:orphan: .. _ahelp_@Install_NMT: ************ @Install_NMT ************ .. contents:: :local: | Overview ======== .. code-block:: none 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 ======= .. code-block:: none -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 ================= .. code-block:: none 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.