Dear Colleagues,

Hi. I was born in 1976. My mother and father were both hairdressers in New York City; that's how they met. ... Sorry, let me skip ahead. In the last year or so, I have been refreshing, updating, and solidifying my AFNI skills a little by rereading some AFNI Bootcamp materials and rerunning the associated hands-on exercises. In doing so, I put together a syllabus of sorts. See below.

Please give me some feedback on it or let me know if I missed something similar in the AFNI documentation because I plan to require my trainees to complete everything on it, especially the hands-on material (with my help and yours of course), and would like to optimize it before subjecting them to it. Also, what would be a reasonable amount of time for someone to complete it? Someone who has lots of other responsibilities. Someone who is very smart and maybe has a little computer-programming experience but has never heard the words Unix or Linux before. Maybe three months?

Sincerely,

Dante

INTRODUCTION:
Reading:
afni00_unix.pdf
afni01_intro.pdf
afni02_to3d.pdf
afni03_interactive.pdf

FUNCTIONAL PREPROCESSING:
Reading:
afni16_start_to_finish.pdf (pp. 1-10)
afni_proc.pdf (pp. 1-25)
Output of afni_proc.py -help (program introduction, PROCESSING BLOCKS, DEFAULTS, and the rest as needed)
Video(s):
[AFNI Academy] AFNI Time Series Analysis (part 8/8): Pre-Processing
[AFNI Academy] Start to Finish Hands-On [1-12, 16]

ANATOMICAL PREPROCESSING:
Reading:
afni14_alignment.pdf
Video(s):
[AFNI Academy] Alignment [1-4]

NONLINEAR/PATCH-REFINEMENT/LOCAL-REFINEMENT ALIGNMENT:
afni_proc.pdf (pp. 26-37)

OVERVIEW OF FMRI DESIGNS AND ANALYSES:
Reading:
afni04_fmri.pdf
Video(s):
[AFNI Academy] AFNI Time Series Analysis (part 2/8): FMRI Data

BLOCK DESIGN AND ANALYSIS:
Reading:
afni05_regression.pdf
Video(s):
[AFNI Academy] AFNI Time Series Analysis (part 3/8): FMRI Fixed-Shape Models
[AFNI Academy] Start to Finish Hands-On [13-15]

EVENT-RELATED (ER) DESIGN AND ANALYSIS USING BASIS FUNCTIONS/TENT FUNCTIONS/PIECEWISE LINEAR SPLINES/LINEAR INTERPOLATION/VARIABLE-SHAPE HEMODYNAMIC RESPONSE FUNCTIONS:
Reading:
afni_TimeSeriesAnalysis.pdf (pp. 53-72)
afni06_decon.pdf (pp. 1-25)
Video(s):
[AFNI Academy] AFNI Time Series Analysis (part 4/8): FMRI Variable-Shape Models
Notes:
Note well that the data discussed in afni06_decon.pdf is not available in
[afni.nimh.nih.gov]
and you must get it from
[afni.nimh.nih.gov]

GROUP ANALYSIS:
Reading:
afni16_start_to_finish.pdf (pp. 11-12)
Video(s):
[AFNI Academy] AFNI Population-level modeling: Overview, perspectives and concepts
[AFNI Academy] Start to Finish Hands-On (17/17): t-test

MULTIPLE TESTING CORRECTION:
Reading:
afni07_ETAC.pdf
Output of afni_proc.py -help (-regress_est_blur_epits, -regress_est_blur_errts, -regress_run_clustsim, -regress_CS_NN, and -regress_opts_CS)
[afni.nimh.nih.gov] (Steps 4 and 5)
Video(s):
[fmrif.nimh.nih.gov]
[AFNI Academy] Start to Finish Hands-On (11/17): blur and mask blocks
Notes:
Solution 1 on p. 16 of afni07_ETAC.pdf is a good approach to start with.

PREPARING YOUR TABLE OF CLUSTERS (GENERALLY, THIS IS THE LAST STEP BEFORE SUBMITTING THE PUBLICATION, AND YOU SHOULD TYPICALLY USE A MASK WHEN VIEWING YOUR RESULTS INITIALLY.):
Reading:
[afni.nimh.nih.gov]
Video(s):
[AFNI Academy] AFNI GUI: Clusterizing