History of AFNI updates
Suggested reading for beginners
Add yourself to the AFNI map!
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Author: rick reynolds (---.nimh.nih.gov)
Date: 01-05-07 09:35
Hello,
We have released a new program (afni_proc.py), which can be used to
create a T-shell script for single subject analysis. It is part of
our Python library (contained in files ending in .py).
Aside from naming decisions, there are often not many choices that
are made when writing a processing script for single subject analysis.
Besides the input datasets and stimulus timing files, some choices
include:
- how many pre-steady-state TRs to remove from the start of each run
- if and how to do temporal alignment (with 3dTshift)
- register EPI volumes to volume close to when the anat was acquired
- what blur to apply (if any)
- what masking to apply (if any)
- whether to scale voxel means to 100
- what options to apply to 3dDeconvolve (many are known at this point)
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The afni_proc.py program takes those choices (and others) as inputs
(via either command line parameters, or from an -ask_me session), and
creates a tcsh script to perform all pre-processing steps, along with
3dDeconvolve.
The most simple example would be to specify just datasets and stim
files (applying defaults for the options):
afni_proc.py -dsets epiRT*.HEAD -regress_stim_files stims.1D
This alone would create a full processing script through 3dDeconvolve.
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For an introduction to the program, please see "afni_proc.py -help"
(probably piping the help text through "less", as in the command
"afni_proc.py -help | less"). Reading the introduction through the
first few examples should give the user a good feel for what the
program will do.
Note that most examples in the '-help' can be applied to the data
under AFNI_data2, one of our current sample data trees for classes,
available via wget (or with a browser):
wget http://afni.nimh.nih.gov/pub/dist/edu/data/AFNI_data2.tgz
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The current output of "afni_proc.py -ver" is version 1.7.
Comments and questions are very welcome.
- rick
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NEW: automatic script creation for single subject analysis |
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rick reynolds |
01-05-07 09:35 |
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haibo |
01-07-07 19:54 |
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rick reynolds |
01-07-07 21:10 |
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haibo |
01-09-07 01:45 |
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rick reynolds |
01-09-07 08:41 |
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haibo |
01-09-07 21:03 |
