# subject_working_dir = os.path.join(working_dir, subject_id) # subject_ds_dir = os.path.join(ds_dir, subject_id) ## #### ## indent here test_dir = '/scr/adenauer2/Franz/LeiCA_NKI_test/' # '/Users/franzliem/Desktop/mattest/' subject_working_dir = test_dir + 'wd' subject_ds_dir = test_dir + 'ds' #time_series_file = '/Users/franzliem/Desktop/LeiCA/0144314/residual_filt_norm_warp.nii.gz' time_series_file = '/scr/adenauer2/Franz/LeiCA_NKI/results/0129973/rsfMRI_preprocessing/epis_MNI_3mm/03_denoised_BP_tNorm/TR_645/residual_filt_norm_warp.nii.gz' # INPUT PARAMETERS for pipeline bp_freq_list = [(None,None), (0.01, 0.1)] parcellations_dict = {} parcellations_dict['msdl'] = {'nii_path': os.path.join(template_dir, 'parcellations/msdl_atlas/MSDL_rois/msdl_rois.nii'), 'is_probabilistic': True} extraction_methods_list = ['correlation', 'sparse_inverse_covariance'] calc_con_mats.connectivity_matrix_wf(time_series_file, working_dir=subject_working_dir, ds_dir=subject_ds_dir, parcellations_dict=parcellations_dict, extraction_methods_list=extraction_methods_list, bp_freq_list=bp_freq_list, use_n_procs=use_n_procs, plugin_name=plugin_name)
parcellations_dict = {} # parcellations_dict['msdl'] = { # 'nii_path': os.path.join(template_dir, 'parcellations/msdl_atlas/MSDL_rois/msdl_rois.nii.gz'), # 'is_probabilistic': True} # parcellations_dict['craddock_205'] = { # 'nii_path': os.path.join(template_dir, 'parcellations/craddock_2012/scorr_mean_single_resolution/scorr_mean_parc_n_21_k_205_rois.nii.gz'), # 'is_probabilistic': False} parcellations_dict['gordon'] = { 'nii_path': os.path.join(template_dir, 'parcellations/Gordon_2014_Parcels/Parcels_MNI_111_sorted.nii.gz'), 'is_probabilistic': False} extraction_methods_list = ['correlation', 'sparse_inverse_covariance'] # fixme # ignore warning from np.rank import warnings with warnings.catch_warnings(): warnings.simplefilter("ignore") calc_con_mats.connectivity_matrix_wf(subjects_list=full_subjects_list, preprocessed_data_dir=preprocessed_data_dir, working_dir=working_dir, ds_dir=ds_dir, parcellations_dict=parcellations_dict, extraction_methods_list=extraction_methods_list, bp_freq_list=bp_freq_list, use_n_procs=use_n_procs, plugin_name=plugin_name)