Merge pull request Deep-MI#545 from dkuegler/fix/fs_time

Fix fs_time check for number of arguments and line duplication in recon-surf

Docker/install_fs_pruned.sh

@@ -104,7 +104,6 @@ wget --no-check-certificate -qO- $fslink  | tar zxv --no-same-owner -C $where \
       --exclude='freesurfer/average/Buckner_JNeurophysiol11_MNI152' \
       --exclude='freesurfer/average/Choi_JNeurophysiol12_MNI152' \
       --exclude='freesurfer/average/mult-comp-cor' \
-      --exclude='freesurfer/average/mult-comp-cor' \
       --exclude='freesurfer/average/samseg' \
       --exclude='freesurfer/average/Yeo_Brainmap_MNI152' \
       --exclude='freesurfer/average/Yeo_JNeurophysiol11_MNI152' \
@@ -271,7 +270,6 @@ copy_files="
   bin/mris_extract_main_component
   bin/mris_fix_topology
   bin/mris_inflate
-  bin/mris_inflate
   bin/mris_info
   bin/mris_jacobian
   bin/mris_label2annot

recon_surf/fs_time

@@ -117,18 +117,17 @@ function   arg1err()
 }
 
 inputargs=("$@")
-if [[ "$#" == 1 ]] ; then usage ; exit 0 ; fi
 any_help=$(echo "$@" | grep -e -help)
 if [[ -n "$any_help" ]]
 then
   usage
   help
   exit 0
 fi
-any_version=$(echo $argv | grep -e -version)
+any_version=$(echo "$@" | grep -e -version)
 if [[ -n "$any_version" ]]
 then
-  echo $VERSION
+  echo "$VERSION"
   exit 0
 fi
 
@@ -144,12 +143,12 @@ do
 
   case $flag in
     -o)
-      if [[ "$#" -lt 1 ]] ; then arg1err $flag; fi
+      if [[ "$#" -lt 1 ]] ; then arg1err "$flag"; fi
       outfile=$1
       shift
       ;;
     -k)
-      if [[ "$#" -lt 1 ]] ; then arg1err $flag ; fi
+      if [[ "$#" -lt 1 ]] ; then arg1err "$flag" ; fi
       key=$1
       shift
       ;;
@@ -161,7 +160,6 @@ do
       ;;
     -debug)
       verbose=1
-      echo=1
       ;;
     *)
       # must be at the start of the command to run
@@ -185,16 +183,16 @@ then
 fi
 
 # CHECK PARAMS
-if [[ ! -e /usr/bin/time ]]
+if [[ "${#cmd[@]}" == 0 ]]
 then
-  echo "ERROR: cannot find /usr/bin/time"
+  usage
+  echo "ERROR: no command passed to execute"
   exit 1
 fi
 
-if [[ "${#cmd[@]}" == 0 ]]
+if [[ ! -e /usr/bin/time ]]
 then
-  usage
-  echo "ERROR: no command passed to execute"
+  echo "ERROR: cannot find /usr/bin/time"
   exit 1
 fi
 

recon_surf/recon-surf.sh

@@ -866,11 +866,9 @@ fi
     echo " " | tee -a $LF
     cmd="recon-all -subject $subject -cortparc2 -cortparc3 -pctsurfcon -hyporelabel $hiresflag $fsthreads"
     RunIt "$cmd" $LF
-  RunIt "$cmd" $LF
     cmd="recon-all -subject $subject -apas2aseg -aparc2aseg -wmparc -parcstats -parcstats2 -parcstats3 -segstats $hiresflag $fsthreads"
     RunIt "$cmd" $LF
     # removed -balabels here and do that below independent of fsaparc flag
-  # removed -balabels here and do that below independent of fsaparc flag
   fi  # (FS-APARC)
 
 
@@ -890,9 +888,9 @@ fi
 
   if [ "$fsaparc" == "0" ] ; then
 
-  echo " " | tee -a $LF
-  echo "============= Creating surfaces - pctsurfcon, hypo, segstats ====================" | tee -a $LF
-  echo " " | tee -a $LF
+    echo " " | tee -a $LF
+    echo "============= Creating surfaces - pctsurfcon, hypo, segstats ====================" | tee -a $LF
+    echo " " | tee -a $LF
 
     # pctsurfcon (has no way to specify which annot to use, so we need to link ours as aparc is not available)
     pushd $ldir
@@ -913,7 +911,6 @@ fi
     # -apas2aseg creates aseg.mgz by editing aseg.presurf.hypos.mgz with surfaces
     cmd="recon-all -subject $subject -hyporelabel -apas2aseg $hiresflag $fsthreads"
     RunIt "$cmd" $LF
-  RunIt "$cmd" $LF
   fi
 
 
@@ -927,12 +924,10 @@ fi
 
 # ============================= FASTSURFER - STATS =========================================
 
-if [ "$fsaparc" == "0" ] ; then
   if [ "$fsaparc" == "0" ] ; then
     # get stats for the aseg (note these are surface fine tuned, that may be good or bad, below we also do the stats for the input aseg (plus some processing)
     cmd="recon-all -subject $subject -segstats $hiresflag $fsthreads"
     RunIt "$cmd" $LF
-  RunIt "$cmd" $LF
   fi