def run_cli(args):
try:
karawun.import_tractography_study(origdcm=args.dicom_template,
niftifiles=args.nifti,
tckfiles=args.tract_files,
labelfiles=args.label_files,
destdir=args.output_dir)
except karawun.RawToLabelImMismatch:
print("One of the label images is not derived from any of the raw images")
except karawun.MissingUIDList:
print("A UID list is required iternally somewhere - this error shouldn't happen")
def converter(targetd):
test_data = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'Data')
t1dcm = os.path.join(test_data, "Dicom",
("1.3.12.2.1107.5.2.43."
"167031.2019040213095021814319052.dcm"))
MR = [
'T1brain.nii.gz', 'FLAIRbrain.nii.gz', 'FAbrain.nii.gz',
'FAbrain_reoriented.nii.gz'
]
MR = [os.path.join(test_data, "Tractography", nii) for nii in MR]
TCK = ['Left_PT_final.tck', 'Right_PT_final.tck']
TCK = [os.path.join(test_data, "Tractography", tck) for tck in TCK]
karawun.import_tractography_study(origdcm=t1dcm,
niftifiles=MR,
tckfiles=TCK,
labelfiles=None,
destdir=targetd)
def label_converter_fail(targetd):
# This should fail as there is no
# image in the same space as the segmentation
test_data = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'Data')
t1dcm = os.path.join(test_data, "Dicom",
("1.3.12.2.1107.5.2.43."
"167031.2019040213095021814319052.dcm"))
MR = ['FAbrain.nii.gz']
MR = [os.path.join(test_data, "Tractography", nii) for nii in MR]
MR_LAB = ['words.nii.gz', 'globes.nii.gz']
MR_LAB = [os.path.join(test_data, "Tractography", nii) for nii in MR_LAB]
TCK = ['Left_PT_final.tck', 'Right_PT_final.tck']
TCK = [os.path.join(test_data, "Tractography", tck) for tck in TCK]
karawun.import_tractography_study(origdcm=t1dcm,
niftifiles=MR,
tckfiles=TCK,
labelfiles=MR_LAB,
destdir=targetd)