def __init__(self):
self.vars = {}
api.set_standard_defaults(self.vars)
self.threads = 4
self.subjects = []
self.exclude_dirs = []
self.data_type = []
self.func_names = []
#cni:
self.anat_scan_num = []
self.func_scan_nums = []
#preprocess specific:
self.preprocess = True
self.do_anat_reconstruction = True
self.do_func_reconstruction = True
self.do_warp_anatomical = True
self.do_correct_motion = True
self.do_normalize = True
self.do_highpass_filter = True
self.do_warp_functionals = True
self.do_mask_functionals = True
self.do_convert_to_nifti = True
#requirements:
self.__preprocess_reqs = ['data_type','anat_scan_num','func_scan_nums',
'func_names']
self.__generic_exclude = ['exclude','scripts','spanprocessor',
'timecourses','ttest','skripts']
data_type = 'cni'
# list the subjects to be processed:
exclude_dirs = ['exclude','scripts','spanprocessor','timecourses','ttest',\
'dd083111','dk091611','ju083111','mm110111','reg_output']
subjects = []
vars['subjects'] = subjects
# cni variables:
raw_anat = '0006_01_T1w_9mm_BRAVO.nii.gz'
raw_funcs = ['0004_01_BOLD_EPI_29mm_2sec.nii.gz','0005_01_BOLD_EPI_29mm_2sec.nii.gz']
raw_funcs_alternate = ['04_BOLD_EPI_29mm_2sec_1_0.nii.gz','05_BOLD_EPI_29mm_2sec_1_0.nii.gz']
func_names = ['pasreg','actreg']
# set standard variable defaults:
api.set_standard_defaults(vars)
#api.set_regreg_defaults(vars)
# running from scripts directory?
run_from_scripts_dir = True
# scripts directory name (OPTIONAL):
scripts_dir = 'reg_output'
vars['scripts_dir'] = scripts_dir
# change directory if neccessary:
if run_from_scripts_dir:
os.chdir('../')
# load in variables: