def create_files_in_directory():
outdir = mkdtemp()
cwd = os.getcwd()
os.chdir(outdir)
filelist = ['a.nii','b.nii']
for f in filelist:
hdr = nif.Nifti1Header()
shape = (3,3,3,4)
hdr.set_data_shape(shape)
img = np.random.random(shape)
nif.save(nif.Nifti1Image(img,np.eye(4),hdr),
os.path.join(outdir,f))
return filelist, outdir, cwd
import nipype.externals.pynifti as nb import numpy as np image_filename2 = "/media/sdb2/laura_study/DATA_4_chis/SPGRs/AG_1247/T2.hdr" nii2 = nb.load(image_filename2) affine = nii2.get_affine() flip_matrix = np.eye(4) #flip_matrix[0,0] = -1 affine = np.dot(flip_matrix,affine) data = nii2.get_data() nb.save(nb.Nifti1Image(data, affine, nii2.get_header()), "new_T2.nii")
# #mean_dist = np.mean(dist_matrix) # #print mean_dist border1 = findBorder(origdata1) print np.sum(border1) nb.save(nb.Nifti1Image(border1, nii1.get_affine(), nii1.get_header()), "border1.nii") nii2 = nb.load(image_filename2) origdata2 = nii2.get_data().astype(np.bool) border2 = findBorder(origdata2) print np.sum(border2) nb.save(nb.Nifti1Image(border2, nii2.get_affine(), nii2.get_header()), "border2.nii") set1_coordinates = getCoordinates(border1, nii1.get_affine()) print set1_coordinates.T.shape set2_coordinates = getCoordinates(origdata2, nii2.get_affine()) print set2_coordinates.T.shape dist_matrix = cdist(set1_coordinates.T, set2_coordinates.T) print dist_matrix.shape