Assignment 3 (due Wednesday, Feb. 1)

• Complete your scripts for checking the existence of data in all of your studies
  • Check existence of functional data
  • Check existence of anatomical data
  • The existence data should be stored in variables that you can save in a Matlab .mat file so that you can later load that file and use the information without having to re-run the existence check. You can have a single .mat file for each study or a single file that has information for all of the studies. Your save command might look something like this:

save(mat_fname, 'exist_epi','exist_hires','exist_coplanar')

where mat_fname is the name of the .mat file that you want to store the information list, and the remaining arguments are a "comma-separated list" of the variables that you want to save. By default, save will save your entire workspace (which can be unnecessarily large if you've loaded EPI images for example).

• Turn in the assignment as follows
• Create a directory called assign3 in your matlab directory, e.g. /qfs3/home/ucd_g1/matlab/assign3
• Deposit a copy of your scripts that are used to run the existence check in that directory. You will continue development of the scripts in your matlab directory, so the scripts you copy to the assign3 directory are simply snapshots of your scripts at the time that this particular assignment was due.

Hints

The challenge in this assignment is handling the variability across studies in the naming at different levels of the data hierarchy. For example, run names appear to differ frequently, and some studies have one experiment whereas others have two.

If one of your studies has more than one experiment, then you need to add a for-loop to loop over each experiment. When placing the for and end statements, remember that subjects, sessions, and runs are nested within experiment.

Run naming schemes appear to differ by experiment. This means that you need to set run_stub conditionally, depending on the experiment. There are two types of conditional statements in Matlab that are commonly used for this purpose. One is if-then-else and the other is switch. They accomplish the same thing. Switch statements are useful if you are doing conditional branching based on the value of a string, for example your study's accession number, e.g. 2-2003-113K5.

Much of the information about run variability can be contained in structure arrays, where each element in the array pertains to a study, experiment, or subject.

If you get stuck, feel free to look at other groups' code for ideas about how to structure your code. You should all have read-permissions on each other's files. Also, if you find yourself beating your head against a coding problem and are not making headway, ask me for help.

Petr's Programming Tips