This assumes you have a working AFNI package installed on your system.


1. Get sample data to play with.
    The class handouts apply to the following datasets.  Either get all
    current class data, or just a couple direcotry trees.

    These instructions apply to putting data under the home directory.

    1a. Start in the home directory (or where ever the data should go).

          cd

    1b. Get all AFNI class data.  (as opposed to 1c)
        If doing this, then skip the following 1c step.

          curl -O http://afni.nimh.nih.gov/pub/dist/edu/data/CD.tgz
          tar xfz CD.tgz

        The s2.cp.files script in the CD directory simply goes to the given
        destination directory (in this case '..', the parent of CD, i.e. the
        'data' directory from above) and extracts all of the packages
        (CD/*.tgz) into it.

          cd CD
          tcsh s2.cp.files . ..

        That's it.  Just get rid of the old CD directory and .tgz file.
        The '\' before 'rm' is so any alias is not applied.

          cd ..
          \rm -fr CD CD.tgz


    1c. Get only some AFNI class data.  (as oppsed to 1b)
        Only do this if step 1b was skipped.

          curl -O http://afni.nimh.nih.gov/pub/dist/edu/data/suma_demo.tgz
          curl -O http://afni.nimh.nih.gov/pub/dist/edu/data/AFNI_data6.tgz
          curl -O http://afni.nimh.nih.gov/pub/dist/edu/data/AFNI_data5.tgz

          tar xfz AFNI_data6.tgz
          tar xfz AFNI_data5.tgz
          tar xfz suma_demo.tgz

          rm -f AFNI_data?.tgz suma_demo.tgz


    It is good to review the handouts while looking that the relevant data.

2. Review key Handouts
    The class handouts apply to the above datasets.

    2a. top-level directories (data and handouts)



Main Tree
 pub/dist/edu/latest 
complete handouts tree
Data Tree
 pub/dist/edu/data 
top-level data tree
Class Directory
 afni_handouts 
current hanounts directory (pdf/txt only)
Web Descriptions
 class handouts 
web description page



    2a. data and select class handounts



Main Data Package
 pub/dist/edu/data/CD.tgz 
current class data package





Unix Overview
afni00_unix.pdf
Unix, the t-shell and use with FMRI processing


Interactive AFNI
afni03_interactive.pdf
guide to the afni GUI


Intro to FMRI
afni04_fmri.pdf
introduction to FMRI and linear regression


Start to Finish
afni16_start_to_finish.pdf
full analysis: single subject and group ANOVA


Group Analysis
GroupAna.pdf
overview of group analysis methods and programs