Threshold distance map by spheres

#Threshold distance map by spheres

module load Anaconda3/2024.02-1
module load fsl/6.0.6

eval "$(conda shell.bash hook)"
conda activate BENCH

#Script to create a distance map of the distance from a WMH for each participant

sub_list="/well/miller/users/uai965/UKBB/Subjects_100/sub_list_100"
core_path="/well/miller/users/uai965/UKBB/Subjects_100"

while read -r ID; do 
    dist_lesion_mask="${core_path}/${ID}/T2_FLAIR/lesions/output/distance_map_lesion_mask_resampled.nii.gz"
    output_dir="${core_path}/${ID}/T2_FLAIR/lesions/output"

    fslmaths "${dist_lesion_mask}" -mas "${output_dir}/lesion_mask_resampled__sphere_2_NL.nii.gz" "${output_dir}/lesion_mask_resampled__sphere_2_NL_distance_mask.nii.gz"
    fslmaths "${dist_lesion_mask}" -mas "${output_dir}/lesion_mask_resampled__sphere_5_NL.nii.gz" "${output_dir}/lesion_mask_resampled__sphere_5_NL_distance_mask.nii.gz"
    fslmaths "${dist_lesion_mask}" -mas "${output_dir}/lesion_mask_resampled__sphere_8_NL.nii.gz" "${output_dir}/lesion_mask_resampled__sphere_8_NL_distance_mask.nii.gz"
    fslmaths "${dist_lesion_mask}" -mas "${output_dir}/lesion_mask_resampled__sphere_10_NL.nii.gz" "${output_dir}/lesion_mask_resampled__sphere_10_NL_distance_mask.nii.gz"
    
    echo "A distance map has been thresholded for the spheres of $ID"
done < "$sub_list"

echo "A distance map has been thresholded for the spheres for all participants"