if platform == 'darwin':
is_hpc = False
else:
is_hpc = True
#
# Initial checks
#
# Check that bids directory is not empty(TODO)
project_root = args.in_dir[0]
print(project_root)
layout = bids.layout.BIDSLayout([(project_root, 'bids')],
exclude='derivatives/')
assert len(layout.get_subjects()) > 0, "No subjects in directory!"
# Create img list
files = layout.get(extensions='.nii.gz', modality='anat')
n_total_jobs = int(args.num_threads[0])
if not args.histmatch:
assert args.template_file is None and not args.template_norm, "Unnecessary template if not histmatch"
if args.histmatch:
assert args.template_file is not None, "Need template for histogram matching"
if args.template_file is not None:
assert os.path.exists(args.template_file[0]), "Template file not found"
if platform == 'darwin':
is_hpc = False
else:
is_hpc = True
#
# Initial checks
#
os.environ["ANTSPATH"] = "/homedtic/gmarti/LIB/ANTsbin/bin"
os.environ["ANTSSCRIPTS"] = "/homedtic/gmarti/LIB/ANTs/Scripts"
# Check that bids directory is not empty(TODO)
project_root = args.in_dir[0]
layout = bids.layout.BIDSLayout([(project_root, 'bids')], exclude='derivatives/')
assert len(layout.get_subjects()) > 0, "No subjects in directory!"
# Create img list
files = layout.get(extensions='.nii.gz', modality='anat', session='M00')
# Keep only the baselines and the files from the subject_file
df_subjects = pd.read_csv(args.subject_file[0])
files_true = [x for x in layout.get_subjects() if str(x[4:7] + "_S_" + x[8:12]) in df_subjects.PTID.values]
print(len(files))
print(len(files_true))
# create output directory
out_dir = args.output_path[0]
if not os.path.exists(out_dir):
os.makedirs(out_dir)