From 9849b7707d12e6230b1f4052ee91adc1fd12b4dc Mon Sep 17 00:00:00 2001 From: Philip Cook Date: Mon, 6 May 2024 10:25:09 -0400 Subject: [PATCH 1/2] DOC: document reg initial transform Make clear that SynOnly needs an initial transform --- ants/registration/interface.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/ants/registration/interface.py b/ants/registration/interface.py index dd481e35..5568ce1b 100644 --- a/ants/registration/interface.py +++ b/ants/registration/interface.py @@ -66,7 +66,7 @@ def registration( See Notes below for more. initial_transform : list of strings (optional) - transforms to prepend + transforms to prepend. If None, a translation is computed to align the image centers of mass. outprefix : string output will be named with this prefix. @@ -193,10 +193,12 @@ def registration( with mutual information as optimization metric. - "SyNRA": Symmetric normalization: Rigid + Affine + deformable transformation, with mutual information as optimization metric. - - "SyNOnly": Symmetric normalization: no initial transformation, - with mutual information as optimization metric. Assumes - images are aligned by an inital transformation. Can be - useful if you want to run an unmasked affine followed by + - "SyNOnly": Symmetric normalization with no rigid or affine stages. + using mutual information as optimization metric. Affine alignment is + provided by the initial_transform arg, either provide the .mat + from linear registration or use initial_transform='Identity' if the + images are already affinely aligned. + Can be useful if you want to run an unmasked affine followed by masked deformable registration. - "SyNCC": SyN, but with cross-correlation as the metric. - "SyNabp": SyN optimized for abpBrainExtraction. From ac62a9658cc617e155c29f0c48285a5de45bee63 Mon Sep 17 00:00:00 2001 From: Philip Cook Date: Mon, 6 May 2024 10:42:09 -0400 Subject: [PATCH 2/2] DOC: formatting --- ants/registration/interface.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/ants/registration/interface.py b/ants/registration/interface.py index 5568ce1b..3777c347 100644 --- a/ants/registration/interface.py +++ b/ants/registration/interface.py @@ -194,10 +194,10 @@ def registration( - "SyNRA": Symmetric normalization: Rigid + Affine + deformable transformation, with mutual information as optimization metric. - "SyNOnly": Symmetric normalization with no rigid or affine stages. - using mutual information as optimization metric. Affine alignment is - provided by the initial_transform arg, either provide the .mat - from linear registration or use initial_transform='Identity' if the - images are already affinely aligned. + Uses mutual information as optimization metric. Affine alignment is + from the initial_transform arg, either provide the .mat from linear + registration or use initial_transform='Identity' if the images are + already affinely aligned. Can be useful if you want to run an unmasked affine followed by masked deformable registration. - "SyNCC": SyN, but with cross-correlation as the metric.