj sess],'dummyscans','output');
spm_file_merge(char(src_dummy,src_main),src);
else
src = src_main;
end
fhdr = aas_getfiles_bystream(aap,'session',[subj sess],'epi_dicom_header','output');

isRun = regexp(taskname,'[_-]?[rR]un[0-9]*$');
if isRun
taskname = taskname(1:isRun-1);
runNo = str2double(regexp(aap.acq_details.sessions(sess).name(isRun:end),'[0-9]*','match'));
end

aas_makedir(aap,fullfile(subjpath,'func'));
dest = fullfile(subjpath,'func',sprintf('%s_task-%s_bold.nii',suboutname,valueValidate(aap.acq_details.sessions(sess).name)));
copyfile(src,dest); gzip(dest); delete(dest);
dest = fullfile(subjpath,'func',sprintf('%s_task-%s_bold.nii',suboutname,valueValidate(taskname)));
if isRun, dest = strrep(dest,'bold.nii',sprintf('run-%d_bold.nii',runNo)); end
copyfile(src,dest); gzip(dest); delete(dest); if exist('src_dummy','var'), delete(src); clear src_dummy; end

% header
loaded = load(fhdr); hdr = loaded.DICOMHEADERS{1};
Expand All @@ -234,19 +256,28 @@ function aa_export_toBIDS(varargin)
'PhaseEncodingDirection',[...
sliceaxes{cell_index(sliceaxes(:,1),deblank(hdr.InPlanePhaseEncodingDirection)),2}{aas_get_numaris4_numval(hdr.CSAImageHeaderInfo,'PhaseEncodingDirectionPositive')+1}...
],...
'TaskName',aap.acq_details.sessions(sess).name ...
'TaskName',taskname ...
);
savejson('',json,spm_file(dest,'ext','json'));
end

% events

if ~isfield(aap.tasksettings,'aamod_firstlevel_model')
stageModels = aap.tasklist.main.module(strcmp({aap.tasklist.main.module.name},'aamod_firstlevel_model'));

if isempty(stageModels)
aas_log(aap,false,'WARNING: No model information is available!')
continue
end
end

models = aap.tasksettings.aamod_firstlevel_model(1).model(2:end);
switch args.model
case 'session'
stageindex = strcmp(arrayfun(@(x) x.extraparameters.aap.acq_details.selected_sessions, stageModels,'UniformOutput',false),aas_getsessname(aap,sess));
otherwise
stageindex = args.model;
end

models = aap.tasksettings.aamod_firstlevel_model(stageindex).model(2:end);
selected_model = (strcmp({models.subject},aas_getsubjname(aap,subj)) | strcmp({models.subject},'*')) & ...
(strcmp({models.session},aap.acq_details.sessions(sess).name) | strcmp({models.session},'*'));
if ~any(selected_model)
Expand Down Expand Up @@ -328,19 +359,28 @@ function aa_export_toBIDS(varargin)
aap = aas_setcurrenttask(aap,stage_dwi);
for sess = 1:numel(aap.acq_details.diffusion_sessions)
aas_log(aap,false,['\tINFO: Exporting DWI session: ' aas_getsessname(aap,sess)])
src = aas_getfiles_bystream(aap,'diffusion_session',[subj sess],'diffusion_data','output');
aap.options.verbose = -1;
fhdr = aas_getfiles_bystream(aap,'diffusion_session',[subj sess],'diffusion_dicom_header','output');
aap.options.verbose = 2;

src_main = aas_getfiles_bystream(aap,'diffusion_session',[subj sess],'diffusion_data','output');

% image
if isempty(src)
if isempty(src_main)
aas_log(aap,false,'WARNING: No image is available!')
continue;
end

if any(strcmp(aas_getstreams(aap,'output'),'dummyscans'))
src = spm_file(tempname,'ext','nii');
src_dummy = aas_getfiles_bystream(aap,'session',[subj sess],'dummyscans','output');
spm_file_merge(char(src_dummy,src_main),src);
else
src = src_main;
end
aap.options.verbose = -1;
fhdr = aas_getfiles_bystream(aap,'diffusion_session',[subj sess],'diffusion_dicom_header','output');
aap.options.verbose = 2;

aas_makedir(aap,fullfile(subjpath,'dwi'));
dest = fullfile(subjpath,'dwi',sprintf('%s_dwi.nii',suboutname));
copyfile(src,dest); gzip(dest); delete(dest);
copyfile(src,dest); gzip(dest); delete(dest); if exist('src_dummy','var'), delete(src); clear src_dummy; end

% header
if isempty(fhdr)
Expand Down

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