apply coverage mask to softseg to make sure coverage is the same as seg

sct-pipeline · Jul 7, 2021 · 88fbfc3 · 88fbfc3
1 parent a90fbeb
commit 88fbfc3
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/process_data.sh b/process_data.sh
@@ -185,6 +185,8 @@ for file_path in "${inc_contrasts[@]}";do
 
   # Bring softseg to native space
   sct_apply_transfo -i ${file_softseg}.nii.gz -d ${file_path}.nii.gz -w ${warping_field_inv}.nii.gz -x linear -o ${file_path}_softseg.nii.gz
+  # Apply coverage mask to softseg
+  sct_maths -i ${file_path}_softseg.nii.gz -o ${file_path}_softseg.nii.gz -mul ${file_path}_ones.nii.gz
   # Generate QC report
   sct_qc -i ${file_path}.nii.gz -s ${file_path}_softseg.nii.gz -p sct_deepseg_sc -qc ${PATH_QC} -qc-subject ${SUBJECT}
 done