Assignment 4 (due Wednesday, Feb. 8)

• The purpose of this assignment is to run the basic image volume integrity checks that I've been talking about. There is now a clean version of the check_fmridc_data.m script that you can use as a template to see how this is done and how you can generate figures with the images that you need to inspect. I encourage you to look at this script and ask me about stuff you don't understand. You can look in
  ~petr/data/2-2002-112K5/figures
  for .ps and .pdf files that show what the output should look like.
• The create 4D Nifti part of the code is now working and should generate Nifti (.nii) files by default for all of you. The 4D Nifti files load somewhat more quickly than the directory full of .img files, but they do take some time to create.
• Fslview should be working and is useful for viewing 4D volumes in movie mode. Aberrant volumes pop right out. Fslview can be used to inspect timepoints that the CALC_MEAN_INTENSITY and PLOT_DATA parts of the code identify as bad.
• The assignment is to run this integrity check on all of your functional data and identify volumes that are bad.
  • Create a text (.txt) file that notes the artifacts you have found. Put this text file and your scripts in a directory called assign4.
  • Be prepared to quickly point me to the files, both the PDF and EPI files, which illustrate the artifact, as we will look at some of these during the beginning of class next week.
• A prize will be awarded for the strangest artifact! We already have a couple of doozies.

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