From 4fdff74130fc684300b720974610aeaaaeb10b05 Mon Sep 17 00:00:00 2001
From: Clemens Pollak <ClePol@users.noreply.github.com>
Date: Mon, 29 Sep 2025 17:01:06 +0200
Subject: [PATCH 1/3] Allow relative paths in run_fastsurfer.sh

---
 run_fastsurfer.sh | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/run_fastsurfer.sh b/run_fastsurfer.sh
index 98cf79203..36295c3c0 100755
--- a/run_fastsurfer.sh
+++ b/run_fastsurfer.sh
@@ -504,6 +504,48 @@ 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="$1"
+  local var_value="${!var_name}"
+  
+  if [[ -n "$var_value" ]]; then
+    if [[ -e "$var_value" ]] || [[ "$var_value" == *"/"* ]]; then
+      # Path exists or contains directory separators - convert to absolute
+      local abs_path
+      abs_path=$(realpath -m "$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")"

From ccdb420a83a15c4e5a0157f424ffdf01405b908a Mon Sep 17 00:00:00 2001
From: ClePol <clemens.pollak@gmail.com>
Date: Mon, 29 Sep 2025 17:24:41 +0200
Subject: [PATCH 2/3] simplified for compatibility with older bash versions

---
 run_fastsurfer.sh | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/run_fastsurfer.sh b/run_fastsurfer.sh
index 36295c3c0..6d61a7118 100755
--- a/run_fastsurfer.sh
+++ b/run_fastsurfer.sh
@@ -508,14 +508,15 @@ 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="$1"
-  local var_value="${!var_name}"
+  local var_value
+  eval "var_value=\$$var_name"
   
-  if [[ -n "$var_value" ]]; then
-    if [[ -e "$var_value" ]] || [[ "$var_value" == *"/"* ]]; then
+  if [ -n "$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 -m "$var_value" 2>/dev/null)
-      if [[ $? -eq 0 && -n "$abs_path" ]]; then
+      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}"

From e816cdd56771267d2aab782c1d74cd1ad1f29f16 Mon Sep 17 00:00:00 2001
From: Martin Reuter <m-reuter@users.noreply.github.com>
Date: Tue, 30 Sep 2025 14:04:32 +0200
Subject: [PATCH 3/3] remove space

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 run_fastsurfer.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/run_fastsurfer.sh b/run_fastsurfer.sh
index 6d61a7118..7d1b749ac 100755
--- a/run_fastsurfer.sh
+++ b/run_fastsurfer.sh
@@ -515,7 +515,7 @@ convert_to_absolute_path() {
     if [ -e "$var_value" ] || [ "${var_value#*/}" != "$var_value" ]; then
       # Path exists or contains directory separators - convert to absolute
       local abs_path
-      abs_path=$(realpath  "$var_value" 2>/dev/null)
+      abs_path=$(realpath "$var_value" 2>/dev/null)
       if [ $? -eq 0 ] && [ -n "$abs_path" ]; then
         eval "$var_name=\"$abs_path\""
       else