sergivalverde/campinas_template

Calgary / Campinas T1 template

Calgary / Campinas template

Build a common T1-w and brain mask template from the Calgary-Campinas-359 dataset.

Requisites:

• ANTS
• Numpy

Method

All images are registered to the first case CC0001 using either linear or deformable registration.

How to generate new templates

Just select the parameters from the beginning of the build_template.py file:

IMAGE_PATH = '/home/sergivalverde/DATA/campinas/all'
T1_NAME = 'T1.nii.gz'  # T1 name, originally was CC...vendor...
BRAINMASK_NAME = 'brainmask_ss.nii.gz'  # brainmask name

# registration options
REG_METHOD = 'Affine'  # choose 'Syn' for deformable, etc...
INTERP = 'linear'   # hwo t

# output names
T1_OUT_TEMPLATE_PATH = 'CC351_lin_t1.nii.gz'
BRAINMASK_OUT_TEMPLATE_PATH = 'CC351_lin_brainmask.nii.gz'