def main(mp_rage_images_folder, pet_images_folder, segmented_regions_folder,
output_folder):
mp_rage_images = FileUtils.get_files_name_in(mp_rage_images_folder)
for mp_rage_image in mp_rage_images:
try:
patient_id = FileUtils.extract_patient_id_from(mp_rage_image)
pet_image = FileUtils.get_file_of_patient_with_id_from_folder(
patient_id, pet_images_folder)
subject_folder = os.path.join(output_folder, patient_id)
# Register the mp rage to the pet space
CoRegistrationProcessFactory.create_co_registration_process_with(
mp_rage_image, pet_image, subject_folder).run()
segmented_regions_image = FileUtils.get_file_of_patient_with_id_from_folder(
patient_id, segmented_regions_folder)
transformation_matrix_path = \
CoRegistrationProcessFactory.get_transformation_matrix_file_name_from(subject_folder, mp_rage_image)
# Register the mask to the subject space using the transformation matrix
CoRegistrationProcessFactory \
.create_co_registration_process_with(segmented_regions_image, pet_image, subject_folder,
transformation_matrix_path).run()
except IndexError as e:
print("Unable to read file for patient with id {}".format(
patient_id))
def main(subjects_folder_path, masks_folder_path, template_path,
output_folder):
subjects = FileUtils.get_files_name_in(subjects_folder_path)
masks = FileUtils.get_files_name_in(masks_folder_path)
for subject in subjects:
patient_id = FileUtils.extract_patient_id_from(subject)
subject_folder = os.path.join(output_folder, patient_id)
# Register the template to the subject space
CoRegistrationProcessFactory.create_co_registration_process_with(
template_path, subject, subject_folder).run()
for mask in masks:
transformation_matrix_path = \
CoRegistrationProcessFactory.get_transformation_matrix_file_name_from(subject_folder, template_path)
# Register the mask to the subject space using the transformation matrix
CoRegistrationProcessFactory \
.create_co_registration_process_with(mask, subject, subject_folder, transformation_matrix_path).run()