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The following is a simple script, named myscript, that I wrote in order to run a command.

dcmpath='$HOME/Data'
dcmfile='IM1'
dcm2nii $dcmpath/$dcmfile

Unfortunately, bash does not recognize the path in front of dcm2nii and I cannot run the last command in the file. I would be thankful if someone could let me know what I am missing. What would be the best way of customizing the path and file name which is the argument of a command?

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"bash does not recognize the path in front of dcm2nii" - What path? dcm2nii is the first thing on the line, there's nothing in front of it. –  Patrick May 19 '14 at 3:27
    
I meant dcm2nii does not find the file with the full path: $dcmpath/$dcmfile although the file really exist. –  A2009 May 19 '14 at 3:41

1 Answer 1

up vote 3 down vote accepted 
dcmpath="$HOME/Data"
dcmfile="IM1"
dcm2nii "$dcmpath/$dcmfile"

In the first line, you should use double quotes instead of single quotes. Single quotes prevent variables like $HOME from being expanded; they're interpreted literally. You can see the bash manual for details: http://www.gnu.org/software/bash/manual/bashref.html#Quoting

It doesn't matter in the second line; both single or double quotes will work fine.

It's also good idea to (double) quote the argument in the last line, in case the variables contain a space.

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Thank you. It worked perfectly. What is the difference between defining the variable surrounded by single quotation and double quotation? –  A2009 May 19 '14 at 3:27
    
@A2009 lk has explained that in the edit. –  Hauke Laging May 19 '14 at 5:31

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