14.1. Overview

14.1.1. Introduction

Publications in the Codex are listed in (approximate) reverse chronological order.

Some programs from other software are listed here, because they were included in the processing. In such cases, the other software package is noted, for example with FreeSurfer: recon-all (FS).

Many thanks to the authors who have made their coding/scripting work available for general benefit.

14.1.2. Program names and keywords for searching

Below are lists of main programs used in Codex scripts (some of the smaller/incidental programs are not used here) and also study keywords. Searching with these might/should make it easier to find examples of interest. These lists will likely grow over time.

Main Program List

  • 3dANOVA2

  • 3dclust

  • 3dClusterize

  • 3dClustSim

  • 3dmask_tool

  • 3dMEMA

  • 3dttest++

  • afni_proc.py

  • BayesianGroupAna.py

  • gen_group_command.py

  • MBA

  • recon-all (FS)

  • @SSwarper

  • @SUMA_Make_Spec_FS

Study keywords by category

FMRI paradigm

task-block, task-event, resting, naturalistic

FMRI dset

EPI, dual phase (AP-PA)

Anatomical dset

MPRAGE, T1w, T2w, T1ma

Subject population

human, nonhuman primate, macaque, rat, simulation

Subject characteristic

patient, control

Subject age group

prenatal, newborn, infant, child, juvenile, adult, senior

Template space

MNI, Talairach, Haskins-ped, native,

Template align method

linear, nonlinear

Geometry of final analysis

volumetric (default), surface

Tissue segmentation method

3dSeg, FreeSurfer

Tissue regression

ANATICOR, fANATICOR, PCA, WM+Vent