From 811354209d079d146cbb30c55821817f5d421cf5 Mon Sep 17 00:00:00 2001
From: muschellij2 <muschellij2@gmail.com>
Date: Fri, 23 Nov 2018 12:08:39 -0500
Subject: [PATCH] fixed bug in kmeansSegmentation

---
 DESCRIPTION            | 2 +-
 R/kmeansSegmentation.R | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9489a12a..c3cd12aa 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ANTsRCore
 Type: Package
 Title: Core Software Infrastructure for 'ANTsR'
-Version: 0.6.2.2
+Version: 0.6.3
 Date: 2018-11-02
 Authors@R: c(
     person(given = "Brian B.", family = "Avants", role = "cre", 
diff --git a/R/kmeansSegmentation.R b/R/kmeansSegmentation.R
index 9f449bb3..7feefc27 100644
--- a/R/kmeansSegmentation.R
+++ b/R/kmeansSegmentation.R
@@ -46,8 +46,8 @@ kmeansSegmentation <- function(img, k, kmask = NA, mrf = 0.1, verbose=FALSE,
                                ...) {
   img = check_ants(img)
   dim <- img@dimension
+  kmimg = iMath(img, "Normalize")
   if (is.na(kmask)) {
-    kmimg = iMath(img, "Normalize")
     kmask <- getMask(kmimg, 0.01, 1, cleanup = 2)
   } else {
     kmask = check_ants(kmask)
@@ -55,7 +55,7 @@ kmeansSegmentation <- function(img, k, kmask = NA, mrf = 0.1, verbose=FALSE,
   kmask = iMath(kmask, "FillHoles") %>% thresholdImage(1,2)
   nhood <- paste(rep(1, dim), collapse = "x")
   mrf <- paste("[", mrf, ",", nhood, "]", sep = "")
-  kmimg <- atropos( a = kmimg, m = mrf, c = "[5,0]",
+  kmimg <- atropos( a = img, m = mrf, c = "[5,0]",
     i = paste("kmeans[",k, "]", sep = ""),
     verbose = verbose,
     x = kmask,