@Install_NMT


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.

The NMT v2 and the CHARM are described in:

   Jung B, Taylor PA, Seidlitz PA, Sponheim C, Glen DR, Messinger A
   (2020).  "A Comprehensive Macaque FMRI Pipeline and Hierarchical
   Atlas."  NeuroImage, submitted.

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.  https://doi.org/10.1016/j.neuroimage.2017.04.063.

** Please cite Jung et al. (2020) 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.

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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 = 2.0; valid = 1.2, 1.3, 2.0)

-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")

-set_env         :allows the script to modify the ~/.afnirc file to increase
                  NMT compatibility with AFNI (recommended if you do only
                  macaque work, but not default; please inquire on the
                  AFNI Message Board if you have any questions about this)

-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

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Please contact Dr. Adam Messinger (messinga@nih.gov) or Ben Jung
(benjamin.jung@nih.gov) with any questions or concerns regarding the
NMT.