I am new to bash scripting and struggle to update a parameter with a default value. I observe some of my optional parameters are not getting updated according to the user input.
Below is the interesting part of my bash script. For instance, I set the variable REGISTRATION to 1, then the user can chose to set it to 0 instead.
# default values
DIM=3
BIASFIELDCORRECTION=1
SKULLSTRIPPING=0
REGISTRATION=1
RESAMPLRES=0
# reading command line arguments
while getopts ":s:d:b:res:reg:h:" OPT
do
case $OPT in
h) #help
Help
exit 0
;;
d) # dimension
DIM=$OPTARG
;;
b) # bias field correction
BIASFIELDCORRECTION=$OPTARG
;;
s) # skull stripping
SKULLSTRIPPING=$OPTARG
;;
res) # resampling resolution
RESAMPLRES=$OPTARG
;;
reg) # resampling resolution
REGISTRATION=$OPTARG
;;
\?) # getopts issues an error message
exit 1
;;
esac
done
echo "Registration:" $REGISTRATION
The problem is that the last line always outputs Registration: 1, even when the user set the variable to 0 with the following syntax:
bash preprocessingPipeline.sh -reg 0
I checked all my parameters and it appears that only res, reg and s present this problem. d and b are correctly updated. Can someone tell my what's wrong with my approach?
