7 Comments

1. 

   Markus

    /  March 13, 2014

   Hi!

   I very much like your blog!

   I just tried your line with GNU parallel, however, I have a problem with the $SUBJECTS_DIR, apparently it is not adapted every time.

   I have a folder for each subject (s01 s02 etc) in which the T1 is contained.

   The $SUBJECTS_DIR should actually follow the recon-all, shouldn’t it?

   Thanks!
   Markus

2. 

   pete

    /  March 25, 2014

   I usually specify the SUBJECTS_DIR each time I open a terminal window. An easy way to do this is to change into the SUBJECTS_DIR and then type:

   export SUBJECTS_DIR=`pwd`

   This will automatically plug the current working directory into the export command. Then any command you run should work within that single window. My general workflow is to set the SUBJECTS_DIR and then cd into another directory that has all of the raw NIFTI files. Then I run the recon-all via:

   ls -d *.nii | parallel recon-all -s {.} -i {} -all -3T -qcache

   The {.} will remove the single extension .nii. If you have .nii.gz files you could pipe it through sed:

   ls -d *.nii.gz | sed ‘s/.nii.gz//’ | parallel recon-all -s {} -i {}.nii.gz -all -3T -qcache

3. 

   Markus

    /  March 25, 2014

   Thanks Pete!

   Actually, I realized that the above mentioned problem was more a problem of how to start recon all. I notice then that having a folder with all {subject}_T1s in it is the best thing to start, and that recon all would create the {subject} folders itself. So the SUBJECTS_DIR is organized by recon all itself too.

   Another question concerning parallel:
   I love the possibility to ls the subjects and pipe them to sed and then to recon all.
   However, is it also possible to run two commands within parallel ?In the sense of a subjects loop:
   for subjects in subjectlist ; do
   command 1 on subject
   command 2 on subject
   done

   I imagine something like:

   ls -d ??? | sed what_ever | parallel command 1 ; command 2

   but I am not sure and I do not want o mess up with my data!

   What do you think?

4. 

   pete

    /  March 25, 2014

   The easiest thing to do is to put your commands into a text file (in this example commands.txt). The basic rule is that commands on the same line will be performed sequentially and commands on different lines will be performed in parallel.

   So something like this:
   echo 1; echo 2;
   echo 3; echo 4;
   echo 5; echo 6;

   might produce:
   3
   4
   1
   2
   5
   6

   To execute this, you can do: parallel < commands.txt

   • 

     Markus

      /  April 11, 2014

     Thank you Pete,

     Do you know how I would call the {} inside de command.txt?

     pure
     cd {}
     it does not work

     Example:
     cat subjectlist.txt | parralel –jobs 5 < command.txt
     (with inside command:
     cd {}
     ls -l
     )

     Thanks!
     Markus

     • 

       pete

        /  April 21, 2014

       I think you’d need to put the subject list into the command file.

5. 

   Markus

    /  April 22, 2014

   Thanks Pete,

   Just to complete here:

   I actually managed to do it using the specification “–workdir” of GNU parallels:

   cat ../Scripts/do_graphcut.txt | parallel –jobs 4 –workdir $SUBJECTS_DIR/{} mri_gcut -T 0.65 $SUBJECTS_DIR/{}/mri/T1.mgz $SUBJECTS_DIR/{}/mri/brainmask.gcuts.T-0.65.mgz

   Best,
   Markus