From f4be657031a5ffb1fb9b43202a72d4b7f1aebe92 Mon Sep 17 00:00:00 2001
From: PEI-MAO <86906938+Pei-mao@users.noreply.github.com>
Date: Thu, 30 May 2024 17:15:57 +0800
Subject: [PATCH] Change MNI152 position, update reg_v002 evaluation (#73)

* Update README.md

* Update README.md

* Add affine and registration

* Update setup.py

* Update setup.py

* Modify MNI152

* add Evaluate_registration

* Update validation.md

* Modify the validate call

* Change MNI152 position, updata reg_v002 evaluation
---
 doc/validation.md                             |  52 +++++++++---------
 tigerbx/lib_tool.py                           |   4 +-
 .../{ => template}/MNI152_cropped_norm.nii.gz | Bin
 .../MNI152_cropped_norm_aseg.nii.gz           | Bin
 4 files changed, 28 insertions(+), 28 deletions(-)
 rename tigerbx/{ => template}/MNI152_cropped_norm.nii.gz (100%)
 rename tigerbx/{ => template}/MNI152_cropped_norm_aseg.nii.gz (100%)

diff --git a/doc/validation.md b/doc/validation.md
index d7c7232..8d48a07 100644
--- a/doc/validation.md
+++ b/doc/validation.md
@@ -49,32 +49,32 @@
 
     | Structure                | Dice    |
     |--------------------------|---------|
-    | Left-Cerebral WM         | 0.857104|
-    | Right-Cerebral WM        | 0.858439|
-    | Left-Cerebral Cortex     | 0.728526|
-    | Right-Cerebral Cortex    | 0.736365|
-    | Left-Lateral Ventricle   | 0.803578|
-    | Right-Lateral Ventricle  | 0.793350|
-    | Left-Cerebellum WM       | 0.807485|
-    | Right-Cerebellum WM      | 0.809267|
-    | Left-Cerebellum Cortex   | 0.869220|
-    | Right-Cerebellum Cortex  | 0.879554|
-    | Left-Thalamus            | 0.851638|
-    | Right-Thalamus           | 0.887088|
-    | Left-Caudate             | 0.813050|
-    | Right-Caudate            | 0.830947|
-    | Left-Putamen             | 0.849082|
-    | Right-Putamen            | 0.853028|
-    | Left-Pallidum            | 0.786699|
-    | Right-Pallidum           | 0.775344|
-    | Left-Hippocampus         | 0.804197|
-    | Right-Hippocampus        | 0.822381|
-    | Left-Amygdala            | 0.773281|
-    | Right-Amygdala           | 0.792968|
-    | Left-VentralDC           | 0.805002|
-    | Right-VentralDC          | 0.815977|
-    | Brain Stem               | 0.886675|
-    | CSF                      | 0.666240|
+    | Left-Cerebral WM         | 0.824035|
+    | Right-Cerebral WM        | 0.828217|
+    | Left-Cerebral Cortex     | 0.707702|
+    | Right-Cerebral Cortex    | 0.717348|
+    | Left-Lateral Ventricle   | 0.786622|
+    | Right-Lateral Ventricle  | 0.769482|
+    | Left-Cerebellum WM       | 0.812269|
+    | Right-Cerebellum WM      | 0.813486|
+    | Left-Cerebellum Cortex   | 0.880312|
+    | Right-Cerebellum Cortex  | 0.885760|
+    | Left-Thalamus            | 0.877530|
+    | Right-Thalamus           | 0.894954|
+    | Left-Caudate             | 0.829615|
+    | Right-Caudate            | 0.819476|
+    | Left-Putamen             | 0.864166|
+    | Right-Putamen            | 0.865252|
+    | Left-Pallidum            | 0.828596|
+    | Right-Pallidum           | 0.806082|
+    | Left-Hippocampus         | 0.827217|
+    | Right-Hippocampus        | 0.833771|
+    | Left-Amygdala            | 0.799048|
+    | Right-Amygdala           | 0.810998|
+    | Left-VentralDC           | 0.834296|
+    | Right-VentralDC          | 0.844643|
+    | Brain Stem               | 0.894280|
+    | CSF                      | 0.700577|
 #### Skull Stripping
     bet_NFBS: 0.969
     bet_synstrip: 0.971
diff --git a/tigerbx/lib_tool.py b/tigerbx/lib_tool.py
index e884cb7..caedc55 100644
--- a/tigerbx/lib_tool.py
+++ b/tigerbx/lib_tool.py
@@ -44,11 +44,11 @@ def download(url, file_name):
 
 def get_mni152():
 
-    return join(application_path, 'MNI152_cropped_norm.nii.gz')
+    return join(application_path, 'template', 'MNI152_cropped_norm.nii.gz')
 
 def get_mni152_seg():
 
-    return join(application_path, 'MNI152_cropped_norm_aseg.nii.gz')
+    return join(application_path, 'template', 'MNI152_cropped_norm_aseg.nii.gz')
 
 def get_model(f):
     from os.path import join, isfile
diff --git a/tigerbx/MNI152_cropped_norm.nii.gz b/tigerbx/template/MNI152_cropped_norm.nii.gz
similarity index 100%
rename from tigerbx/MNI152_cropped_norm.nii.gz
rename to tigerbx/template/MNI152_cropped_norm.nii.gz
diff --git a/tigerbx/MNI152_cropped_norm_aseg.nii.gz b/tigerbx/template/MNI152_cropped_norm_aseg.nii.gz
similarity index 100%
rename from tigerbx/MNI152_cropped_norm_aseg.nii.gz
rename to tigerbx/template/MNI152_cropped_norm_aseg.nii.gz