modification of header

seeg_reconstruction.sh

@@ -16,7 +16,7 @@ c3d ct_post.nii.gz -threshold 4000 7000 2 -1 -o seeg_extremity.nii.gz
 c3d seeg_body.nii.gz seeg_extremity.nii.gz -add -o seeg_electrode.nii.gz
 
 
-# Delete the brain skull to get only the electrode (first part)
+# Delete the brain skull to get only the electrode (method 1)
 # Do the brain mask in binary image 
 c3d brain_mask.nii.gz -replace 1 1 -o brain_mask_seeg.nii.gz
 # Setup value in the brain mask 
@@ -25,17 +25,17 @@ c3d DE_seeg.nii.gz -replace -2 0 DE_2_seeg.nii.gz # get 0 and 1: bone
 
 # Add brainMask to get the electrodes inside the brain 
 c3d DE_2_seeg.nii.gz brain_mask_seeg.nii.gz -add -o DE_mask.nii.gz
-# Replace value to get the electrode inside (1) 
+# Replace value to setup brain area as background (= 0) and get electrodes inside brain
 c3d DE_mask.nii.gz -replace 1 0 -o elec_inside.nii.gz
 
-# Add extrem part of electrode 
+# Add extrem part of electrodes 
  c3d elec_inside.nii.gz seeg_extremity.nii.gz -add -o electrode_without_skullbone.nii.gz
 
-# Make image binary for a better representation 
+# Re-thresholding image to correctly define background and electrodes 
 c3d electrode_without_skullbone.nii.gz -threshold 0 6 1 0 -o final_seeg.nii.gz
 
 
-# Additional method to smoother the skull bone (part 2)
+# Additional method to get rid of the skull bone (Method 2)
 # Define the skull bone based on CT scan  
 c3d ct_post.nii.gz -threshold 900 1400 0 1 -o skull_seeg.nii.gz 
 
@@ -45,7 +45,7 @@ c3d skull_seeg.nii.gz DE_2_seeg.nii.gz -add -o skull_DE.nii.gz
 # Setup overlapping image as background 
 c3d skull_DE.nii.gz -replace 1 0 -o skull_DE.nii.gz
 
-# Combine with the previous SEEg segmentation obtained in part 1
+# Combine with the previous SEEg segmentation obtained with Method 1 
 c3d skull_DE.nii.gz final_seeg.nii.gz -add -o combine_tworepresentation.nii.gz
 
 # Setup overlapping image as a background to get better rid of remaining skull brain