def get_files():
with open('dset_config.json', 'r') as fo:
CONFIG = json.load(fo)
DATA_DIR = op.abspath('/home/data/nbc/external-datasets/ds001491/')
all_info = {}
for dset_name in list(CONFIG.keys())[:3]:
layout = BIDSLayout(op.join(DATA_DIR, dset_name))
cfg = CONFIG[dset_name]
task = cfg['task']
dset_info = {}
for sub in layout.get_subjects():
runs = layout.get_runs(subject=sub, task=task)
sub_info = {}
for run in runs:
run_info = {}
run_info['files'] = []
run_info['echo_times'] = []
for echo in sorted(
layout.get_echoes(subject=sub, task=task, run=run)):
raw_files = layout.get(subject=sub,
task=task,
run=run,
echo=echo,
extensions='.nii.gz')
preproc_files = layout.get(subject=sub,
task=task,
run=run,
root='afni-step1',
echo=echo,
extensions='.nii.gz',
desc='realign')
preproc_files = raw_files[:]
if len(preproc_files) != 1:
print(preproc_files)
raise Exception('BAD')
# Replace filename with path when using new version of bids
run_info['files'].append(preproc_files[0].filename)
metadata = layout.get_metadata(preproc_files[0].filename)
run_info['echo_times'].append(metadata['EchoTime'])
sub_info[run] = run_info
dset_info[sub] = sub_info
all_info[dset_name] = dset_info
with open('all_files.json', 'w') as fo:
json.dump(all_info, fo, indent=4, sort_keys=True)
def get_files():
DSET_DIR = op.abspath('/home/data/nbc/external-datasets/ds001491/')
layout = BIDSLayout(DSET_DIR)
layout.add_derivatives(
'/home/data/nbc/external-datasets/ds001491/derivatives/afni-step1/')
task = 'images'
info = {}
for sub in sorted(layout.get_subjects()):
print(sub)
sub_info = {'files': [], 'echo_times': []}
for echo in sorted(layout.get_echoes(subject=sub, task=task)):
raw_files = layout.get(subject=sub,
task=task,
echo=echo,
extensions='.nii.gz')
preproc_files = layout.get(subject=sub,
task=task,
root='afni-step1',
extensions='.nii.gz')
# For some reason pybids doesn't index echo in derivatives
preproc_files = [
p for p in preproc_files
if 'echo-{0}'.format(echo) in p.filename
]
if len(preproc_files) != 1:
print(preproc_files)
raise Exception('BAD')
# Replace filename with path when using new version of bids
sub_info['files'].append(preproc_files[0].path)
metadata = raw_files[0].metadata
sub_info['echo_times'].append(metadata['EchoTime'])
info[sub] = sub_info
with open('preproc_files.json', 'w') as fo:
json.dump(info, fo, indent=4, sort_keys=True)
