def main():
try:
DATA_PATH = sys.argv[1]
except IndexError:
raise RuntimeError("Pass data path on command line")
N_SLICES = 40
TR = 2.5
SLICE_AXIS = 0
# 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
# This time, don't add half a slice - nifti won't accept it.
slice_times = space_to_order * time_one_slice
subjects = get_subjects(DATA_PATH)
for name, subject in subjects.items():
for run in subject['functionals']:
fname = run['filename']
print("Fixing functional " + fname)
fixnifti.fixup_nifti_file(fname, 'f', TR, SLICE_AXIS,
slice_times) # changed filename to fname
for anat_fname in subject['anatomicals']:
print("Fixing anatomical " + anat_fname)
fixnifti.fixup_nifti_file(anat_fname)
def main():
try:
DATA_PATH = sys.argv[1]
except IndexError:
raise RuntimeError("Pass data path on command line")
N_SLICES = 40
TR = 2.5
SLICE_AXIS=0
# 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
# This time, don't add half a slice - nifti won't accept it.
slice_times = space_to_order * time_one_slice
subjects = get_subjects(DATA_PATH)
for name, subject in subjects.items():
for run in subject['functionals']:
fname = run['filename']
print("Fixing functional " + fname)
fixnifti.fixup_nifti_file(fname, 'f', TR, SLICE_AXIS, slice_times)
for anat_fname in subject['anatomicals']:
print("Fixing anatomical " + anat_fname)
fixnifti.fixup_nifti_file(anat_fname)
def test_fixup_nifti_file():
# Test fixup_nifti_file function
data = np.arange(24).reshape((2, 3, 4))
img = nib.Nifti1Image(data, None)
hdr = img.get_header()
assert_equal(hdr['pixdim'][4], 1)
assert_equal(hdr.get_dim_info(), (None, None, None))
def_aff = img.get_header().get_best_affine()
tmpdir = tempfile.mkdtemp()
try:
fname = os.path.join(tmpdir, 'test.nii')
new_fname = os.path.join(tmpdir, 'ftest.nii')
nib.save(img, fname)
# Just running without params sets the affine
fixup_nifti_file(fname)
img2 = nib.load(new_fname)
assert_almost_equal(img2.get_affine(), def_aff)
hdr2 = img2.get_header()
assert_almost_equal(hdr2.get_sform(), def_aff)
assert_almost_equal(hdr2.get_qform(), def_aff)
# set prefix
fixup_nifti_file(fname, 'pre')
img2 = nib.load(os.path.join(tmpdir, 'pretest.nii'))
assert_almost_equal(img2.get_affine(), def_aff)
# Set TR
fixup_nifti_file(fname, 'f', 2.1)
img2 = nib.load(new_fname)
hdr2 = img2.get_header()
assert_almost_equal(hdr2['pixdim'][4], 2.1, 6)
# Set slice axis
fixup_nifti_file(fname, 'f', None, 1)
img2 = nib.load(new_fname)
hdr2 = img2.get_header()
assert_equal(hdr2.get_dim_info(), (None, None, 1))
# And slice times
times = np.array([0, 1, 2]) * 3 / 2.1
fixup_nifti_file(fname, 'f', 2.1, 1, times)
img2 = nib.load(new_fname)
hdr2 = img2.get_header()
assert_almost_equal(hdr2.get_slice_times(), times)
del img, img2
finally:
shutil.rmtree(tmpdir)
def test_fixup_nifti_file():
# Test fixup_nifti_file function
data = np.arange(24).reshape((2, 3, 4))
img = nib.Nifti1Image(data, None)
hdr = img.get_header()
assert_equal(hdr['pixdim'][4], 1)
assert_equal(hdr.get_dim_info(), (None, None, None))
def_aff = img.get_header().get_best_affine()
tmpdir = tempfile.mkdtemp()
try:
fname = os.path.join(tmpdir, 'test.nii')
new_fname = os.path.join(tmpdir, 'ftest.nii')
nib.save(img, fname)
# Just running without params sets the affine
fixup_nifti_file(fname)
img2 = nib.load(new_fname)
assert_almost_equal(img2.get_affine(), def_aff)
hdr2 = img2.get_header()
assert_almost_equal(hdr2.get_sform(), def_aff)
assert_almost_equal(hdr2.get_qform(), def_aff)
# set prefix
fixup_nifti_file(fname, 'pre')
img2 = nib.load(os.path.join(tmpdir, 'pretest.nii'))
assert_almost_equal(img2.get_affine(), def_aff)
# Set TR
fixup_nifti_file(fname, 'f', 2.1)
img2 = nib.load(new_fname)
hdr2 = img2.get_header()
assert_almost_equal(hdr2['pixdim'][4], 2.1, 6)
# Set slice axis
fixup_nifti_file(fname, 'f', None, 1)
img2 = nib.load(new_fname)
hdr2 = img2.get_header()
assert_equal(hdr2.get_dim_info(), (None, None, 1))
# And slice times
times = np.array([0, 1, 2]) * 3 / 2.1
fixup_nifti_file(fname, 'f', 2.1, 1, times)
img2 = nib.load(new_fname)
hdr2 = img2.get_header()
assert_almost_equal(hdr2.get_slice_times(), times)
del img, img2
finally:
shutil.rmtree(tmpdir)
import os, os.path as op
import glob
from nipype.utils.filemanip import split_filename
import os.path as op
import nipype.interfaces.ants as ants
import fixnifti # Borrowed from https://github.com/practical-neuroimaging/pna-utils
list_to_reg = glob.glob("p0*_maths_rl.nii")
for in_file in list_to_reg:
path, name, ext = split_filename(in_file)
fixnifti.fixup_nifti_file(in_file)