def download_from_xnat(args,subdir): args['keepdata'] = True #use default download username if (len(args['xnat_username'])<1) or (len(args['xnat_password'])<1): xnat_tools.down_subject_dicoms(args['xnat_server'], os.path.join(subdir,'raw'), args['xnat_project'], args['subcode']) else: xnat_tools.down_subject_dicoms(args['xnat_server'], os.path.join(subdir,'raw'), args['xnat_project'], args['subcode'], xnat_username=args['xnat_username'], xnat_password=args['xnat_password'])
def download_from_xnat(args,subdir): args['keepdata'] = True #use default download username if (len(args['xnat_username'])<1) or (len(args['xnat_password'])<1): xnat_tools.down_subject_dicoms(args['xnat_server'], os.path.join(subdir,'raw'), args['xnat_project'], args['subcode']) else: xnat_tools.down_subject_dicoms(args['xnat_server'], os.path.join(subdir,'raw'), args['xnat_project'], args['subcode'], xnat_username=args['xnat_username'], xnat_password=args['xnat_password'])
def download_from_xnat(args, subdir):
args["keepdata"] = True
# use default download username
if (len(args["xnat_username"]) < 1) or (len(args["xnat_password"]) < 1):
xnat_tools.down_subject_dicoms(
args["xnat_server"], os.path.join(subdir, "raw"), args["xnat_project"], args["subcode"]
)
else:
xnat_tools.down_subject_dicoms(
args["xnat_server"],
os.path.join(subdir, "raw"),
args["xnat_project"],
args["subcode"],
xnat_username=args["xnat_username"],
xnat_password=args["xnat_password"],
)
sys.stderr.write(indent + " for help use --help\n")
return 2
if opts.get_data :
import xnat_tools
#we aren't doing this with an XNATSource node because the current implementation cannot download
#more than 10 files at once
if DEBUG:
print XNAT_SERVER
print os.path.join(opts.data_directory, 'raw')
print opts.project
print opts.subject
print "Type your XNAT username and password below"
if not os.path.exists(os.path.join(opts.data_directory, opts.subject, 'raw')):
os.makedirs(os.path.join(opts.data_directory, opts.subject, 'raw'))
xnat_tools.down_subject_dicoms(XNAT_SERVER, os.path.join(opts.data_directory, opts.subject, 'raw'), opts.project, opts.subject)
if opts.dicom_to_nifti:
if opts.subject == "all":
for subject in os.listdir(opts.data_directory):
workflow = openfmri_dicom_to_nifti(opts.data_directory, subject)
workflow.run()
else:
workflow = openfmri_dicom_to_nifti(opts.data_directory, opts.subject)
workflow.run()
if any([opts.autorecon_all, opts.melodic, opts.motion_correction, opts.skull_strip, opts.dti_qa, opts.fmri_qa, opts.process_fieldmap]):
workflow = preprocess_dataset(opts.data_directory, opts.subject, model_id=opts.model_id, task_id=opts.task_id,
work_directory=opts.work_directory, xnat_datasource=opts.get_data,
run_motion_correction=opts.motion_correction, run_skull_strip=opts.skull_strip,
