cmind.pipeline.cmind_age_to_template

Choose an age-appropriate pediatric template. utility to autogenerate a list of standard volumes and transforms for the CMIND study. Creates a file reg_struct.csv with the following rows

#The following entries correspond to the age-specific template and brain masks: StudyTemplate,<filename> StudyTemplate_brain,<filename> StudyTemplate_brain_mask,<filename>

#additional, optional cerebrum masks priors StudyTemplate_cerebrum,<filename> StudyTemplate_cerebrum_mask,<filename>

#optional tissue priors StudyTemplate_pve1_prior,<filename> StudyTemplate_pve2_prior,<filename> StudyTemplate_pve3_prior,<filename>

#Nonlinear affine & warp to MNI space (precomputed) ANTS_StudyTemplate_to_MNI_Aff,<filename> ANTS_StudyTemplate_to_MNI_Warp,<filename>

#StudyTemplate warped to MNI space (precomputed) ANTS_StudyTemplate_to_MNI_img,<filename>

#Linear affine to MNI space (precomputed) FLIRT_StudyTemplate_to_MNI_Aff,<filename>

#StudyTemplate affine transformed to MNI space (precomputed) FLIRT_StudyTemplate_to_MNI_img,<filename>

Functions

cmind_age_to_template(age_months, ...[, ...])

choose appropriate pediatric template based on the subject age

cmind.pipeline.cmind_age_to_template.cmind_age_to_template(age_months, ped_template_path, output_dir, resolution_string='2mm', ForceUpdate=False, verbose=False, logger=None)

choose appropriate pediatric template based on the subject age

Parameters:

age_months : float

age of subject in months

ped_template_path : directory

path to the directory containing the pediatric templates

output_dir : str

output directory in which to store reg_struct.csv

resolution_str : {‘1mm’,‘2mm’}, optional

resolution of the templates to use (default = ‘2mm’)

ForceUpdate : bool, optional

if True, rerun and overwrite any previously existing results

verbose : bool, optional

print additional output (to terminal and log)

logger : logging.Logger or str, optional

logging.Logger object (or string of a filename to log to)

Returns:

reg_struct : dict

dictionary of registration related atlases and transforms

reg_struct_file : str

filename of the .csv file containing reg_struct

Notes

initialize a registration structure, reg_struct and save it to reg_struct.csv in output_dir.

based on age, a specific study-specific template will be assigned

study template for age_months < 6 months

study template for 6 < age_months < 24

study template for 24 < age_months < 48

study template for age_months > 48