# 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)
