parcellations_dict['basc_197'] = {
'nii_path':
os.path.join(
template_dir,
'basc_multiscale_2015/template_cambridge_basc_multiscale_nii_sym/template_cambridge_basc_multiscale_sym_scale197.nii.gz'
),
'is_probabilistic':
False
}
use_n_procs = 5
# plugin_name = 'MultiProc'
plugin_name = 'CondorDAGMan'
for subject_id in subjects_list:
working_dir = os.path.join(working_dir_base, subject_id)
ds_dir = os.path.join(ds_dir_base, subject_id)
print('\n\nsubmitting %s' % subject_id)
calc_local_metrics(brain_mask=brain_mask,
preprocessed_data_dir=in_data_root_path,
subject_id=subject_id,
parcellations_dict=parcellations_dict,
bp_freq_list=bp_freq_list,
TR=TR,
selectfiles_templates=selectfiles_templates,
working_dir=working_dir,
ds_dir=ds_dir,
use_n_procs=use_n_procs,
plugin_name=plugin_name)
parcellations_dict['basc_444'] = {
'nii_path': os.path.join(template_dir,
'basc_multiscale_2015/template_cambridge_basc_multiscale_nii_sym/template_cambridge_basc_multiscale_sym_scale444.nii.gz'),
'is_probabilistic': False}
parcellations_dict['basc_197'] = {
'nii_path': os.path.join(template_dir,
'basc_multiscale_2015/template_cambridge_basc_multiscale_nii_sym/template_cambridge_basc_multiscale_sym_scale197.nii.gz'),
'is_probabilistic': False}
use_n_procs = 5
# plugin_name = 'MultiProc'
plugin_name = 'CondorDAGMan'
for subject_id in subjects_list:
working_dir = os.path.join(working_dir_base, subject_id)
ds_dir = os.path.join(ds_dir_base, subject_id)
print('\n\nsubmitting %s' % subject_id)
calc_local_metrics(brain_mask=brain_mask,
preprocessed_data_dir=in_data_root_path,
subject_id=subject_id,
parcellations_dict=parcellations_dict,
bp_freq_list=bp_freq_list,
TR=TR,
selectfiles_templates=selectfiles_templates,
working_dir=working_dir,
ds_dir=ds_dir,
use_n_procs=use_n_procs,
plugin_name=plugin_name)
for subject_id in subjects_list:
subject_working_dir = os.path.join(working_dir, subject_id)
subject_ds_dir = os.path.join(ds_dir, subject_id, 'metrics')
# INPUT PARAMETERS for pipeline
cfg = {}
cfg['subject_id'] = subject_id
cfg['dicom_dir'] = dicom_dir
cfg['preprocessed_data_dir'] = preprocessed_data_dir
cfg['working_dir'] = subject_working_dir
cfg['freesurfer_dir'] = freesurfer_dir
cfg['template_dir'] = template_dir
cfg['script_dir'] = script_dir
cfg['ds_dir'] = subject_ds_dir
cfg['TR_list'] = TR_list
cfg['vols_to_drop'] = vols_to_drop
cfg['rois_list'] = rois_list
cfg['lp_cutoff_freq'] = lp_cutoff_freq
cfg['hp_cutoff_freq'] = hp_cutoff_freq
cfg['use_fs_brainmask'] = use_fs_brainmask
cfg['use_n_procs'] = use_n_procs
cfg['plugin_name'] = plugin_name
calc_metrics.calc_local_metrics(cfg)