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 |
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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)[source]¶ 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