Fix smaller issues in srun_fastsurfer.sh

srun_fastsurfer.sh

@@ -43,7 +43,7 @@ subject_list_awk_code_sid="\$1"
 subject_list_awk_code_args="\$2"
 subject_list_delim="="
 jobarray=""
-timelimit_seg=10
+timelimit_seg=15
 # 1mm can take 1h per hemi plus 1h extra on a single core (depending on cpu speed)
 timelimit_surf=$((4 * 60))
 # the memory required for the surface and the segmentation pipeline depends on the
@@ -419,23 +419,23 @@ fi
 wait # for directories to be made
 
 # step one: copy singularity image to hpc
-all_cases_file="/$hpc_work/scripts/subject_list"
+all_cases_file="$hpc_work/scripts/subject_list"
 
 log "cp \"$singularity_image\" \"$hpc_work/images/fastsurfer.sif\""
 script_dir="$(dirname "$THIS_SCRIPT")"
 log "cp \"$script_dir/brun_fastsurfer.sh\" \"$script_dir/stools.sh\" \"$hpc_work/scripts\""
 log "cp \"$fs_license\" \"$hpc_work/scripts/.fs_license\""
 log "Create Status/Success file at $hpc_work/scripts/subject_success"
 
-tofile="cat"
+tofile=("cat")
 if [[ "$submit_jobs" == "true" ]]
 then
   cp "$singularity_image" "$hpc_work/images/fastsurfer.sif" &
   cp "$script_dir/brun_fastsurfer.sh" "$script_dir/stools.sh" "$hpc_work/scripts" &
   cp "$fs_license" "$hpc_work/scripts/.fs_license" &
   log "#Status/Success file of srun_fastsurfer-run $(date)" > "$hpc_work/scripts/subject_success" &
 
-  tofile="tee $all_cases_file"
+  tofile=("tee" "$all_cases_file")
 fi
 
 # step two: copy input data to hpc
@@ -451,9 +451,9 @@ then
     log ""
   fi
 
-  cases=$(translate_cases "$in_dir" "$subject_list" "/source" "${subject_list_delim}" "${subject_list_awk_code_sid}" "${subject_list_awk_code_args}" | $tofile)
+  cases=$(translate_cases "$in_dir" "$subject_list" "/source" "${subject_list_delim}" "${subject_list_awk_code_sid}" "${subject_list_awk_code_args}" | "${tofile[@]}")
 else
-  cases=$(read_cases "$in_dir" "$pattern" "/source" | $tofile)
+  cases=$(read_cases "$in_dir" "$pattern" "/source" | "${tofile[@]}")
 fi
 num_cases=$(echo "$cases" | wc -l)
 
@@ -548,6 +548,7 @@ then
   seg_cmd_filename=$hpc_work/scripts/slurm_cmd_seg.sh
   if [[ "$submit_jobs" == "true" ]] ; then seg_cmd_file=$seg_cmd_filename ; else seg_cmd_file=$(mktemp) ; fi
 
+  IFS=" "
   slurm_part_=$(first_non_empty_arg "$partition_seg" "$partition")
   if [[ -z "$slurm_part_" ]] ; then slurm_partition=() ; else slurm_partition=(-p "$slurm_part_") ; fi
   {
@@ -573,16 +574,12 @@ then
   fi
   # note that there can be a decent startup cost for each run, running multiple cases
   # per task significantly reduces this
-  seg_slurm_sched=("--mem=${mem_seg}G" "--cpus-per-task=$num_cpus_per_task"
+  seg_slurm_sched=("--mem=${mem_seg}G" "--cpus-per-task=$num_cpus_per_task" -J "FastSurfer-Seg-$USER"
                    --time=$((timelimit_seg * real_num_cases_per_task + 5))
-                   "${slurm_partition[@]}" "${slurm_email[@]}"
-                   "${jobarray_option[@]}" -J "FastSurfer-Seg-$USER"
+                   "${slurm_partition[@]}" "${slurm_email[@]}" "${jobarray_option[@]}"
                    -o "$hpc_work/logs/seg_%A_%a.log" "$seg_cmd_filename")
-  if [[ "$cpu_only" == "true" ]]
-  then
-    debug "Schedule SLURM job without gpu"
-  else
-    seg_slurm_sched=(--gpus=1 "${seg_slurm_sched[@]}")
+  if [[ "$cpu_only" == "true" ]] ; then debug "Schedule SLURM job without gpu"
+  else seg_slurm_sched+=(--gpus-per-task=1)
   fi
   log "chmod +x $seg_cmd_filename"
   chmod +x "$seg_cmd_file"
@@ -630,13 +627,9 @@ then
                            "${fastsurfer_surf_options[@]}"
                            "${POSITIONAL_FASTSURFER[@]}")
   surf_cmd_filename=$hpc_work/scripts/slurm_cmd_surf.sh
-  if [[ "$submit_jobs" == "true" ]]; then surf_cmd_file=$surf_cmd_filename
-  else surf_cmd_file=$(mktemp)
-  fi
+  if [[ "$submit_jobs" == "true" ]]; then surf_cmd_file=$surf_cmd_filename ; else surf_cmd_file=$(mktemp) ; fi
   mem_per_core=$((mem_surf / num_cpus_surf))
-  if [[ "$mem_surf" -gt "$((mem_per_core * num_cpus_surf))" ]]; then
-    mem_per_core=$((mem_per_core+1))
-  fi
+  if [[ "$mem_surf" -gt "$((mem_per_core * num_cpus_surf))" ]]; then mem_per_core=$((mem_per_core+1)) ; fi
   slurm_part_=$(first_non_empty_arg "$partition_surf" "$partition")
   if [[ -z "$slurm_part_" ]] ; then slurm_partition=() ; else slurm_partition=(-p "$slurm_part_") ; fi
   {

stools.sh

@@ -170,6 +170,8 @@ function check_subject_images ()
   missing_subject_imgs=""
   symlink_subject_imgs=""
   data_dir="$1"
+  #remove training /
+  while [[ "${data_dir:$((${#data_dir} - 1))}" == "/" ]] ; do data_dir=${data_dir:0:$((${#data_dir} - 1))} ; done
   OLD_IFS=$IFS
   IFS=$'\n'
   for subject in $2
@@ -196,7 +198,6 @@ function check_subject_images ()
         arg0="${arg:0:${#data_dir}}"
         if [[ "$real_data" != "$(realpath "$arg0")" ]] || [[ "${real_arg:${#real_data}}" != "${arg:${#data_dir}}" ]] # this is a symlink
         then
-          echo ":$(realpath "$arg"):=?=:$arg:"
           if [[ $first_img == 1 ]]; then missing_subject_ids+=", $subject_id" ; first_img=0 ; fi
           symlink_subject_imgs+=", $arg => $(realpath "$arg")"
         fi