CODEWITHSUNDEEP
bashshellunix
Antonio
Antonio

Reputation: 327

Finding filenames with specific string in a shell script

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

Upvotes: 1

Views: 157

Answers (3)

Jithin Scaria
Jithin Scaria

Reputation: 1309

try changing the line

anatomical_scans=$find$inputpath-name *mprage

to

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

Upvotes: 4

Nic Olas
Nic Olas

Reputation: 471

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!!!'

Upvotes: 1

M. Becerra
M. Becerra

Reputation: 659

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!!!"

Upvotes: 1

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