def main():
parser = _build_arg_parser()
args = parser.parse_args()
try:
devnull = open(os.devnull)
subprocess.call(args.eddy_cmd, stderr=devnull)
except:
parser.error("Please download the {} command.".format(args.eddy_cmd))
if args.verbose:
logging.basicConfig(level=logging.INFO)
required_args = [args.input_dwi, args.bvals, args.bvecs, args.mask]
assert_inputs_exist(parser, required_args)
if os.path.splitext(args.output_prefix)[1] != '':
parser.error('The prefix must not contain any extension.')
bvals, bvecs = read_bvals_bvecs(args.bvals, args.bvecs)
bvals_min = bvals.min()
b0_threshold = args.b0_thr
if bvals_min < 0 or bvals_min > b0_threshold:
raise ValueError('The minimal b-value is lesser than 0 or greater '
'than {0}. This is highly suspicious. Please check '
'your data to ensure everything is correct. '
'Value found: {1}'.format(b0_threshold, bvals_min))
gtab = gradient_table(bvals, bvecs, b0_threshold=b0_threshold)
acqparams = create_acqparams(gtab, args.readout, args.encoding_direction)
index = create_index(bvals)
bvecs = create_non_zero_norm_bvecs(bvecs)
if not os.path.exists(args.output_directory):
os.makedirs(args.output_directory)
acqparams_path = os.path.join(args.output_directory, 'acqparams.txt')
np.savetxt(acqparams_path, acqparams, fmt='%1.4f', delimiter=' ')
bvecs_path = os.path.join(args.output_directory, 'non_zero_norm.bvecs')
np.savetxt(bvecs_path, bvecs.T, fmt="%.8f")
index_path = os.path.join(args.output_directory, 'index.txt')
np.savetxt(index_path, index, fmt='%i', newline=" ")
additional_args = ""
if args.topup is not None:
additional_args += "--topup={} ".format(args.topup)
if args.slice_drop_correction:
additional_args += "--repol "
if args.fix_seed:
additional_args += "--initrand "
output_path = os.path.join(args.output_directory, args.output_prefix)
eddy = '{0} --imain={1} --mask={2} --acqp={3} --index={4}' \
' --bvecs={5} --bvals={6} --out={7} --data_is_shelled {8}' \
.format(args.eddy_cmd, args.input_dwi, args.mask, acqparams_path,
index_path, bvecs_path, args.bvals, output_path,
additional_args)
if args.output_script:
with open("eddy.sh", 'w') as f:
f.write(eddy)
else:
print(eddy)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
try:
devnull = open(os.devnull)
subprocess.call("topup", stderr=devnull)
except:
logging.warning(
"topup not found. If executing locally, please install "
"the command from the FSL library and make sure it is "
"available in your path.")
if args.verbose:
logging.basicConfig(level=logging.INFO)
required_args = [args.in_forward_b0, args.in_reverse_b0]
assert_inputs_exist(parser, required_args)
assert_outputs_exist(parser, args, [], args.out_b0s)
assert_fsl_options_exist(parser, args.topup_options, 'topup')
if os.path.splitext(args.out_prefix)[1] != '':
parser.error('The prefix must not contain any extension.')
b0_img = nib.load(args.in_forward_b0)
b0 = b0_img.get_fdata(dtype=np.float32)
if len(b0.shape) == 4 and b0.shape[3] > 1:
logging.warning("B0 is 4D. To speed up Topup, we recommend "
"using only one b0 in both phase encoding "
"direction, unless necessary.")
elif len(b0.shape) == 3:
b0 = b0[..., None]
rev_b0_img = nib.load(args.in_reverse_b0)
rev_b0 = rev_b0_img.get_fdata(dtype=np.float32)
if len(rev_b0.shape) == 4 and rev_b0.shape[3] > 1:
logging.warning("Reverse B0 is 4D. To speed up Topup, we "
"recommend using only one b0 in both phase "
"encoding direction, unless necessary.")
elif len(rev_b0.shape) == 3:
rev_b0 = rev_b0[..., None]
fused_b0s = np.concatenate((b0, rev_b0), axis=-1)
fused_b0s_path = os.path.join(args.out_directory, args.out_b0s)
nib.save(nib.Nifti1Image(fused_b0s, b0_img.affine), fused_b0s_path)
acqparams = create_acqparams(args.readout, args.encoding_direction,
b0.shape[-1], rev_b0.shape[-1])
if not os.path.exists(args.out_directory):
os.makedirs(args.out_directory)
acqparams_path = os.path.join(args.out_directory, args.out_params)
np.savetxt(acqparams_path, acqparams, fmt='%1.4f', delimiter=' ')
output_path = os.path.join(args.out_directory, args.out_prefix)
fout_path = os.path.join(args.out_directory, "correction_field")
iout_path = os.path.join(args.out_directory, "corrected_b0s")
additional_args = ""
if args.topup_options:
additional_args = args.topup_options
topup = 'topup --imain={0} --datain={1}'\
' --config={2} --verbose --out={3}'\
' --fout={4} --iout={5} --subsamp=1 {6}\n'\
.format(fused_b0s_path, acqparams_path, args.config, output_path,
fout_path, iout_path, additional_args)
if args.out_script:
with open("topup.sh", 'w') as f:
f.write(topup)
else:
print(topup)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
try:
devnull = open(os.devnull)
subprocess.call(args.eddy_cmd, stderr=devnull)
except:
logging.warning("{} not found. If executing locally, please install "
"the command from the FSL library and make sure it is "
"available in your path.".format(args.eddy_cmd))
if args.verbose:
logging.basicConfig(level=logging.INFO)
required_args = [args.in_dwi, args.in_bvals, args.in_bvecs, args.in_mask]
assert_inputs_exist(parser, required_args)
assert_fsl_options_exist(parser, args.eddy_options, 'eddy')
if os.path.splitext(args.out_prefix)[1] != '':
parser.error('The prefix must not contain any extension.')
if args.n_reverse and not args.lsr_resampling:
logging.warning(
'Multiple reverse phase images supplied, but least-square '
'resampling is disabled. If the reverse phase image was acquired '
'with the same sampling as the forward phase image, '
'use --lsr_resampling for better results from Eddy.')
bvals, bvecs = read_bvals_bvecs(args.in_bvals, args.in_bvecs)
bvals_min = bvals.min()
b0_threshold = args.b0_thr
if bvals_min < 0 or bvals_min > b0_threshold:
raise ValueError('The minimal b-value is lesser than 0 or greater '
'than {0}. This is highly suspicious. Please check '
'your data to ensure everything is correct. '
'Value found: {1}'.format(b0_threshold, bvals_min))
n_rev = args.n_reverse
if args.topup_params:
acqparams = np.loadtxt(args.topup_params)
if acqparams.shape[0] == 2:
index = create_index(bvals, n_rev=n_rev)
elif acqparams.shape[0] == np.sum(bvals <= b0_threshold):
index = create_multi_topup_index(bvals, 'none', n_rev,
b0_threshold)
else:
b_mask = np.ma.array(bvals, mask=[bvals > b0_threshold])
n_b0_clusters = len(np.ma.clump_unmasked(b_mask[:n_rev])) + \
len(np.ma.clump_unmasked(b_mask[n_rev:]))
if acqparams.shape[0] == n_b0_clusters:
index = create_multi_topup_index(bvals, 'cluster', n_rev,
b0_threshold)
else:
raise ValueError('Could not determine a valid index file '
'from the provided acquisition parameters '
'file: {}'.format(args.topup_params))
else:
acqparams = create_acqparams(args.readout,
args.encoding_direction,
nb_rev_b0s=int(n_rev > 0))
index = create_index(bvals, n_rev=n_rev)
bvecs = create_non_zero_norm_bvecs(bvecs)
if not os.path.exists(args.out_directory):
os.makedirs(args.out_directory)
acqparams_path = os.path.join(args.out_directory, 'acqparams.txt')
np.savetxt(acqparams_path, acqparams, fmt='%1.4f', delimiter=' ')
index_path = os.path.join(args.out_directory, 'index.txt')
np.savetxt(index_path, index, fmt='%i', newline=" ")
bvecs_path = os.path.join(args.out_directory, 'non_zero_norm.bvecs')
np.savetxt(bvecs_path, bvecs.T, fmt="%.8f")
additional_args = ""
if args.topup is not None:
additional_args += "--topup={} ".format(args.topup)
if args.slice_drop_correction:
additional_args += "--repol "
if args.fix_seed:
additional_args += "--initrand "
if args.lsr_resampling:
if len(bvals) - n_rev == n_rev:
forward_bb = bvals[:n_rev, None] * bvecs[:n_rev, :]
reverse_bb = bvals[n_rev:, None] * bvecs[n_rev:, :]
if np.allclose(forward_bb, reverse_bb):
additional_args += "--resamp=lsr --fep=true "
else:
logging.warning('Least-square resampling disabled since '
'directions in both phase directions differ.')
else:
logging.warning('Least-square resampling disabled since number of '
'directions in both phase directions differ.')
if args.eddy_options:
additional_args += args.eddy_options
output_path = os.path.join(args.out_directory, args.out_prefix)
eddy = '{0} --imain={1} --mask={2} --acqp={3} --index={4}' \
' --bvecs={5} --bvals={6} --out={7} --data_is_shelled {8}' \
.format(args.eddy_cmd, args.in_dwi, args.in_mask, acqparams_path,
index_path, bvecs_path, args.in_bvals, output_path,
additional_args)
if args.out_script:
with open("eddy.sh", 'w') as f:
f.write(eddy)
else:
print(eddy)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
if args.verbose:
logging.basicConfig(level=logging.INFO)
required_args = [args.input_dwi, args.bvals, args.bvecs, args.reverse_b0]
assert_inputs_exist(parser, required_args)
assert_outputs_exist(parser, args, [], args.output_b0s)
if os.path.splitext(args.output_prefix)[1] != '':
parser.error('The prefix must not contain any extension.')
bvals, bvecs = read_bvals_bvecs(args.bvals, args.bvecs)
bvals_min = bvals.min()
# TODO refactor this
b0_threshold = args.b0_thr
if bvals_min < 0 or bvals_min > b0_threshold:
raise ValueError('The minimal b-value is lesser than 0 or greater '
'than {0}. This is highly suspicious. Please check '
'your data to ensure everything is correct. '
'Value found: {1}'.format(b0_threshold, bvals_min))
gtab = gradient_table(bvals, bvecs, b0_threshold=b0_threshold)
acqparams = create_acqparams(gtab, args.readout, args.encoding_direction)
if not os.path.exists(args.output_directory):
os.makedirs(args.output_directory)
acqparams_path = os.path.join(args.output_directory, 'acqparams.txt')
np.savetxt(acqparams_path, acqparams, fmt='%1.4f', delimiter=' ')
rev_b0_img = nib.load(args.reverse_b0)
rev_b0 = rev_b0_img.get_data()
dwi_image = nib.load(args.input_dwi)
dwi = dwi_image.get_data()
b0s = dwi[..., gtab.b0s_mask]
b0_idx = np.where(gtab.b0s_mask)[0]
fused_b0s = np.zeros(b0s.shape[:-1] + (len(b0_idx) + 1, ))
fused_b0s[..., 0:-1] = b0s
fused_b0s[..., -1] = rev_b0
fused_b0s_path = os.path.join(args.output_directory, args.output_b0s)
nib.save(nib.Nifti1Image(fused_b0s, rev_b0_img.affine), fused_b0s_path)
output_path = os.path.join(args.output_directory, args.output_prefix)
fout_path = os.path.join(args.output_directory, "correction_field")
iout_path = os.path.join(args.output_directory, "corrected_b0s")
topup = 'topup --imain={0} --datain={1}'\
' --config={2} --verbose --out={3}'\
' --fout={4} --iout={5} --subsamp=1 \n'\
.format(fused_b0s_path, acqparams_path, args.config, output_path,
fout_path, iout_path)
if args.output_script:
with open("topup.sh", 'w') as f:
f.write(topup)
else:
print(topup)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
if args.verbose:
logging.basicConfig(level=logging.INFO)
required_args = [args.in_dwi, args.in_bvals, args.in_bvecs,
args.in_reverse_b0]
assert_inputs_exist(parser, required_args)
assert_outputs_exist(parser, args, [], args.out_b0s)
if os.path.splitext(args.out_prefix)[1] != '':
parser.error('The prefix must not contain any extension.')
bvals, bvecs = read_bvals_bvecs(args.in_bvals, args.in_bvecs)
bvals_min = bvals.min()
# TODO refactor this
b0_threshold = args.b0_thr
if bvals_min < 0 or bvals_min > b0_threshold:
raise ValueError('The minimal b-value is lesser than 0 or greater '
'than {0}. This is highly suspicious. Please check '
'your data to ensure everything is correct. '
'Value found: {1}'.format(b0_threshold, bvals_min))
rev_b0_img = nib.load(args.in_reverse_b0)
rev_b0 = rev_b0_img.get_fdata(dtype=np.float32)
if len(rev_b0.shape) == 4:
logging.warning("Reverse B0 is 4D. To speed up Topup, the mean of all "
"reverse B0 will be taken.")
rev_b0 = np.mean(rev_b0, axis=3)
gtab = gradient_table(bvals, bvecs, b0_threshold=b0_threshold)
dwi_image = nib.load(args.in_dwi)
dwi = dwi_image.get_fdata(dtype=np.float32)
b0 = dwi[..., gtab.b0s_mask]
if b0.shape[3] > 1:
logging.warning("More than one B0 was found. To speed up Topup, "
"the mean of all B0 will be taken.")
b0 = np.mean(b0, axis=3)
else:
b0 = np.squeeze(b0, axis=3)
fused_b0s = np.zeros(b0.shape+(2,))
fused_b0s[..., 0] = b0
fused_b0s[..., 1] = rev_b0
fused_b0s_path = os.path.join(args.out_directory, args.out_b0s)
nib.save(nib.Nifti1Image(fused_b0s,
rev_b0_img.affine),
fused_b0s_path)
acqparams = create_acqparams(args.readout, args.encoding_direction)
if not os.path.exists(args.out_directory):
os.makedirs(args.out_directory)
acqparams_path = os.path.join(args.out_directory, 'acqparams.txt')
np.savetxt(acqparams_path, acqparams, fmt='%1.4f', delimiter=' ')
output_path = os.path.join(args.out_directory, args.out_prefix)
fout_path = os.path.join(args.out_directory, "correction_field")
iout_path = os.path.join(args.out_directory, "corrected_b0s")
topup = 'topup --imain={0} --datain={1}'\
' --config={2} --verbose --out={3}'\
' --fout={4} --iout={5} --subsamp=1 \n'\
.format(fused_b0s_path, acqparams_path, args.config, output_path,
fout_path, iout_path)
if args.out_script:
with open("topup.sh", 'w') as f:
f.write(topup)
else:
print(topup)