clear path_data = [pwd filesep]; [status,msg,data_fmri] = niak_wget('cobre_lightweight20_nii'); file_pheno = [data_fmri.path filesep 'phenotypic_data.tsv.gz']; tab = niak_read_csv_cell(file_pheno); list_subject = tab(2:end,1); files_in = struct; for ss = 1:length(list_subject) files_in.fmri.(list_subject{ss}).sess1.rest = [data_fmri.path filesep 'fmri_' list_subject{ss} '.nii.gz']; end [status,msg,data_template] = niak_wget('cambridge_template_mnc1'); files_in.network = [data_template.path filesep 'template_cambridge_basc_multiscale_sym_scale007.mnc.gz']; files_in.seeds = [path_data 'list_seeds.csv']; opt_csv.labels_x = { 'MOTOR' , 'DMN' }; % The labels for the network opt_csv.labels_y = { 'index' }; tab = [3 ; 5]; niak_write_csv(files_in.seeds,tab,opt_csv); opt.folder_out = [path_data 'connectome']; opt.flag_p2p = false; % No parcel-to-parcel correlation values opt.flag_global_prop = false; % No global graph properties opt.flag_local_prop = false; % No local graph properties opt.flag_rmap = true; % Generate correlation maps opt.flag_test = false; [pipeline,opt] = niak_pipeline_connectome(files_in,opt); file_dmn = [opt.folder_out filesep 'rmap_seeds' filesep 'average_rmap_DMN.nii.gz']; file_motor = [opt.folder_out filesep 'rmap_seeds' filesep 'average_rmap_MOTOR.nii.gz']; [hdr,rmap_dmn] = niak_read_vol(file_dmn); [hdr,rmap_motor] = niak_read_vol(file_motor); size(rmap_dmn) size(rmap_motor) % The default-mode network opt_v = struct; opt_v.vol_limits = [0.25 0.7]; opt_v.type_color = 'hot_cold'; niak_montage(rmap_dmn,opt_v) % The sensorimotor network opt_v = struct; opt_v.vol_limits = [0.25 0.7]; opt_v.type_color = 'hot_cold'; niak_montage(rmap_motor,opt_v) file_mask_dmn = [opt.folder_out filesep 'rmap_seeds' filesep 'mask_DMN.nii.gz']; [hdr,mask_dmn] = niak_read_vol(file_mask_dmn); opt_v = struct; opt_v.vol_limits = [0 1]; opt_v.type_color = 'hot_cold'; niak_montage(mask_dmn,opt_v) file_dmn_40003 = [opt.folder_out filesep 'rmap_seeds' filesep 'rmap_40003_DMN.nii.gz']; [hdr,rmap_dmn_40003] = niak_read_vol(file_dmn_40003); opt_v = struct; opt_v.vol_limits = [0.4 1]; opt_v.type_color = 'hot_cold'; niak_montage(rmap_dmn_40003,opt_v) file_connectome_40003 = [opt.folder_out filesep 'connectomes' filesep 'connectome_rois_40003.mat']; data = load(file_connectome_40003); size(data.conn) conn = niak_lvec2mat(data.conn); size(conn) data.ind_roi niak_visu_matrix(conn) files = niak_grab_connectome(opt.folder_out)