def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv if argv else ['--help'])
verbose = arguments.v
set_global_loglevel(verbose=verbose)
printv('Load data...', verbose)
nii_mt = Image(arguments.mt)
nii_pd = Image(arguments.pd)
nii_t1 = Image(arguments.t1)
if arguments.b1map is None:
nii_b1map = None
else:
nii_b1map = Image(arguments.b1map)
if arguments.trmt is None:
arguments.trmt = fetch_metadata(
get_json_file_name(arguments.mt, check_exist=True),
'RepetitionTime')
if arguments.trpd is None:
arguments.trpd = fetch_metadata(
get_json_file_name(arguments.pd, check_exist=True),
'RepetitionTime')
if arguments.trt1 is None:
arguments.trt1 = fetch_metadata(
get_json_file_name(arguments.t1, check_exist=True),
'RepetitionTime')
if arguments.famt is None:
arguments.famt = fetch_metadata(
get_json_file_name(arguments.mt, check_exist=True), 'FlipAngle')
if arguments.fapd is None:
arguments.fapd = fetch_metadata(
get_json_file_name(arguments.pd, check_exist=True), 'FlipAngle')
if arguments.fat1 is None:
arguments.fat1 = fetch_metadata(
get_json_file_name(arguments.t1, check_exist=True), 'FlipAngle')
# compute MTsat
nii_mtsat, nii_t1map = compute_mtsat(nii_mt,
nii_pd,
nii_t1,
arguments.trmt,
arguments.trpd,
arguments.trt1,
arguments.famt,
arguments.fapd,
arguments.fat1,
nii_b1map=nii_b1map)
# Output MTsat and T1 maps
printv('Generate output files...', verbose)
nii_mtsat.save(arguments.omtsat)
nii_t1map.save(arguments.ot1map)
display_viewer_syntax([arguments.omtsat, arguments.ot1map],
colormaps=['gray', 'gray'],
minmax=['-10,10', '0, 3'],
opacities=['1', '1'],
verbose=verbose)
def test_compute_mtsat():
img_mtsat, img_t1map = mt.compute_mtsat(nii_mt=make_sct_image(1500),
nii_pd=make_sct_image(2000),
nii_t1=make_sct_image(1500),
tr_mt=30,
tr_pd=30,
tr_t1=15,
fa_mt=9,
fa_pd=9,
fa_t1=15)
assert img_mtsat.data[0] == pytest.approx(1.5327, 0.0001)
def main():
parser = get_parser()
args = parser.parse_args(args=None if sys.argv[1:] else ['--help'])
verbose = args.v
sct.init_sct(log_level=verbose, update=True) # Update log level
sct.printv('Load data...', verbose)
nii_mt = Image(args.mt)
nii_pd = Image(args.pd)
nii_t1 = Image(args.t1)
if args.b1map is None:
nii_b1map = None
else:
nii_b1map = Image(args.b1map)
# compute MTsat
nii_mtsat, nii_t1map = compute_mtsat(nii_mt,
nii_pd,
nii_t1,
args.trmt,
args.trpd,
args.trt1,
args.famt,
args.fapd,
args.fat1,
nii_b1map=nii_b1map)
# Output MTsat and T1 maps
# by default, output in the same directory as the input images
sct.printv('Generate output files...', verbose)
if args.omtsat is None:
fname_mtsat = os.path.join(os.path.dirname(nii_mt.absolutepath),
"mtsat.nii.gz")
else:
fname_mtsat = args.omtsat
nii_mtsat.save(fname_mtsat)
if args.ot1map is None:
fname_t1map = os.path.join(os.path.dirname(nii_mt.absolutepath),
"t1map.nii.gz")
else:
fname_t1map = args.ot1map
nii_t1map.save(fname_t1map)
sct.display_viewer_syntax([fname_mtsat, fname_t1map],
colormaps=['gray', 'gray'],
minmax=['-10,10', '0, 3'],
opacities=['1', '1'],
verbose=verbose)