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,