Merge pull request Deep-MI#511 from Deep-MI/fix/older-bash-srun-fasts…

…urfer

Remove strings from arithmetic expressions

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
@@ -318,18 +319,19 @@ 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 +490,4 @@ then
 fi
 
 # always exit successful
-exit 0
+exit 0

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" ]]