def __init__(self, imgfile, datafile=None, subject=None, group=None, convert=True):
self.name = imgfile.split('/')[-1].split('.')[0]
self.json = imageutils.img_to_json(imgfile)
# If image is in Analyze format, write NIFTI copy
if convert and re.match('img', imgfile):
img = NiftiImage(imgfile)
img.save('%s.nii.gz' % self.name)
def __init__(self,
imgfile,
datafile=None,
subject=None,
group=None,
convert=True):
self.name = imgfile.split('/')[-1].split('.')[0]
self.json = imageutils.img_to_json(imgfile)
# If image is in Analyze format, write NIFTI copy
if convert and re.match('img', imgfile):
img = NiftiImage(imgfile)
img.save('%s.nii.gz' % self.name)
def save(self, image):
nifti_image = NiftiImage(image.data)
spacing = image.spacing.tolist()
spacing.reverse()
nifti_image.pixdim = spacing
# logging.warning("Image direction and origin will not be saved")
nifti_image.save(self._filename)
# Save gradient direction file if saving NIfTI
if "mr_diffusion_sequence" in image.metadata:
gradients = [[], [], []]
b_values = []
for diffusion in image.metadata["mr_diffusion_sequence"]:
gradient = diffusion.diffusion_gradient_direction_sequence[
0].diffusion_gradient_orientation
b_value = diffusion.diffusion_bvalue
for index, value in enumerate(gradient):
gradients[index].append(str(value))
b_values.append(str(b_value))
gradients = "\n".join(
[" ".join(direction) for direction in gradients])
b_values = " ".join(b_values)
base_name = os.path.splitext(self._filename)[0]
if base_name.endswith(".nii"):
base_name = os.path.splitext(base_name)[0]
gradients_file = open("{0}.bvec".format(base_name), "w")
gradients_file.write(gradients)
gradients_file.close()
bvalues_file = open("{0}.bval".format(base_name), "w")
bvalues_file.write(b_values)
bvalues_file.close()
def write_nifti_file(settings, basename):
"""Write data <basename>.nii."""
nim = NiftiImage(get_data(settings))
filename = basename + '.nii'
print 'Writing data to the nifti file ' + filename + '.'
nim.save(filename)
def write_nifti_file(settings, basename):
"""Write data <basename>.nii."""
nim = NiftiImage(get_data(settings))
filename = basename+'.nii'
print 'Writing data to the nifti file '+filename+'.'
nim.save(filename)