Exercise: play with text-based data file


Please try not just copy-n-pasting the commands provided in the hands-on exercises!! Typing (and eventually making typos) is an essential part of the learning process.


Download this data file using the following command:

$ wget https://raw.githubusercontent.com/Donders-Institute/hpc-wiki-v2/master/docs/linux/exercise/gcutError_recon-all.log

This data file is an example output file from a freesurfer command submitted to the cluster using qsub. In this simple task we are going to try to extract some information from it using a few commands.

Your Task

  1. Construct a Linux command pipeline to get the subject ID associated with the log file. The subejct ID is of the form Subject##, i.e Subject01, Subject02, Subject03, etc. Use one command to send input to grep, and then use grep to search for a pattern. If you’re a bit confused, take a look at the hints and the example grep command below. You’ll have to modify it to get the result you want.


    • Commands separated with a pipe, the | character, send the output of the command to the left of the pipe as input to the command on the right of the pipe.

    • Think back on the exercise about wildcards. grep uses something called regular expressions that are similar to wildcards, but much more extensive. For grep regexps, * and [] work the same way as they do in wildcards. For a fuller treatment of regexps, click here. For a quick example see below. You can grep for a search term in a file with something like the following:

      #example grep command
      $ cat file.txt | grep SEARCHTERM
      # where searchterm can be something like
      $ cat file.txt | grep "[0-9][0-9].*"
      # this search term would find matches in strings that start with two numbers followed by anything
  2. If you completed Task 1, you were able to find the output you wanted, but there was much more output sent to the screen than you needed. Construct another pipeline to limit the output of grep to only the first line.


    Think of a command that prints the first n lines of a file. You can always google the task if you can’t think of the right tool for the job.


Solution to Task 1

$ cat gcutError_recon-all.log | grep "Subject[0-9][0-9]"
-subjid FreeSurfer -i /home/language/dansha/Studies/LaminarWord/SubjectData/Subject05/Scans/Anatomical/MP2RAGE/MP2RAGE.nii -all
setenv SUBJECTS_DIR /home/language/dansha/Studies/LaminarWord/SubjectData/Subject05
mri_convert /home/language/dansha/Studies/LaminarWord/SubjectData/Subject05/Scans/Anatomical/MP2RAGE/MP2RAGE.nii /home/language/dansha/Studies/LaminarWord/SubjectData/Subject05/FreeSurfer/mri/orig/001.mgz
mri_convert /home/language/dansha/Studies/LaminarWord/SubjectData/Subject05/Scans/Anatomical/MP2RAGE/MP2RAGE.nii /home/language/dansha/Studies/LaminarWord/SubjectData/Subject05/FreeSurfer/mri/orig/001.mgz
reading from /home/language/dansha/Studies/LaminarWord/SubjectData/Subject05/Scans/Anatomical/MP2RAGE/MP2RAGE.nii...
writing to /home/language/dansha/Studies/LaminarWord/SubjectData/Subject05/FreeSurfer/mri/orig/001.mgz...
cp /home/language/dansha/Studies/LaminarWord/SubjectData/Subject05/FreeSurfer/mri/orig/001.mgz /home/language/dansha/Studies/LaminarWord/SubjectData/Subject05/FreeSurfer/mri/rawavg.mgz


Note that you could also have run the command

$ grep "Subject[0-9][0-9]" gcutError_recon-all.log

to get the same results. The traditional unix command line tools typically provide many ways of doing the same thing. It’s up to the user to find the best way to accomplish each task. grep is an excellent tool. To learn more about what you can search, try man grep. You can also google for something like “cool stuff I can do with grep.”

Solution to Task 2

$ grep "Subject[0-9][0-9]" gcutError_recon-all.log | head -1

You could have also done

$ grep -m 1 "Subject[0-9][0-9]" gcutError_recon-all.log
$ cat gcutError_recon-all.log | grep "Subject[0-9][0-9]" | head -1
$ cat gcutError_recon-all.log | grep -m 1 "Subject[0-9][0-9]"

There are usually many ways to do the same thing. Look up the -m option in the grep man page if you’re curious!

Closing Remarks

These are just simple examples. You see the real power of the unix command line tools when you add a little, soon to come, scripting know-how. A simple example of a more powerful way to use grep is in a case where you have 543 subject logs (not impossible!), and you need to search through all of them for subjects who participated in a version of your experiment with a bad stimuli list. grep is an excellent tool for this!