From 3d7bcb9539a9d160906428581789c467e79e972b Mon Sep 17 00:00:00 2001 From: Andrew Hoopes Date: Tue, 22 Dec 2020 11:35:29 -0500 Subject: [PATCH] nf: full path reading of subfield input files --- BrainstemSS/segmentBS.sh | 2 +- HippoSF/segmentHA_T1.sh | 2 +- HippoSF/segmentHA_T1_long.sh | 2 +- HippoSF/segmentHA_T2.sh | 4 ++-- ThalamicNuclei/segmentThalamicNuclei.sh | 4 ++-- 5 files changed, 7 insertions(+), 7 deletions(-) diff --git a/BrainstemSS/segmentBS.sh b/BrainstemSS/segmentBS.sh index a95b00035a1..e7106bb7c1f 100755 --- a/BrainstemSS/segmentBS.sh +++ b/BrainstemSS/segmentBS.sh @@ -88,7 +88,7 @@ endif # If SUBJECTS_DIR is provided, just set it if ($#argv == 2) then - set SUBJECTS_DIR = $2 + set SUBJECTS_DIR = `getfullpath $2` endif # Set name of subject diff --git a/HippoSF/segmentHA_T1.sh b/HippoSF/segmentHA_T1.sh index 2fde77d287e..d816f8903e0 100755 --- a/HippoSF/segmentHA_T1.sh +++ b/HippoSF/segmentHA_T1.sh @@ -97,7 +97,7 @@ endif # If SUBJECTS_DIR is provided, just set it if ($#argv == 2) then - set SUBJECTS_DIR = $2 + set SUBJECTS_DIR = `getfullpath $2` endif # Set name of subject diff --git a/HippoSF/segmentHA_T1_long.sh b/HippoSF/segmentHA_T1_long.sh index e9faf98e5e5..a7975da13fb 100755 --- a/HippoSF/segmentHA_T1_long.sh +++ b/HippoSF/segmentHA_T1_long.sh @@ -106,7 +106,7 @@ endif # If SUBJECTS_DIR is provided, just set it if ($#argv == 2) then - set SUBJECTS_DIR = $2 + set SUBJECTS_DIR = `getfullpath $2` endif # Set base subject diff --git a/HippoSF/segmentHA_T2.sh b/HippoSF/segmentHA_T2.sh index 16cee54b093..73abad8eddc 100755 --- a/HippoSF/segmentHA_T2.sh +++ b/HippoSF/segmentHA_T2.sh @@ -118,12 +118,12 @@ endif # If SUBJECTS_DIR is provided, just set it if ($#argv == 5) then - set SUBJECTS_DIR = $5 + set SUBJECTS_DIR = `getfullpath $5` endif # Set name of subject set SUBJECTNAME = $1 -set T2VOL = $2 +set T2VOL = `getfullpath $2` set ANALYSISID = $3 set USET1 = $4 diff --git a/ThalamicNuclei/segmentThalamicNuclei.sh b/ThalamicNuclei/segmentThalamicNuclei.sh index aa235b27cb1..fb5fbd40ddc 100755 --- a/ThalamicNuclei/segmentThalamicNuclei.sh +++ b/ThalamicNuclei/segmentThalamicNuclei.sh @@ -104,7 +104,7 @@ endif # If SUBJECTS_DIR is provided, just set it if ($#argv == 2) then - set SUBJECTS_DIR = $2 + set SUBJECTS_DIR = `getfullpath $2` endif # Set name of subject @@ -133,7 +133,7 @@ endif # Set additional parameters, if necessary set ANALYSISID="mainFreeSurferT1"; if ($#argv > 2) then - set ADDVOL="$3"; + set ADDVOL="`getfullpath $3`"; set ANALYSISID="$4"; set BBREGMODE="$5"; set DOBIASFIELDCORR="1";