interpolate_WLS_with_first_echo

#!/bin/bash
wls_map=$1 ### R2s_rbc_0p3_run01_brain_masked.nii
firstecho_map=$2
bubble_mask_final=$3
out_map=$4
temp_folder=$5

fslmaths ${bubble_mask_final} -bin ${temp_folder}/killmebubble.nii
fslmaths ${temp_folder}/killmebubble.nii -mul -1 -add 1 -bin ${temp_folder}/killmebubbleinvert.nii

### WLS
fslmaths $wls_map -mul ${temp_folder}/killmebubbleinvert.nii ${temp_folder}/killmeWLS.nii

### first echo 
fslmaths $firstecho_map -mul ${temp_folder}/killmebubble.nii ${temp_folder}/killmefirstecho.nii

### add 

fslmaths ${temp_folder}/killmeWLS.nii -add ${temp_folder}/killmefirstecho.nii ${out_map}