parser.add_argument('--interp', action='store', metavar='String',
help="'Interpolation method.One of 'pv': Partial volume, 'tri':Trilinear, 'rand': Random interpolation'",
default='pv')
params = parser.parse_args()
if __name__ == '__main__':
fmoving = params.in_file
fstatic = params.reference
baseFixed=baseFixed=rcommon.getBaseFileName(fstatic)
print(fmoving + ' --> ' + fstatic)
static=nib.load(fstatic)
static=nib.Nifti1Image(static.get_data().squeeze(), static.get_affine())
static = nifti2nipy(static)
moving=nib.load(fmoving)
moving=nib.Nifti1Image(moving.get_data().squeeze(), moving.get_affine())
moving= nifti2nipy(moving)
similarity = params.similarity #'crl1' 'cc', 'mi', 'nmi', 'cr', 'slr'
interp = params.interp #'pv', 'tri',
renormalize = True
optimizer = 'powell'
print('Setting up registration...')
print 'Similarity:',similarity
tic = time.time()
R = HistogramRegistration(moving, static, similarity=similarity,
interp=interp, renormalize=renormalize)
read_sherbrooke_3shell)
from dipy.segment.mask import median_otsu
fetch_sherbrooke_3shell()
img, gtab = read_sherbrooke_3shell()
data = img.get_data()
data, mask = median_otsu(data)
affine = img.get_affine()
static_id = 0
moving_id = 20
static = nifti2nipy(nib.Nifti1Image(data[..., static_id], affine))
moving = nifti2nipy(nib.Nifti1Image(data[..., moving_id], affine))
similarity = 'crl1' # 'cc', 'mi', 'nmi', 'cr', 'slr'
interp = 'pv' # 'tri',
renormalize = True
optimizer = 'powell'
print('Setting up registration...')
tic = time.time()
R = HistogramRegistration(moving, static, similarity=similarity,
interp=interp, renormalize=renormalize)
T = R.optimize('affine', optimizer=optimizer)
toc = time.time()
print(' Registration time: %f sec' % (toc - tic))
parser.add_argument('--interp', action='store', metavar='String',
help="'Interpolation method.One of 'pv': Partial volume, 'tri':Trilinear, 'rand': Random interpolation'",
default='pv')
params = parser.parse_args()
if __name__ == '__main__':
fmoving = params.in_file
fstatic = params.reference
fmoved = params.out_file
print(fmoving + ' --> ' + fstatic)
static = nifti2nipy(nib.load(fstatic))
moving = nifti2nipy(nib.load(fmoving))
similarity = params.similarity #'crl1' 'cc', 'mi', 'nmi', 'cr', 'slr'
interp = params.interp #'pv', 'tri',
renormalize = True
optimizer = 'powell'
print('Setting up registration...')
tic = time.time()
R = HistogramRegistration(moving, static, similarity=similarity,
interp=interp, renormalize=renormalize)
T = R.optimize('affine', optimizer=optimizer)
toc = time.time()
print('Registration time: %f sec' % (toc - tic))
metavar='String',
help=
"'Interpolation method.One of 'pv': Partial volume, 'tri':Trilinear, 'rand': Random interpolation'",
default='pv')
params = parser.parse_args()
if __name__ == '__main__':
fmoving = params.in_file
fstatic = params.reference
baseFixed = baseFixed = rcommon.getBaseFileName(fstatic)
print(fmoving + ' --> ' + fstatic)
static = nib.load(fstatic)
static = nib.Nifti1Image(static.get_data().squeeze(), static.get_affine())
static = nifti2nipy(static)
moving = nib.load(fmoving)
moving = nib.Nifti1Image(moving.get_data().squeeze(), moving.get_affine())
moving = nifti2nipy(moving)
similarity = params.similarity #'crl1' 'cc', 'mi', 'nmi', 'cr', 'slr'
interp = params.interp #'pv', 'tri',
renormalize = True
optimizer = 'powell'
print('Setting up registration...')
print 'Similarity:', similarity
tic = time.time()
R = HistogramRegistration(moving,
static,
similarity=similarity,
