From 7593b4024b5e8ea9c7e617f1e407d113417c8e8f Mon Sep 17 00:00:00 2001
From: muschellij2 <muschellij2@gmail.com>
Date: Sun, 24 Nov 2019 22:09:20 -0500
Subject: [PATCH] fixing bug in mid_sagittal align

---
 R/mid_sagittal_align.R | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/R/mid_sagittal_align.R b/R/mid_sagittal_align.R
index c690874..44053da 100644
--- a/R/mid_sagittal_align.R
+++ b/R/mid_sagittal_align.R
@@ -70,10 +70,14 @@ mid_sagittal_align = function(
     verbose = verbose,
     retimg = FALSE,
     outfile = tfile)
-  centered = reverse_rpi_orient_file(
-    file = tfile, 
-    orientation = rp$orientation,
-    convention = rp$convention)
+  if (force_rpi) {
+    centered = reverse_rpi_orient_file(
+      file = tfile, 
+      orientation = rp$orientation,
+      convention = rp$convention)
+  } else {
+    centered = tfile
+  }
   if (retimg) {
     centered = readnii(centered)
   }