Fix: passthrough of arguments to run_prediction.py (previous commit b…

…roke this, but this adds some more options)

Fix fs_license definition via --fs_license for long_prepare_template.sh
Fix shellcheck warnings
Consolidate checks for whether a subject_dir is a longitudinal template

long_fastsurfer.sh

@@ -165,6 +165,7 @@ case $key in
   --parallel_long) parallel=1 ;;
   --py) python="$1" ; shift ;;
   -h|--help) usage ; exit ;;
+  --remove_suffix) echo "ERROR: The --remove_suffix option is not supported by long_prepare_template.sh" ; exit 1 ;;
   --sid|--t1|--t2)
     echo "ERROR: --sid, --t1 and --t2 are not valid for long_fastsurfer.sh, these values are"
     echo "  populated via --tpids, --tid and --t1s, respectively."

recon_surf/functions.sh

@@ -190,4 +190,17 @@ function echo_quoted()
     sep=" "
   done
   echo ""
-}
+}
+
+function check_is_template()
+{
+  # params:
+  # 1: subjects_dir
+  # 2: subject_if
+  if [ ! -f "$1/$2/base-tps.fastsurfer" ] ; then
+    echo "ERROR: $2 is either not found in \$SUBJECTS_DIR or it is not a longitudinal template"
+    echo "  directory (base), which needs to contain base-tps.fastsurfer file. Please ensure that"
+    echo "  the base (template) has been created with long_prepare_template.sh."
+    exit 1
+  fi
+}

recon_surf/long_prepare_template.sh

@@ -68,11 +68,7 @@ interpol="cubic"    # for the final interpolation of all time points in median i
 robust_template_avg_arg=1  # median for template creation (if more than 1 time point)
 
 # default arguments
-batch_size=1
-device="auto"
-viewagg="auto"
 python="python3.10 -s" # avoid user-directory package inclusion
-vox_size="min"
 sd="$SUBJECTS_DIR"
 
 # init variables that need to be passed
@@ -154,6 +150,7 @@ fi
 # PARSE Command line
 inputargs=("$@")
 POSITIONAL_FASTSURFER=()
+run_pred_flags=()
 i=0
 while [[ $# -gt 0 ]]
 do
@@ -179,23 +176,18 @@ case $key in
     done
     ;;
   --sd) sd="$1" ; export SUBJECTS_DIR="$1" ; shift  ;;
-  --vox_size) vox_size="$1" ; shift ;;
+  # these flags are passed through to run_prediction.py
+  --vox_size|--device|--viewagg_device|--conform_to_1mm_threshold|--threads)
+    run_pred_flags+=("$key" "$1") ; shift ;;
+  --batch) run_pred_flags+=("--batch_size" "$1") ; shift ;;
+  # these known arguments get ignored
+  --aseg_name|--conformed_name|--asegdkt_segfile|--brainmask_name|--seg_log|--qc_log) shift ;;
+  --async_io) ;;
+  --fs_license) export FS_LICENSE="$1" ; shift ;;
+  --remove_suffix) echo "ERROR: The --remove_suffix option is not supported by long_prepare_template.sh" ; exit 1 ;;
   -h|--help) usage ; exit ;;
   --py) python="$1" ; shift ;;
-  --device) device="$1" ; shift ;;
-  --batch) batch_size="$1" ; shift ;;
-  --viewagg_device)
-    case "$1" in
-      check)
-        echo "WARNING: the option \"check\" is deprecated for --viewagg_device <device>, use \"auto\"."
-        viewagg="auto"
-        ;;
-      gpu) viewagg="cuda" ;;
-      *) viewagg="$1" ;;
-    esac
-    shift # past value
-    ;;
-  *)    # unknown options get forwarded to run_fastsurfer (or ignored)
+  *)    # unknown options also get ignored, but also print warnings
     POSITIONAL_FASTSURFER[i]="$arg"
     i=$((i + 1))
     ;;
@@ -209,28 +201,34 @@ done
 
 ################################## CHECKS ##############################
 
+if [[ "${#POSITIONAL_FASTSURFER[@]}" -gt 0 ]]
+then
+  echo "WARNING: The arguments ${POSITIONAL_FASTSURFER[*]}"
+  echo "  are not recognized and therefore ignored!"
+fi
+
 if [ "${#t1s[@]}" -lt 1 ]
 then
-  echo "ERROR: must supply T1 inputs (full head) via --t1s"
+  echo "ERROR: You must supply T1 inputs (full head) via --t1s!"
   exit 1
 fi
 
 if [ "${#tpids[@]}" -lt 1 ]
 then
-  echo "ERROR: must supply time points ids via --tpids"
+  echo "ERROR: You must supply time points ids via --tpids!"
   exit 1
 fi
 
 if [ -z "$tid" ]
 then
-  echo "ERROR: must supply subject template name via --tid"
+  echo "ERROR: You must supply subject template name via --tid!"
   exit 1
 fi
 
 # check that t1s list is same length as tpids
 if [ "${#tpids[@]}" -ne "${#t1s[@]}" ]
 then
-  echo "ERROR: length of tpids must equal t1s"
+  echo "ERROR: The length of tpids must equal t1s!"
   exit 1
 fi
 
@@ -247,8 +245,9 @@ then
 fi
 if [[ "$(stat -c "%u:%g" "$SUBJECTS_DIR")" == "0:0" ]] && [[ "$(id -u)" != "0" ]] && [[ "$(stat -c "%a" "$SUBJECTS_DIR" | tail -c 2)" -lt 6 ]]
 then
-  echo "ERROR: The subject directory ($SUBJECTS_DIR) is owned by root and is not writable. FastSurfer cannot write results! "
-  echo "This can happen if the directory is created by docker. Make sure to create the directory before invoking docker!"
+  echo "ERROR: The subject directory ($SUBJECTS_DIR) is owned by root and is not writable."
+  echo "  FastSurfer cannot write results! This can happen if the directory is created by"
+  echo "  docker. Make sure to create the directory before invoking docker!"
   exit 1;
 fi
 
@@ -288,6 +287,7 @@ echo "Log file for long_prepare_template" >> "$LF"
 
 
 ### IF THE SCRIPT GETS TERMINATED, ADD A MESSAGE
+# shellcheck disable=SC2064
 trap "{ echo \"long_prepare_template.sh terminated via signal at \$(date -R)!\" >> \"$LF\" ; }" SIGINT SIGTERM
 
 
@@ -354,7 +354,7 @@ for ((i=0;i<${#tpids[@]};++i)); do
   RunIt "$cmd" "$LF"
 
   # conform !!!!!!! should we conform to some common value, determined from all time points?? !!!!!!
-  # this is relevant if input resolutions differe (which they should not), currently conform min may not work as expected
+  # this is relevant if input resolutions different (which they should not), currently conform min may not work as expected
   #conform="$mdir/T1_conform${extension}"
   #cmd="mri_convert -c ${t1s[i]} $conform"
   #cmd="$python $fastsurfercnndir/data_loader/conform.py -i ${t1s[i]} -o $conform --vox_size $vox_size --dtype any --verbose"
@@ -368,21 +368,19 @@ for ((i=0;i<${#tpids[@]};++i)); do
   mask_name="$mdir/cross_mask${extension}"
   aseg_segfile="$mdir/cross_aseg.auto_noCCseg${extension}"
   seg_log="/dev/null"
-  cmd=($python "$fastsurfercnndir/run_prediction.py"
-         "${POSITIONAL_FASTSURFER[@]}" --t1 "$t1input"
+  cmda=($python "$fastsurfercnndir/run_prediction.py" --t1 "$t1input" --async_io
          --asegdkt_segfile "$asegdkt_segfile" --conformed_name "$conformed_name"
          --brainmask_name "$mask_name" --aseg_name "$aseg_segfile" --sid "${tpids[i]}"
-         --seg_log "$seg_log" --vox_size "$vox_size" --batch_size "$batch_size"
-         --viewagg_device "$viewagg" --device "$device")
-  run_it "$LF" "${cmd[@]}"
+         --seg_log "$seg_log" "${run_pred_flags[@]}")
+  run_it "$LF" "${cmda[@]}"
 
   # remove mri subdirectory (run_prediction creates 001 there)
-  cmd=(rm -rf "$mdir/mri")
-  run_it "$LF" "${cmd[@]}"
+  cmda=(rm -rf "$mdir/mri")
+  run_it "$LF" "${cmda[@]}"
 
   # mask is binary, we need to use on conformed image:
-  cmd=(mri_mask "$conformed_name" "$mask_name" "$mdir/cross_brainmask${extension}")
-  run_it "$LF" "${cmd[@]}"
+  cmda=(mri_mask "$conformed_name" "$mask_name" "$mdir/cross_brainmask${extension}")
+  run_it "$LF" "${cmda[@]}"
 done
 
 # skip intensity normalization or bias field removal for now
@@ -401,30 +399,29 @@ done
 # create a file with all time points names
 # this cannot be "base-tps" else recon-surf (and inside recon-all) will fail
 BaseSubjsListFname="$SUBJECTS_DIR/$tid/base-tps.fastsurfer"
-rm -f ${BaseSubjsListFname}
-mkdir -p $SUBJECTS_DIR/$tid/mri/transforms
+rm -f "${BaseSubjsListFname}"
+mkdir -p "$SUBJECTS_DIR/$tid/mri/transforms"
 subjInVols=()
 normInVols=()
 ltaXforms=()
 
 for s in "${tpids[@]}"
 do
-  echo $s
-  echo "${s}" >> ${BaseSubjsListFname}
+  echo "$s" | tee -a "${BaseSubjsListFname}"
   mdir="$SUBJECTS_DIR/$tid/long-inputs/${s}"
   invol="$mdir/cross_conform${extension}"
-  subjInVols+=($invol)
+  subjInVols+=("$invol")
   normvol="$mdir/cross_brainmask${extension}"
-  normInVols+=($normvol)
-  ltaname=${s}_to_${tid}.lta
-  ltaXforms+=(${SUBJECTS_DIR}/$tid/mri/transforms/${ltaname})
+  normInVols+=("$normvol")
+  ltaname="${s}_to_${tid}.lta"
+  ltaXforms+=("${SUBJECTS_DIR}/$tid/mri/transforms/${ltaname}")
 done
 
 
 if [ ${#tpids[@]} == 1 ]
 then
   # if only a single time point, create fake 'base' by making the image upright
-  # this assures that also subjects with a single time point get processes as the other
+  # this assures that also subjects with a single time point get processed as the other
   # subjects in the longitudinal stream
 
   # 1. make the norm upright (base space)
@@ -441,17 +438,17 @@ else #more than 1 time point:
 
 
   # create the 'mean/median' norm volume:
-  cmd="mri_robust_template --mov ${normInVols[@]}"
-  cmd="$cmd --lta ${ltaXforms[@]}"
+  cmd="mri_robust_template --mov ${normInVols[*]}"
+  cmd="$cmd --lta ${ltaXforms[*]}"
   cmd="$cmd --template ${SUBJECTS_DIR}/$tid/mri/base_brainmask${extension}"
   cmd="$cmd --average ${robust_template_avg_arg}"
   cmd="$cmd --sat 4.685"
   RunIt "$cmd" "$LF"
 
   # create the 'mean/median' input (orig) volume:
-  cmd="mri_robust_template --mov ${subjInVols[@]}"
+  cmd="mri_robust_template --mov ${subjInVols[*]}"
   cmd="$cmd --average ${robust_template_avg_arg}"
-  cmd="$cmd --ixforms ${ltaXforms[@]}"
+  cmd="$cmd --ixforms ${ltaXforms[*]}"
   cmd="$cmd --noit"
   t1=${SUBJECTS_DIR}/$tid/mri/orig.mgz
   cmd="$cmd --template $t1"

run_fastsurfer.sh

@@ -697,12 +697,7 @@ fi
 
 if [[ "$base" == "1" ]]
 then
-  if [ ! -f "$sd/$subject/base-tps.fastsurfer" ] ; then
-    echo "ERROR: $subject is either not found in \$SUBJECTS_DIR or it is not a longitudinal template"
-    echo "  directory (base), which needs to contain base-tps.fastsurfer file. Please ensure that"
-    echo "  the base (template) has been created with long_prepare_template.sh."
-    exit 1
-  fi
+  check_is_template "$sd" "$subject"
   if [[ -n "$t1" ]] && [[ "$t1" != "from-base" ]]; then
     echo "WARNING: --t1 was passed but will be overwritten with T1 from base template."
   fi
@@ -713,12 +708,7 @@ fi
 
 if [[ "$long" == "1" ]]
 then
-  if [ ! -f "$sd/$baseid/base-tps.fastsurfer" ] ; then
-    echo "ERROR: $baseid is either not found in \$SUBJECTS_DIR or it is not a longitudinal template"
-    echo "  directory (base), which needs to contain base-tps.fastsurfer file. Please ensure that"
-    echo "  the base (template) has been created with long_prepare_template.sh."
-    exit 1
-  fi
+  check_is_template "$sd" "$baseid"
   if ! grep -Fxq "$subject" "$sd/$baseid/base-tps.fastsurfer" ; then
     echo "ERROR: $subject id not found in base-tps.fastsurfer. Please ensure that this time point"
     echo "  was included during creation of the base (template)."