nf: full path reading of subfield input files

ayendiki · Dec 22, 2020 · 3d7bcb9 · 3d7bcb9
1 parent d9ed621
commit 3d7bcb9
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Showing 5 changed files with 7 additions and 7 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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";