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Copy pathAPOE_to_RASer.py
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APOE_to_RASer.py
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from transform_handler import img_transform_exec
from file_tools import mkcdir
import os, socket, glob
subjects_list = ["N58214", "N58215",
"N58216", "N58217", "N58218", "N58219", "N58221", "N58222", "N58223", "N58224",
"N58225", "N58226", "N58228",
"N58229", "N58230", "N58231", "N58232", "N58633", "N58634", "N58635", "N58636", "N58649", "N58650",
"N58651", "N58653", "N58654",
'N58408', 'N58714', 'N58740', 'N58477', 'N58734', 'N58309', 'N58792', 'N58302',
'N58784', 'N58706', 'N58361', 'N58355', 'N58712', 'N58790', 'N58606', 'N58350', 'N58608',
'N58779', 'N58500', 'N58604', 'N58749', 'N58510', 'N58394', 'N58346', 'N58344', 'N58788', 'N58305',
'N58514', 'N58794', 'N58733', 'N58655', 'N58735', 'N58310', 'N58400', 'N58708', 'N58780', 'N58512',
'N58747', 'N58303', 'N58404', 'N58751', 'N58611', 'N58745', 'N58406', 'N58359', 'N58742', 'N58396',
'N58613', 'N58732', 'N58516', 'N58402']
subjects_list = ["N58831","N59022","N59026","N59033","N59035","N59039","N59041","N59065","N59066","N59072","N59076","N59078","N59080","N59097","N59099","N59109","N59116","N59118","N59120"]
#removed 'N58398' could not find
computer_name = socket.gethostname()
if 'santorini' in computer_name:
DWI_folder = '/Users/alex/jacques/APOE_test/DWI_allsubj'
labels_folder = '/Users/alex/jacques/APOE_test/DWI_allsubj'
output_folder = '/Users/alex/jacques/APOE_test/DWI_allsubj_RAS/'
if 'samos' in computer_name:
DWI_folder = '/mnt/paros_MRI/jacques/APOE/DWI_allsubj/'
labels_folder = '/mnt/paros_MRI/jacques/APOE/DWI_allsubj/'
output_folder = '/mnt/paros_MRI/jacques/APOE/DWI_allsubj_RAS/'
subjects_all = glob.glob(os.path.join(DWI_folder,'*_subjspace_coreg.nii.gz'))
subjects_list = []
for subject in subjects_all:
subject_name = os.path.basename(subject)
subjects_list.append(subject_name[:6])
subjects_list.sort()
subjects_list = subjects_list[:]
print(subjects_list)
mkcdir(output_folder)
for subject in subjects_list:
coreg_file = os.path.join(DWI_folder,f'{subject}_subjspace_coreg.nii.gz')
labels_file = os.path.join(labels_folder,f'{subject}_labels.nii.gz')
labels_lr_file = os.path.join(labels_folder,f'{subject}_labels_lr_ordered.nii.gz')
mask_file = os.path.join(DWI_folder, f'{subject}_subjspace_mask.nii.gz')
coreg_RAS_file = os.path.join(output_folder,f'{subject}_coreg_RAS.nii.gz')
labels_RAS_file = os.path.join(output_folder,f'{subject}_labels_RAS.nii.gz')
labels_RAS_lr_file = os.path.join(output_folder,f'{subject}_labels_lr_ordered_RAS.nii.gz')
mask_RAS_file = os.path.join(output_folder, f'{subject}_RAS_mask.nii.gz')
transferred=0
if not os.path.exists(coreg_RAS_file):
img_transform_exec(coreg_file,'ARI','RAS',coreg_RAS_file)
transferred=1
if not os.path.exists(labels_RAS_file):
img_transform_exec(labels_file,'ARI','RAS',labels_RAS_file)
transferred=1
if not os.path.exists(labels_RAS_lr_file):
if os.path.exists(labels_lr_file):
img_transform_exec(labels_lr_file,'ARI','RAS',labels_RAS_lr_file)
transferred=1
if not os.path.exists(mask_RAS_file):
img_transform_exec(mask_file,'ARI','RAS',mask_RAS_file)
transferred=1
if transferred:
print(f'transferred subject {subject}')
else:
print(f'already transferred subject {subject}')