From 063ef8773252b71f43d03a549ff08dc91fb5ab3d Mon Sep 17 00:00:00 2001
From: Tom Close <tclose@oist.jp>
Date: Tue, 25 Dec 2012 15:31:19 +0900
Subject: [PATCH] removed normalise option from estimate_response (which is
 commented out anyway) because it doesn't seem to be working as I thought it
 would.

---
 bash/get_dw_response | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bash/get_dw_response b/bash/get_dw_response
index 63c4066..a448c68 100755
--- a/bash/get_dw_response
+++ b/bash/get_dw_response
@@ -38,7 +38,7 @@ gen_WM_mask $dwi_file ${pfx}mask.mif - | threshold - ${pfx}wm_mask.mif -abs $WM_
 dwi2tensor $dwi_file - | tensor2FA - - | mrmult - ${pfx}wm_mask.mif - | threshold - ${pfx}sf_mask.mif -abs $SF_FA_THRESHOLD
 
 # Mask single_fibre mask with whole brain mask 
-#estimate_response $dwi_file ${pfx}sf_mask.mif $output -lmax 8 -normalise
+#estimate_response $dwi_file ${pfx}sf_mask.mif $output -lmax 8
 
 # Save the average b0 to file for use in scaling the base intensity of the expected image
 get_b0 $dwi_file ${pfx}sf_mask.mif -method median > ${output_base}.b0.$output_ext