From a32b2bb0d5c33da70b4ae53aefba23980fb80d27 Mon Sep 17 00:00:00 2001
From: Stephen Smith <steve@fmrib.ox.ac.uk>
Date: Tue, 12 Mar 2019 12:26:58 +0000
Subject: [PATCH] add back mean to detrended fmri timeseries in hcp_fix
---
hcp_fix | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/hcp_fix b/hcp_fix
index 8cd6f31..433d9ef 100755
--- a/hcp_fix
+++ b/hcp_fix
@@ -47,7 +47,8 @@ echo "processing FMRI file $fmri with highpass $hp"
if [ $hp -gt 0 ] ; then
echo "running highpass"
hptr=`echo "10 k $hp 2 / $tr / p" | dc -`
- ${FSLDIR}/bin/fslmaths $fmri -bptf $hptr -1 ${fmri}_hp$hp
+ ${FSLDIR}/bin/fslmaths $fmri -Tmean ${fmri}_hp$hp
+ ${FSLDIR}/bin/fslmaths $fmri -bptf $hptr -1 -add ${fmri}_hp$hp ${fmri}_hp$hp
fmri=${fmri}_hp$hp
fi
--
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