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R3
students
seeg
Commits
a24de974
Commit
a24de974
authored
5 years ago
by
Loic Marx
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modification of header
parent
b3356677
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1 merge request
!1
bash script for SEEG electrodes reconstruction
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seeg_reconstruction.sh
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seeg_reconstruction.sh
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seeg_reconstruction.sh
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a24de974
...
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@@ -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
g
et
the
electrode inside
(1)
# Replace value to
s
et
up brain area as background (= 0) and get
electrode
s
inside
brain
c3d DE_mask.nii.gz
-replace
1 0
-o
elec_inside.nii.gz
# Add extrem part of electrode
# Add extrem part of electrode
s
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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