From 90d08b3af975d32f5162e8894d00aca14ab3743c Mon Sep 17 00:00:00 2001 From: Philip Cook Date: Tue, 20 Feb 2024 12:49:06 -0500 Subject: [PATCH] ENH: Support different segmentation labels in kelly_kapowski For example, BIDS common image-derived labels do not follow the same numbering scheme as ANTs. Add the ability to specify the GM and WM labels. --- ants/segmentation/kelly_kapowski.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/ants/segmentation/kelly_kapowski.py b/ants/segmentation/kelly_kapowski.py index f63c22b2..6684487a 100644 --- a/ants/segmentation/kelly_kapowski.py +++ b/ants/segmentation/kelly_kapowski.py @@ -8,7 +8,7 @@ from .. import utils -def kelly_kapowski(s, g, w, its=45, r=0.025, m=1.5, **kwargs): +def kelly_kapowski(s, g, w, its=45, r=0.025, m=1.5, gm_label=2, wm_label=3, **kwargs): """ Compute cortical thickness using the DiReCT algorithm. @@ -36,6 +36,12 @@ def kelly_kapowski(s, g, w, its=45, r=0.025, m=1.5, **kwargs): m : scalar gradient field smoothing parameter + gm_label : integer + label for gray matter in the segmentation image + + wm_label : integer + label for white matter in the segmentation image + kwargs : keyword arguments anything else, see KellyKapowski help in ANTs @@ -60,7 +66,7 @@ def kelly_kapowski(s, g, w, its=45, r=0.025, m=1.5, **kwargs): d = s.dimension outimg = g.clone() kellargs = {'d': d, - 's': s, + 's': "[{},{},{}]".format(utils.get_pointer_string(s),gm_label,wm_label), 'g': g, 'w': w, 'c': "[{}]".format(its),