NHP-pRF/FitResults/Reference/Volumes/atlas/M01/atlas2funcspace.sh

#!/bin/bash

if [ -f /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-danny/atlas/D99_in_Danny_adj_inFunc.nii.gz ]; then
    DATE=$( date '+%F_%H%M' )
    cp /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-danny/atlas/D99_in_Danny_adj_inFunc.nii.gz \
       /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-danny/atlas/D99_in_Danny_adj_inFunc_${DATE}.nii.gz
fi

flirt -in /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-danny/atlas/D99_in_Danny_adj.nii.gz \
    -ref /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-danny/func/sub-danny_ref_func_brain_res-1x1x1.nii.gz \
    -applyxfm -init /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-danny/warps/sub-danny_anat2func.mat \
    -out /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-danny/atlas/D99_in_Danny_adj_inFunc.nii.gz -interp nearestneighbour

gunzip /Users/chris/Dropbox/GIT_Support/NHP-BIDS/manual-masks/sub-danny/atlas/D99_in_Danny_adj_inFunc.nii.gz