AFNI Class Notes 8/16/2019 (update 10/20/2026):

Helpful AFNI links:

• AFNI lessons:
  • https://afni.nimh.nih.gov/pub/dist/edu/2016_0222_lister_hill/
• AFNI data example:
  • https://afni.nimh.nih.gov/pub/dist/edu/data/CD.expanded/AFNI_data6/

Today's Objectives:

We will do a quick introduction to linux and important commandline tools. This will include a discussion on dicoms, niftis, and field maps. We will also discuss multiband acquisition.

Tools discussed:

• Have linux, or virtual box (neurodebian or VM)
• Critical Linux commands:
  • ssh or mobaXterm: getting to a linux box 
  • ls, cd, pwd: moving on command line
  • tcsh, bash: shell options
  • screen, env, DISPLAY: working with system
  • grep, find, xargs, sed, awk: working with files
• Dicom-to-BRIK/NIFTI tools:
  • dicom_hdr: outputs dicom information to commandline
  • dcm2nii: part of MRIcro package that reads header details
  • dcm2niix: part of MRIcroGL package that fits BIDS 
  • to3d: afni, defaults to AFNI but can do NIFTI
  • Dimon: afni function that reads dicom header designed for real time
• Distortion correction:
  • field map correction: FUGUE but use Keck fieldmap.html
  • topup correction: topup  but use Keck run_topup can be done in afni using unWarpEPI.py
  • epi_reg: a combination fieldmap and registration 
  • First Step in processing:
    • uber_subject.py: gui for creation of afni_proc.py
  • @SSwarper or sswarper2: skull stripping and alignment [also addressed later]
• Quick Comment about Multiband [example GE] (pptx)