This document shows how to use a shell script to submit a batch of scans to Fsurf for processing.

Important note on data privacy: In order to protect the privacy of your participants’ scans, we request that you submit only defaced and fully deidentified scans for processing by fsurf. Images can be anonymized and deidentified before they are uploaded to OSG servers as described in the article on anonymizing images.

Preparing to submit scans

There are a few things that will be needed before you can start:

  • Terminal access on a computer with the following:
  • Bash installed
  • Wired internet access (preferable) or very fast wireless access
  • A directory with anonymized and defaced MRI brain scans
  • Knowledge of using a text editor within a terminal (e.g. vi, nano, emacs, etc.)

Running fsurf non-interactively

By default, fsurf asks if an image has defaced and anonymized when it is submitted for processing. However, if fsurf is given --defaced and --deidentified as options, these prompts will not appear.

Scripting fsurf submissions

The basic approach we will take is to generate a text file with scan and subject information. Then we'll use a script that will read this text file to submit each subject for processing using Fsurf.

Generating the text file

First, we'll generate a list of subjects. Assuming, the scans that we'd like to process are at ~/scans, run:

$ for i in `ls ~/scans/*`; do python -c 'import os,sys;print(os.path.realpath(sys.argv[1]))' $i; done > scan_list

This will generate a file with each scan on a separate line. Now edit the file using a text editor and add the subject for each scan file. After you're done, the file should look something like this:

 /home/user/scans/subject_1_defaced.mgz subject_1
 /home/user/scans/MRN_1_defaced.mgz MRN_1
 /home/user/scans/MRN_3_defaced.mgz MRN_3

Each line should have the filename for the scan, a space, and then the name of the subject.

Submission script

Now that we have a file that has information on the scans that should be submitted, let's write a script that will use that to call fsurf with the proper options.

Open a file called submit_multiple.sh in your text editor and cut and paste the following in it :


 while IFS= read -r line;
   input_file=`echo $line | cut -f 1 -d' '`
   subject=`echo $line | cut -f 2 -d' '`
   if [[ ! -z ${input_file} && ! -z ${subject} ]];
     ./fsurf submit --input=$input_file --subject=$subject --defaced --deidentified
 done < "$1"

Now make the script executable and run it:

 $ chmod a+x submit_multiple.sh
 $ ./submit_multiple.sh scan_list

The script may take a while to complete if you have a slow connection or if you are processing a lot of scans. If you're processing many scans, it's best that you run this on a computer that's connected using a wired connection.


This page was updated on Nov 11, 2019 at 23:00 from examples/FsurfRemote/ScriptingFsurf.md.