Finding filenames with specific string in a shell script

Question

I am trying to write a bash script to do a batch processing of some fMRI data. My problem is that I am not able to get the filenames that match a specific pattern within the directory of interest.

My scripts looks like this

#!/bin/bash

inputpath="/Volumes/External_HD/Experiments/MRI_Data"
outputpath="/Volumes/External_HD/Experiments/MRI_Data_output"

anatomical_scans=$find `$inputpath` -name *mprage

# RUN BET
bet $anatomical_scans $outputpath

echo 'Finished!!!'

The only output that I get is the following error message

-name: command not found

I am definetely not familiar with shell scripting so I am sorry if the question may sound trivial. Any help will be much appreciated.

Antonio

EDIT:: SOLVED

Exploring the suggestions I found the correct way to make it running with no errors

anatomical_scans=$(find $input_path -name "*mprage*")

Thanks

You miss some ''.. Take a look at this: stackoverflow.com/questions/8509226/… — Fabio_MO
– Fabio_MO, Commented Dec 6, 2017 at 16:20
Learn to use shellcheck.net before you post your code here ;-) . When you use shellcheck, you need to include a proper "she-bang" line as the first line, usually #!/bin/bash . AND avoid the top 10 shell script beginner mistakes by reading stackoverflow.com/tags/bash/info multiple times. Good luck. — shellter
– shellter, Commented Dec 6, 2017 at 16:26

hek2mgl · Accepted Answer · 2017-12-07 09:41:18Z

4

try changing the line

anatomical_scans=$find$inputpath-name *mprage

to

anatomical_scans=$(find "${inputpath}" -name "*mprage")

edited Dec 7, 2017 at 9:41

hek2mgl

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answered Dec 6, 2017 at 17:46

Jithin Scaria

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Comments

M. Becerra · Accepted Answer · 2017-12-06 16:18:56Z

1

You can do the following:

#!/bin/bash

inputpath="/Volumes/External_HD/Experiments/MRI_Data"
outputpath="/Volumes/External_HD/Experiments/MRI_Data_output"

function anatomical_scans {
    find $inputpath -name "*mprage"
}

# RUN BET
bet anatomical_scans $outputpath

echo "Finished!!!"

answered Dec 6, 2017 at 16:18

M. Becerra

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Comments

Nic Olas · Accepted Answer · 2017-12-06 16:58:17Z

1

You can try as below, hope it can help.

#!/bin/bash

inputpath="/Volumes/External_HD/Experiments/MRI_Data"
outputpath="/Volumes/External_HD/Experiments/MRI_Data_output"

anatomical_scans=`find $inputpath -name '*mprage'`

# RUN BET
bet $anatomical_scans $outputpath

echo 'Finished!!!'

answered Dec 6, 2017 at 16:58

Nic Olas

4712 silver badges12 bronze badges

1 Comment

Nic3500 Over a year ago

Although it works, the syntax var=$(command) is preferred since it solves quoting issues, and others as described here: mywiki.wooledge.org/BashFAQ/082

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