From 47568071f068f4b45b691d0516953e97a9522bdd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20K=C3=BCgler?= <david.kuegler@dzne.de>
Date: Sat, 13 Apr 2024 13:57:05 +0200
Subject: [PATCH 1/2] Remove strings from arithmetic expressions

There seems to be an issue with parsing strings as integer/numbers in some bash versions, see #507 . This commit pulls out `num_subjects=${#subjects[@]}` and replaces the string `"${#subjects[@]}"` in the arithmetic expression by `num_subjects`.
---
 brun_fastsurfer.sh | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/brun_fastsurfer.sh b/brun_fastsurfer.sh
index d7114539..a438b54e 100755
--- a/brun_fastsurfer.sh
+++ b/brun_fastsurfer.sh
@@ -318,18 +318,19 @@ then
   fi
 fi
 
+num_subjects=${#subjects[@]}
 if [[ -z "$task_id" ]] && [[ -z "$task_count" ]]
 then
   subject_start=0
-  subject_end="${#subjects[@]}"
+  subject_end=$num_subjects
 elif [[ -z "$task_id" ]] || [[ -z "$task_count" ]]
 then
   echo "Both task_id and task_count have to be defined, invalid --batch argument?"
   exit 1
 else
-  subject_start=$(((task_id - 1) * "${#subjects[@]}" / task_count))
-  subject_end=$((task_id * "${#subjects[@]}" / task_count))
-  subject_end=$((subject_end < "${#subjects[@]}" ? subject_end : "${#subjects[@]}"))
+  subject_start=$(((task_id - 1) * num_subjects / task_count))
+  subject_end=$((task_id * num_subjects / task_count))
+  subject_end=$((subject_end < num_subjects ? subject_end : num_subjects))
   echo "Processing subjects $subject_start to $subject_end"
 fi
 subject_len=$((subject_end - subject_start))
@@ -488,4 +489,4 @@ then
 fi
 
 # always exit successful
-exit 0
\ No newline at end of file
+exit 0

From 5aa851b42e1173b582dd83c6e10992cd44817dab Mon Sep 17 00:00:00 2001
From: David Kuegler <david.kuegler@dzne.de>
Date: Sat, 13 Apr 2024 14:14:57 +0200
Subject: [PATCH 2/2] Add version of the shell to the debug output

---
 brun_fastsurfer.sh | 3 ++-
 srun_fastsurfer.sh | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/brun_fastsurfer.sh b/brun_fastsurfer.sh
index a438b54e..480ff64d 100755
--- a/brun_fastsurfer.sh
+++ b/brun_fastsurfer.sh
@@ -288,7 +288,8 @@ then
   done
   echo ""
   echo ""
-  echo "Running in shell$(ls -l "/proc/$$/exe" | cut -d">" -f2)"
+  shell=$(ls -l "/proc/$$/exe" | cut -d">" -f2)
+  echo "Running in shell $shell: $($shell --version 2>/dev/null | head -n 1)"
   echo ""
   echo "---END DEBUG  ---"
 fi
diff --git a/srun_fastsurfer.sh b/srun_fastsurfer.sh
index 676122aa..49065d56 100755
--- a/srun_fastsurfer.sh
+++ b/srun_fastsurfer.sh
@@ -489,7 +489,8 @@ do
   else debugf " %s" "$p";
   fi
 done
-debug "Running in$(ls -l /proc/$$/exe | cut -d">" -f2)"
+shell=$(ls -l "/proc/$$/exe" | cut -d">" -f2)
+debug "Running in shell $shell: $($shell --version 2>/dev/null | head -n 1)"
 debug ""
 
 if [[ "${pattern/#\/}" != "$pattern" ]]