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Commit a24de974 authored by Loic Marx's avatar Loic Marx
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modification of header

parent b3356677
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1 merge request!1bash script for SEEG electrodes reconstruction
......@@ -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
......
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