Part 1: Getting Data

If you haven't already, follow the Installation Instructions to set up your account on Lonestar 6 and install necessary software. These instructions are written with Lonestar 6 in mind, but they should also work with Stampede and Frontera.

ssh into the login node on Lonestar 6 (replace $username with your TACC username):

ssh -Y $username@ls6.tacc.utexas.edu

For some steps, it may be helpful to use an idev session. idev is a program to claim a compute node for a fixed amount of time, and then ssh into that node. It allows you to test out code or run more computationally intensive programs like fslview. If you try to run something like fslview on a login node (accessed at ls6.tacc.utexas.edu), the process may be killed, and you might be temporarily banned from Lonestar. Be careful, and when in doubt, use an idev session or a remote desktop. If you just run idev with no arguments, you will be a job that will last up to 30 minutes, and that will run on one of the development nodes. You can use the -t option to request more time. For example, to get two hours: idev -t 02:00:00.

Copy the sample data from Corral to your WORK directory:

cp -r /corral-repl/utexas/prestonlab/preproc/part1 $WORK/preproc
cd $WORK/preproc

Take a look at the data using ls:

ls bender_03
ls bender_03/raw/bender_03
ls bender_03/raw/bender_03/2

Each subject was run over two days. For bender_03, the day one data are in the bender_03 directory, and day 2 is in the bender_03a directory. The raw data for each day are placed in a $subject/raw/$subject directory within the main study directory. The raw data for each subject are placed in multiple directories. Each directory corresponds to one scan, which includes many DICOM (.dcm) files. DICOM files have a lot of information, but the format isn't very standardized. Most neuroimaging software packages work with NIfTI files, so our first step is to convert the DICOM files to NIfTI format.

Setting up a Study

Many scripts in the pipeline use some environment variables so you don't have to keep specifying the same things over and over again. These variables are generally set up in your .bashrc script. The .bashrc script is a hidden script in your $HOME directory.

The most important environment variable is $STUDYDIR. This is a base directory with one directory for each subject:

$STUDYDIR/
  $subject1
  $subject2
  ...
  $subjectN

To define the study directory, run this:

export STUDYDIR=$WORK/preproc

As long as this is run before running a given script, it will work. If you put the above line in your $HOME/.bashrc file, it will run as soon as you log into Lonestar, so you won't have to think about it. You can edit your .bashrc file by navigating to your $HOME directory and then using a program like emacs; i.e. in the command line from your home directory you would write: emacs .bashrc