def main():
try:
DATA_PATH = sys.argv[1]
except IndexError:
raise RuntimeError("Pass data path on command line")
N_SLICES = 40
TR = 2.5
# You need to work out slice times here
subjects = get_subjects(DATA_PATH)
for name, subject in subjects.items():
for run in subject['functionals']:
fname = run['filename']
print("Running slice timing on " + fname)
slice_time_file(fname, slice_times, TR)
def main():
try:
DATA_PATH = sys.argv[1]
except IndexError:
raise RuntimeError("Pass data path on command line")
N_SLICES = 40
TR = 2.5
# Figure out slice times.
slice_order = np.array(range(0, N_SLICES, 2) + range(1, N_SLICES, 2))
space_to_order = np.argsort(slice_order)
time_one_slice = TR / N_SLICES
slice_times = space_to_order * time_one_slice + time_one_slice / 2.0
subjects = get_subjects(DATA_PATH)
for name, subject in subjects.items():
for run in subject['functionals']:
fname = run['filename']
print("Running slice timing on " + fname)
slice_time_file(fname, slice_times, TR, slice_axis=0)
def test_slice_time_file():
# Test slice_time_file from slice_time_image
n_slices = 5
n_vols = 4
TR = 2.0
data = np.random.normal(size=(2, 3, n_slices, n_vols))
img = nib.Nifti1Image(data, np.eye(4))
slice_times = np.arange(n_slices) * TR / n_slices + 0.1
tmpdir = tempfile.mkdtemp()
try:
fname = os.path.join(tmpdir, 'myfile.nii')
a_fname = os.path.join(tmpdir, 'amyfile.nii')
nib.save(img, fname)
for order in ('linear', 'cubic', 1, 4):
interped_img = slice_time_image(img, slice_times, TR, order)
slice_time_file(fname, slice_times, TR, order)
a_img = nib.load(a_fname)
assert_almost_equal(interped_img.get_data(), a_img.get_data())
del a_img
finally:
shutil.rmtree(tmpdir)
def test_slice_time_file():
# Test slice_time_file from slice_time_image
n_slices = 5
n_vols = 4
TR = 2.0
data = np.random.normal(size=(2, 3, n_slices, n_vols))
img = nib.Nifti1Image(data, np.eye(4))
slice_times = np.arange(n_slices) * TR / n_slices + 0.1
tmpdir = tempfile.mkdtemp()
try:
fname = os.path.join(tmpdir, 'myfile.nii')
a_fname = os.path.join(tmpdir, 'amyfile.nii')
nib.save(img, fname)
for order in ('linear', 'cubic', 1, 4):
interped_img = slice_time_image(img, slice_times, TR, order)
slice_time_file(fname, slice_times, TR, order)
a_img = nib.load(a_fname)
assert_almost_equal(interped_img.get_data(), a_img.get_data())
del a_img
finally:
shutil.rmtree(tmpdir)
import numpy as np import slicetime fname = 'bold.nii.gz' slice_order = np.array(range(0, 35, 2) + range(1, 35, 2)) TR = 3.0 n_slices = 35 time_one_slice = TR / n_slices space_to_order = np.argsort(slice_order) slice_times = space_to_order * time_one_slice + (time_one_slice / 2) slicetime.slice_time_file(fname, slice_times, TR)