@Install_NMT

Overview

Installs the NIMH Macaque Template (NMT) with the accompanying
Cortical Hierarchy Atlas of the Rhesus Macaque (CHARM).

Note there are multiple versions and variants of the template to
choose from (see the "-ver .." and "-sym .." options, below), with
the default being the symmetric NMT v2.1.

The NMT v2 and the CHARM are described in:

   Jung B, Taylor PA, Seidlitz PA, Sponheim C, Perkins P, Glen DR,
   Messinger A (2021). A Comprehensive Macaque FMRI Pipeline and
   Hierarchical Atlas. NeuroImage 235:117997.
   https://doi.org/10.1016/j.neuroimage.2021.117997.

while the previous template versions (the NMT v1.2 and NMT v1.3) are
described in:

   Seidlitz J, Sponheim C, Glen DR, Ye FQ, Saleem KS, Leopold DA,
   Ungerleider L, Messinger A (2018). A Population MRI Brain
   Template and Analysis Tools for the Macaque. NeuroImage 170:
   121–31. doi: 10.1016/j.neuroimage.2017.04.063.

** Please cite Jung et al. (2021) and/or Seidlitz et al. (2018) if
you make use of the respective templates in your work. **

After the archive is downloaded and unpacked (as the directory
"NMT_*", depending on your selected version+variant), see its
README.txt for details.

Options

-install_dir DD  :the install location for the NMT
                  (default = the PWD)

-nmt_ver VV      :the version of the NMT you wish to install
                  (default = 2.1; valid = 2.1, 2.0, 1.3, 1.2)

-sym SS          :the NMT v2 has both a symmetric and asymmetric variant.
                  Specify the desired variant SS as either "sym" or
                  "asym".  Option is valid for the NMT v2 only--in
                  other cases it is ignored. (default = "sym")

-overwrite       :allows the script to remove a pre-existing NMT directory

-wget            :use wget to download archive. Script chooses by default
                  with preference for curl

-curl            :use curl to download archive. Script chooses by default
                  with preference for curl

-help            :repeats this message

Questions/contact

If you have any NMT or CHARM questions, please contact:

  Adam Messinger : messinga @ nih.gov
  Ben Jung       : benjamin.jung @ nih.gov

For demo or processing (@animal_warper, afni_proc.py, etc.) questions,
please contact:

  Daniel Glen    : glend @ mail.nih.gov
  Paul Taylor    : paul.taylor @ nih.gov

or ask on the AFNI Message Board.