diff --git a/PadsOff b/PadsOff index 87a0d3f..68e1b84 100755 --- a/PadsOff +++ b/PadsOff @@ -75,7 +75,7 @@ function reportParameters() { ${bold} 0. Initialised with $n_threads threads ${normal} -------------------------------------------------------------------------------- ANTs installation found : ${bold} $ANTSPATH ${normal} - FaceOff location : ${bold} $SCRIPT_DIR ${normal} + PadsOff location : ${bold} $SCRIPT_DIR ${normal} Input data : ${bold} $input_file ${normal} Using SyN? : ${bold} $syn ${normal} DePad mask (output) : ${bold} $OUTPUT_MASK_NAME ${normal} @@ -157,11 +157,10 @@ else fi if [ -z "$force_syn" ]; then - force_syn=1 - syn="yes" -else force_syn=0 syn="no" +else + syn="yes" fi ################################################################################ @@ -187,7 +186,7 @@ ${ANTSPATH}/antsAI \ --metric MI[ $TEMPLATE_DIR/OASIS_T1w.nii.gz , $input_file , 32 , Regular , 0.25 ] \ --output $TEMPLATE_DIR/REG_INPUT_TO_TEMP_INIT.mat -echo " ${bold} 1. Mapped to template. ${normal}" +echo " ${bold} 0. Initialised to template. ${normal}" echo "--------------------------------------------------------------------------------" if [ $force_syn -eq 1 ]; then @@ -241,7 +240,7 @@ if [ $force_syn -eq 1 ]; then --transform [ $TEMPLATE_DIR/REG_INPUT_TO_TEMP_0GenericAffine.mat , 1 ] \ --verbose 0 - echo " ${bold} 2. Deface mask created. ${normal}" + echo " ${bold} 2. DePad mask created. ${normal}" echo "--------------------------------------------------------------------------------" else @@ -287,7 +286,7 @@ else --transform [ $TEMPLATE_DIR/REG_INPUT_TO_TEMP_0GenericAffine.mat , 1 ] \ --verbose 0 - echo " ${bold} 2. Deface mask created. ${normal}" + echo " ${bold} 2. DePad mask created. ${normal}" echo "--------------------------------------------------------------------------------" fi @@ -306,7 +305,7 @@ ${ANTSPATH}/ImageMath \ $input_file \ $OUTPUT_MASK_NAME -echo " ${bold} 3. Defacing completed. ${normal}" +echo " ${bold} 3. DePadding completed. ${normal}" echo "--------------------------------------------------------------------------------" end_time0=$(date +%s) @@ -326,5 +325,5 @@ rm $TEMPLATE_DIR/REG_INPUT_TO_TEMP_*.* # ################################################################################ -echo " ${bold} 4. FaceOff ended. It took $(($nettime0 / 3600))h:$(($nettime0 % 3600 / 60))m:$(($nettime0 % 60))s. ${normal}" +echo " ${bold} 4. PadsOff ended. It took $(($nettime0 / 3600))h:$(($nettime0 % 3600 / 60))m:$(($nettime0 % 60))s. ${normal}" echo "================================================================================"