diff --git a/run_fastsurfer.sh b/run_fastsurfer.sh
index 98cf79203..7d1b749ac 100755
--- a/run_fastsurfer.sh
+++ b/run_fastsurfer.sh
@@ -504,6 +504,49 @@ esac
 done
 set -- "${POSITIONAL[@]}" # restore positional parameters
 
+
+# Function to convert path to absolute if it exists and is not empty
+convert_to_absolute_path() {
+  local var_name="$1"
+  local var_value
+  eval "var_value=\$$var_name"
+  
+  if [ -n "$var_value" ]; then
+    if [ -e "$var_value" ] || [ "${var_value#*/}" != "$var_value" ]; then
+      # Path exists or contains directory separators - convert to absolute
+      local abs_path
+      abs_path=$(realpath "$var_value" 2>/dev/null)
+      if [ $? -eq 0 ] && [ -n "$abs_path" ]; then
+        eval "$var_name=\"$abs_path\""
+      else
+        echo "WARNING: Failed to convert $var_name to absolute path: $var_value" | tee -a "${tmpLF:-/dev/null}"
+      fi
+    fi
+  fi
+}
+
+# Convert path variables to absolute paths
+convert_to_absolute_path "sd"
+convert_to_absolute_path "t1"
+convert_to_absolute_path "t2"
+convert_to_absolute_path "seg_log"
+convert_to_absolute_path "conformed_name"
+convert_to_absolute_path "norm_name"
+convert_to_absolute_path "norm_name_t2"
+convert_to_absolute_path "asegdkt_segfile"
+convert_to_absolute_path "mask_name"
+convert_to_absolute_path "merged_segfile"
+convert_to_absolute_path "cereb_segfile"
+convert_to_absolute_path "cereb_statsfile"
+convert_to_absolute_path "hypo_segfile"
+convert_to_absolute_path "hypo_statsfile"
+convert_to_absolute_path "asegdkt_vinn_statsfile"
+convert_to_absolute_path "aseg_vinn_statsfile"
+convert_to_absolute_path "aseg_segfile"
+convert_to_absolute_path "FS_LICENSE"
+
+
+
 # make sure FastSurfer is in the PYTHONPATH
 export PYTHONPATH
 PYTHONPATH="$FASTSURFER_HOME$([[ -n "$PYTHONPATH" ]] && echo ":$PYTHONPATH")"