adhd_pipeline_roi_ohsu_1000.m

% This is a script to run a region growing procedure on the OHSU database.
%
% Copyright (c) Pierre Bellec, Montreal Neurological Institute, 2008-2010.
%               Centre de recherche de l'institut de Gériatrie de Montréal
%               Département d'informatique et de recherche opérationnelle
%               Université de Montréal, 2011.
% Maintainer : pierre.bellec@criugm.qc.ca
% See licensing information in the code.
% Keywords : fMRI, resting-state, ADHD, region growing

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% 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.
%
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% IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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% THE SOFTWARE.

clear

%% Setting input/output files 
path_data = '/media/database2/adhd_niak/ohsu_output/';
opt_g.min_xcorr_func = -Inf;
opt_g.max_translation = Inf;
opt_g.max_rotation = Inf;
files_in = niak_grab_fmri_preprocess(path_data,opt_g);

%% Options
files_in.atoms = '/media/database2/adhd_niak/rois_1000_kki/rois/brain_rois.mnc.gz'; 
path_results   = '/media/database2/adhd_niak/rois_1000_ohsu/';
files_in.areas = [path_results 'roi_aal_3mm.mnc.gz']; % The anatomical areas to contrain the region growing
opt.folder_out = path_results; % Where to store the results
opt.flag_roi   = true; % Only generate the ROI parcelation
opt.region_growing.thre_size = 1000; % The critical size for regions

%% Run the pipeline
opt.flag_test = true;
opt.psom.max_queued = 8;
[pipeline,opt] = niak_pipeline_stability_rest(files_in,opt);