diff --git a/ants/registration/registration.py b/ants/registration/registration.py index 00400a3e..fd7efd22 100644 --- a/ants/registration/registration.py +++ b/ants/registration/registration.py @@ -580,19 +580,20 @@ def registration( ] # ------------------------------------------------------------ elif type_of_transform == "SyNOnly": - args = [ - "--dimensionality", str(fixed.dimension), - "-r"] + initial_transform + [ - "--metric", "%s[%s,%s,1,%s]" % (syn_metric, fixed_str, moving_str, syn_sampling), - "--transform", mysyn, - "--convergence", "[%s,1e-7,8]" % synits, - "--smoothing-sigmas", smoothingsigmas, - "--shrink-factors", shrinkfactors, - "-u", "1", - "-z", "1", - "--output", "[%s,%s,%s]" % (outprefix, warpedmovout_str, warpedfixout_str), - ] - if multivariate_extras is not None: + if multivariate_extras is None: + args = [ + "--dimensionality", str(fixed.dimension), + "-r"] + initial_transform + [ + "--metric", "%s[%s,%s,1,%s]" % (syn_metric, fixed_str, moving_str, syn_sampling), + "--transform", mysyn, + "--convergence", "[%s,1e-7,8]" % synits, + "--smoothing-sigmas", smoothingsigmas, + "--shrink-factors", shrinkfactors, + "-u", "1", + "-z", "1", + "--output", "[%s,%s,%s]" % (outprefix, warpedmovout_str, warpedfixout_str), + ] + else: metrics = [] for mve_idx in range(len(multivariate_extras)): metrics.append("--metric") @@ -613,7 +614,21 @@ def registration( metric_sampling, ) metrics.append(metric_full_string) - args = args + metrics + args_pre = [ + "--dimensionality", str(fixed.dimension), + "-r"] + initial_transform + [ + "--metric", "%s[%s,%s,1,%s]" % (syn_metric, fixed_str, moving_str, syn_sampling), + ] + args_post = [ + "--transform", mysyn, + "--convergence", "[%s,1e-7,8]" % synits, + "--smoothing-sigmas", smoothingsigmas, + "--shrink-factors", shrinkfactors, + "-u", "1", + "-z", "1", + "--output", "[%s,%s,%s]" % (outprefix, warpedmovout_str, warpedfixout_str), + ] + args = args_pre + metrics + args_post args.append("-x") args.append(maskopt) # ------------------------------------------------------------