#!/bin/tcsh

# This script should be sourced, to affect the current environment.
# It is meant to initialize main variables needed by most other scripts.

# study_root_in should basically be a BIDS data source directory
# (subject directoris would be underneath)
# set global_root  = /data/NIMH_SSCC/rickr/UCLA.pamenc.50
# set study_root_in  = /data/NIMH_SSCC/gaia/UCLA_phenomics/data_clean
set study_root_in = /data/NIMH_SSCC/rickr/UCLA.pamenc/pamenc.class.60.links
if ( ! -d $study_root_in ) then
   echo '** missing $study_root_in : ' $study_root_in 
   echo ""
   echo "   please edit $0"
   echo ""
   exit 1
endif

# study_root_out could be the same as study_root_in; it is where
# a derivatives directory should be
# (do we keep it here for now?)
set study_root_out = /data/NIMH_SSCC/rickr/UCLA.pamenc/AFNI
set deriv_dir = $study_root_out/derivatives
if ( ! -d $deriv_dir ) then
   echo '++ making $deriv_dir' $deriv_dir
   mkdir -p $deriv_dir
   if ( $status ) then
      echo "** failed to create deriv_dir: $deriv_dir, failing..."
      exit 1
   endif
endif

# set subject_list
cd $study_root_in
set all_subjects = ( sub-* )
set nsubj = $#all_subjects
cd -