ukbb_grabber_40k.m

function files = ukbb_grabber(path_data,opt)
% Grab the T1w+fMRI scans in a BIDS dataset 
% http://bids.neuroimaging.io
%
% SYNTAX:
% FILES = NIAK_GRAB_BIDS(PATH_DATA,OPT)
%
% _________________________________________________________________________
% INPUTS:
%
% PATH_DATA
%   (string, default [pwd filesep], aka './') full path to one site of 
%   a BIDS dataset
%
% OPT 
%   (structure) grabber options
%    
%   FUNC_HINT
%       (string) A hint to pick one out of many fmri input for exemple 
%       if the fmri study includes "sub-XX_task-rest-a_hint_bold.nii.gz"
%       and "sub-XX_task-rest-a_thing_bold.nii.gz" and the "hint" flavor
%       needs to be selected, opt.func_hint = 'hint', would do the trick.
%       
%   ANAT_HINT
%       (string, defaut = T1w) A hint to pick one out of many anat input. 
%       If no hint is give the first file to be listed by the OS will be picked. 
%       If you want to select a different input than T1w, let say 
%       sub-XX_ses-XX_FLAIR_run-001.nii.gz input the following option:
%       opt.anat_hint = "FLAIR" 
%
%   TASK_TYPE
%       (string, default = rest) The type of task, explicitely named in bids 
%       file name
%
%   MAX_SUBJECTS
%       (int, default = 0) 0 return all subjects. Used to put an upper limit
%       on the number of subjects that are returned (nice an simple 
%       debugging feature).
%
%   SUBJECT_LIST
%       (cellarray of int) The only subject to be returned
%   
% _________________________________________________________________________
% OUTPUTS:
%
% FILES
%   (structure) with the following fields, ready to feed into 
%   NIAK_PIPELINE_FMRI_PREPROCESS :
%
%       <SUBJECT>.FMRI.<SESSION>.<RUN>
%          (string) a list of fMRI datasets, acquired in the 
%          same session (small displacements). 
%          The field names <SUBJECT> and <SESSION> can be any arbitrary 
%          strings. The <RUN> input is optional
%
%      <SUBJECT>.ANAT 
%          (string) anatomical volume, from the same subject as in 
%          FILES_IN.<SUBJECT>.FMRI
% _________________________________________________________________________
% SEE ALSO:
% NIAK_PIPELINE_FMRI_PREPROCESS
%
% _________________________________________________________________________
% COMMENTS:
%
% Copyright (c) P-O Quirion, Pierre Bellec
%               Centre de recherche de l'institut de Griatrie de Montral,
%               Dpartement d'informatique et de recherche oprationnelle,
%               Universit de Montral, 2016-17.
% Maintainer : poq@criugm.qc.ca
% See licensing information in the code.
% Keywords : grabber, brain imaging data structure

% Permission is hereby granted, free of charge, to any person obtaining a copy
% of this software and associated documentation files (the "Software"), to deal
% in the Software without restriction, including without limitation the rights
% to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
% copies of the Software, and to permit persons to whom the Software is
% furnished to do so, subject to the following conditions:
%
% The above copyright notice and this permission notice shall be included in
% all copies or substantial portions of the Software.
%
% THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
% IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
% FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
% AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
% LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
% OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
% THE SOFTWARE.

% Prepare the path for the BIDS data
if nargin == 0
    path_data = pwd;
end
path_data = niak_full_path(path_data);

fprintf(1,"Reading Bids structure %s\n", path_data)
% If no path given, search local dir
if (nargin < 1)||isempty(path_data)
    path_data = [pwd filesep];
elseif nargin < 2
    opt = struct;
end

if ~isdir(path_data)
    error('Bid directory does not exist: %s', path_data)
end


if ~strcmp(path_data(end),filesep);
    path_data = [path_data filesep];
end

if ~isfield(opt,'func_hint')
    func_hint = '';
else
    func_hint = regexptranslate('escape', opt.func_hint);
end

if ~isfield(opt,'anat_hint')
    anat_hint = 'T1w';
else
    anat_hint = regexptranslate('escape', opt.anat_hint);
end

if ~isfield(opt,'max_subjects')
    max_subjects = 0;
else
    max_subjects = opt.max_subjects;
end

if ~isfield(opt,'subject_list')
    subject_list = 0;
else
    subject_list = opt.subject_list;
end



if ~isfield(opt,'task_type')
    task_type = "rest";
else
    task_type = opt.task_type;
end


list_dir = dir(path_data);
files = struct;

for num_f = 1:length(list_dir)	

    if list_dir(num_f).isdir && ~strcmpi(list_dir(num_f).name, '.') ...
       && ~strcmpi(list_dir(num_f).name, '..')
 
        subject_dir = list_dir(num_f).name;

%	dir_name = regexpi(subject_dir,"(sub-(.*))", 'tokens');
%	if ~isempty(dir_name)
%	    sub_id = dir_name{1}{1,2};
%	    % Condition to return only subject in subject list
%	    if ~isa(subject_list,'numeric') && ~any([subject_list{:}]==str2num(sub_id))
%		continue
%	    end
%	else
%	    continue   
%	end   	

	

	sub_str = strsplit(subject_dir,'-'){2};

	if opt.batch == sub_str(1)
		if(~strcmpi(sub_str,'3921443'))
			subject = ['sub' sub_str];
			fmri_tmp = glob([path_data subject_dir filesep 'func' filesep '*_task-rest_bold.nii.gz']){1};
			anat_tmp = glob([path_data subject_dir filesep 'anat' filesep '*_T1w.nii.gz']){1};
		end
		if((exist(fmri_tmp) == 2) && (exist(anat_tmp)==2))	
			files.(subject).fmri.session.run = fmri_tmp;
			files.(subject).anat = anat_tmp;
	
		end
	end
    end
end