1#!/bin/tcsh -fe 2 3# written by Ben Jung (June 30, 2020) 4# additional contact people about NMT issues: 5# * Adam Messinger (re. template/data itself) 6# * Daniel Glen (of course) 7# * Paul Taylor 8 9set stat = 0 10set sdir = $PWD 11 12goto PARSE 13RET_PARSE: 14if ("$nmt_ver" =~ 2*) then 15 set template = NMT_v${nmt_ver}_${sym} 16else 17 set template = NMT_v${nmt_ver} 18endif 19 20if ( -d ${install_dir}/$template) then 21 if (${overwrite} == "0") then 22 echo "" 23 echo "ERROR:" 24 echo " Directory ${install_dir}/$template exists already" 25 echo " If you want to reinstall the NMT, add -overwrite" 26 echo " to your @Install_NMT command" 27 echo "" 28 goto END 29 else if (${overwrite} == "1") then 30 echo "WARNING: Removing currently installed ${install_dir}/$template" 31 \rm -r ${install_dir}/$template 32 endif 33endif 34 35if ($use_curl == -1) then 36 which curl 37 if ($status) then 38 set use_curl = 0; 39 else 40 set use_curl = 1; 41 endif 42endif 43 44cd ${install_dir} 45 46echo "Downloading https://afni.nimh.nih.gov/pub/dist/atlases/macaque/nmt/${template}.tgz" 47if ($use_curl == 0) then 48 wget https://afni.nimh.nih.gov/pub/dist/atlases/macaque/nmt/${template}.tgz 49else 50 curl -O https://afni.nimh.nih.gov/pub/dist/atlases/macaque/nmt/${template}.tgz 51endif 52 53\tar -xvzf $template.tgz 54\rm $template.tgz 55 56cd $template 57 58cat <<EOF 59 60******************************************************** 61Please read ${install_dir}/$template/README.txt for more information 62about this template 63******************************************************** 64 65EOF 66 67### PT: user has to set up the specific format of the dataset they 68### want to be in the env vars: *_05mm, *_fh, or 'default'. This 69### won't work anymore 70#if ($set_env == 1) then 71# set atlas_dir = ${install_dir} 72# @AfniEnv -set AFNI_SUPP_ATLAS_DIR $atlas_dir 73# @AfniEnv -set AFNI_WHEREAMI_DEC_PLACES 2 74# @AfniEnv -set AFNI_TEMPLATE_SPACE_LIST NMT,NMT2,D99_Macaque,D99_Macaque_book 75# @AfniEnv -set AFNI_WEBBY_WAMI YES 76#endif 77 78cd - 79 80 81goto END 82 83PARSE: 84 85#------------------------ process user options -------------------------- 86set use_curl = -1 87set nmt_ver = 2.1 88set sym = sym 89set install_dir = ${sdir} 90set overwrite = 0 91set ac = 1 92set set_env = 0 93while ($ac <= $#argv) 94 if ("$argv[$ac]" == "-help" || "$argv[$ac]" == "-h") then 95 goto HELP 96 97 else if ("$argv[$ac]" == "-curl") then 98 set use_curl = 1 99 100 else if ("$argv[$ac]" == "-wget") then 101 set use_curl = 0 102 103 else if ("$argv[$ac]" == "-install_dir") then 104 set this_opt = "$argv[$ac]" 105 @ ac ++ 106 if ( $ac > $#argv ) then 107 echo "** missing parameter for option '${this_opt}'" 108 exit 1 109 endif 110 set install_dir = $argv[$ac] 111 112 else if ("$argv[$ac]" == "-overwrite") then 113 set overwrite = "1" 114 115 else if ("$argv[$ac]" == "-nmt_ver") then 116 set this_opt = "$argv[$ac]" 117 @ ac ++ 118 if ( $ac > $#argv ) then 119 echo "** missing parameter for option '${this_opt}'" 120 exit 1 121 endif 122 set nmt_ver = $argv[$ac] 123 if (($nmt_ver != "1.2") && \ 124 ($nmt_ver != "1.3") && \ 125 ($nmt_ver != "2.0") && \ 126 ($nmt_ver != "2.1")) then 127 echo "nmt_ver $nmt_ver is not a valid choice" 128 exit 1 129 endif 130 131 else if ("$argv[$ac]" == "-sym") then 132 set this_opt = "$argv[$ac]" 133 @ ac ++ 134 if ( $ac > $#argv ) then 135 echo "** missing parameter for option '${this_opt}'" 136 exit 1 137 endif 138 set sym = $argv[$ac] 139 if ($sym == "symmetric") then 140 set sym = sym 141 else if ($sym == "asymmetric") then 142 set sym = asym 143 endif 144 145 else if ("$argv[$ac]" == "-set_env") then 146 #set set_env = "1" 147 echo "+* WARNING: '-set_env' is no longer a usable option" 148 echo " Instead, after the datadownload has completed," 149 echo " Run the setup*.tcsh script in your NMT data directory" 150 echo " of choice to setup the AFNI environment vars." 151 152 else 153 echo "Error: Option or parameter '$argv[$ac]' not understood" 154 goto END 155 endif 156 @ ac ++ 157end 158 159goto RET_PARSE 160 161HELP: 162cat << EOF 163 164 Overview ~1~ 165 166 Installs the NIMH Macaque Template (NMT) with the accompanying 167 Cortical Hierarchy Atlas of the Rhesus Macaque (CHARM). 168 169 Note there are multiple versions and variants of the template to 170 choose from (see the "-ver .." and "-sym .." options, below), with 171 the default being the ${sym}metric NMT v${nmt_ver}. 172 173 The NMT v2 and the CHARM are described in: 174 175 Jung B, Taylor PA, Seidlitz PA, Sponheim C, Perkins P, Glen DR, 176 Messinger A (2021). A Comprehensive Macaque FMRI Pipeline and 177 Hierarchical Atlas. NeuroImage 235:117997. 178 https://doi.org/10.1016/j.neuroimage.2021.117997. 179 180 while the previous template versions (the NMT v1.2 and NMT v1.3) are 181 described in: 182 183 Seidlitz J, Sponheim C, Glen DR, Ye FQ, Saleem KS, Leopold DA, 184 Ungerleider L, Messinger A (2018). A Population MRI Brain 185 Template and Analysis Tools for the Macaque. NeuroImage 170: 186 121–31. doi: 10.1016/j.neuroimage.2017.04.063. 187 188 ** Please cite Jung et al. (2021) and/or Seidlitz et al. (2018) if 189 you make use of the respective templates in your work. ** 190 191 After the archive is downloaded and unpacked (as the directory 192 "NMT_*", depending on your selected version+variant), see its 193 README.txt for details. 194 195 -------------------------------------------------------------------------- 196 197 Options ~1~ 198 199 -install_dir DD :the install location for the NMT 200 (default = the PWD) 201 202 -nmt_ver VV :the version of the NMT you wish to install 203 (default = ${nmt_ver}; valid = 2.1, 2.0, 1.3, 1.2) 204 205 -sym SS :the NMT v2 has both a symmetric and asymmetric variant. 206 Specify the desired variant SS as either "sym" or 207 "asym". Option is valid for the NMT v2 only--in 208 other cases it is ignored. (default = "${sym}") 209 210 -overwrite :allows the script to remove a pre-existing NMT directory 211 212 -wget :use wget to download archive. Script chooses by default 213 with preference for curl 214 215 -curl :use curl to download archive. Script chooses by default 216 with preference for curl 217 218 -help :repeats this message 219 220 -------------------------------------------------------------------------- 221 222 Questions/contact ~1~ 223 224 If you have any NMT or CHARM questions, please contact: 225 226 Adam Messinger : messinga @ nih.gov 227 Ben Jung : benjamin.jung @ nih.gov 228 229 For demo or processing (@animal_warper, afni_proc.py, etc.) questions, 230 please contact: 231 232 Daniel Glen : glend @ mail.nih.gov 233 Paul Taylor : paul.taylor @ nih.gov 234 235 or ask on the AFNI Message Board. 236 237EOF 238 239 goto END 240 241BEND: 242 echo "Failed" 243 set stat = 1 244 goto END 245 246END: 247 exit $stat 248