signMaps

#!/usr/bin/env bash
exec > >(tee -a ~/signMap_output.log)
exec 2> >(tee -a ~/signMap_error.log >&2)

while getopts s:t:d:m: flag
do
    case "${flag}" in
        s) dirSubs=${OPTARG};;
        t) dirHCP=${OPTARG};;
        d) datasetName=${OPTARG};;
	?)
		echo "script usage: $(basename "$0") [-s path to subs] [-t path to HCP surfaces] [-d name of the dataset]" >&2
		exit 1
	esac
done

echo "Path subs directory: $dirSubs";
echo "Path to fs_LR-deformed_to-fsaverage surfaces: $dirHCP";
echo "Dataset name: $datasetName";


for hemisphere in 'lh' 'rh';
do 
    echo "Generating visual field sign maps from fsaverage predicted maps..."
    4_signmaps.py --path $dirSubs --hemisphere $hemisphere
    
    echo "Resampling fsaverage sign maps to native space..."
    cd $dirSubs
    for dirSub in `ls $dirSubs`; 
    do 
    if [ "$hemisphere" == 'lh' ]; then
        echo $dirSub
        wb_command -metric-resample $dirSub/deepRetinotopy/"$dirSub".fs_predicted_fieldSignMap_"$hemisphere"_average.func.gii \
        $dirHCP/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii \
        $dirSub/surf/"$hemisphere".sphere.reg.surf.gii ADAP_BARY_AREA $dirSub/deepRetinotopy/"$dirSub".predicted_fieldSignMap_average."$hemisphere".native.func.gii \
        -area-surfs $dirSub/surf/"$dirSub"."$hemisphere".midthickness.32k_fs_LR.surf.gii $dirSub/surf/"$hemisphere".midthickness.surf.gii
    else
        wb_command -metric-resample $dirSub/deepRetinotopy/"$dirSub".fs_predicted_fieldSignMap_"$hemisphere"_average.func.gii  \
        $dirHCP/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii \
        $dirSub/surf/"$hemisphere".sphere.reg.surf.gii ADAP_BARY_AREA $dirSub/deepRetinotopy/"$dirSub".predicted_fieldSignMap_average."$hemisphere".native.func.gii \
        -area-surfs $dirSub/surf/"$dirSub"."$hemisphere".midthickness.32k_fs_LR.surf.gii $dirSub/surf/"$hemisphere".midthickness.surf.gii
    fi
    done
done
echo "All done!"