Common abbreviations in AFNI docs and Message Board discussions

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Just as a quick reference, you might see the following abbreviations used a lot in AFNI MB (= Message Board) discussions. Unless otherwise stated, the referenced programs are within the AFNI software distribution. This list will likely grow over time.

  • AP: afni_proc.py, the primary FMRI processing pipeline-generating tool in AFNI.
  • APQC: afni_proc.py's quality control (QC) HTML report.
  • SSW: originally, @SSwarper, the commonly used wrapper program for estimating both skullstripping (SS) of an anatomical dataset and its nonlinear alignment (warping) to a template. Now also referring to the updated program, sswarper2 that has very similar syntax and the same output structure, so they can be used interchangeably. Will also refer to any other updated programs in this family tree with similar names.
  • AW: @animal_warper, an analogous program to SSW, but specifically designed for working on nonhuman data (macaques, marmosets, rats, mice, canines, etc.).
  • NIFTI: (or technically NIfTI) the "Neuroimaging Informatics Technology Initiative" format for data, a standard format for volumetric neuroimaging datasets. Originally developed by Cox et al. (2004) to promote and simplify datasharing across software packages, its standard C libraries continue to be primarily maintained by AFNI developers (namely, Rick Reynolds). AFNI reads and outputs this format, in addition to BRIK/HEAD.
  • GIFTI: (or technically GIfTI) the Geometry format under the Neuroimaging Informatics Technology Initiative. Basically, the surface mesh analogue of NIFTI. The standard C libraries are also primarily maintained by AFNI developers (namely, Rick Reynolds). AFNI reads and outputs this format.
  • FS: the FreeSurfer software distribution (Fischl et al. 2002); this is used fairly often in conjunction with AFNI processing, particularly the recon-all program for estimating surface meshes and anatomical parcellations from a T1w anatomical. The AFNI program @SUMA_Make_Spec_FS is typically run after recon-all to bring the outputs into formats AFNI can process (NIFTI volumes, GIFTI surface meshes, *.niml.dset surface datasets), as well as standardizing the mesh.