#!/bin/bash

if [ -f /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-M01/atlas/D99_in_M01_adj_inFunc.nii.gz ]; then
    DATE=$( date '+%F_%H%M' )
    cp /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-M01/atlas/D99_in_M01_adj_inFunc.nii.gz \
       /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-M01/atlas/D99_in_M01_adj_inFunc_${DATE}.nii.gz
fi

flirt -in /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-M01/atlas/D99_in_M01_adj.nii.gz \
    -ref /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-M01/func/sub-M01_ref_func_brain_res-1x1x1.nii.gz \
    -applyxfm -init /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-M01/warps/sub-M01_anat2func.mat \
    -out /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-M01/atlas/D99_in_M01_adj_inFunc.nii.gz -interp nearestneighbour

gunzip /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-M01/atlas/D99_in_M01_adj_inFunc.nii.gz