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SCT commit: 9a514410590bfcc06cd659b9107f331cd0853c28 SCT commit message: DOC: sct_download_data: updated URL to point toward beta28 Former-commit-id: 73b9ec6c19e0b3a88181e89913e6b7f244d63fb6 [formerly 2f8b827b429850225018e6f5fb67b7fbf03ed8d2] Former-commit-id: 9b832cadbc8bae6701c61fe71eb30b100331df3a Former-commit-id: cfe068e93d316cf9dc67019e9d87acc631e7e082
spinalcordtoolbox · Nov 21, 2016 · 7537a70 · 7537a70
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,24 +1,7 @@
 #PAM50 Template
 
-##2016-09-02 (JCA)
-- Created new WM atlas using commit: 8a91d5fbdba6cf222de3880d9777cef46d736256
-
-##2016-08-30 (JCA)
-- added "8, spine, PAM50_spine.nii.gz" in template/info_label.txt
-
-##2016-08-26 (JCA)
-- modified "PAM50_label_disc.nii.gz"
-- updated PAM50_levels accordingly
-~~~
-sct_process_segmentation -i PAM50_cord.nii.gz -p label-vert -discfile PAM50_label_disc.nii.gz
-~~~
-
-##2016-08-25 (JCA)
-- extended cord segmentation towards caudal end using ITKsnap: only one half, then used a function to copy the other half (see below)
-- extended cord segmentation towards rostral end using:
-~~~
-python $SCT_DIR/dev/atlas/create_atlas/register_AMU_to_PAM.py
-~~~
+##2016-11-21 (JCA)
+- Added #Keyword= entries for cleaner code
 
 ##2016-07-15 (JCA)
 - Modified cord segmentation because slightly too large.

diff --git a/atlas/PAM50_atlas_00.nii.gz b/atlas/PAM50_atlas_00.nii.gz
diff --git a/atlas/PAM50_atlas_01.nii.gz b/atlas/PAM50_atlas_01.nii.gz
diff --git a/atlas/PAM50_atlas_02.nii.gz b/atlas/PAM50_atlas_02.nii.gz
diff --git a/atlas/PAM50_atlas_03.nii.gz b/atlas/PAM50_atlas_03.nii.gz
diff --git a/atlas/PAM50_atlas_04.nii.gz b/atlas/PAM50_atlas_04.nii.gz
diff --git a/atlas/PAM50_atlas_05.nii.gz b/atlas/PAM50_atlas_05.nii.gz
diff --git a/atlas/PAM50_atlas_06.nii.gz b/atlas/PAM50_atlas_06.nii.gz
diff --git a/atlas/PAM50_atlas_07.nii.gz b/atlas/PAM50_atlas_07.nii.gz
diff --git a/atlas/PAM50_atlas_08.nii.gz b/atlas/PAM50_atlas_08.nii.gz
diff --git a/atlas/PAM50_atlas_09.nii.gz b/atlas/PAM50_atlas_09.nii.gz
diff --git a/atlas/PAM50_atlas_10.nii.gz b/atlas/PAM50_atlas_10.nii.gz
diff --git a/atlas/PAM50_atlas_11.nii.gz b/atlas/PAM50_atlas_11.nii.gz
diff --git a/atlas/PAM50_atlas_12.nii.gz b/atlas/PAM50_atlas_12.nii.gz
diff --git a/atlas/PAM50_atlas_13.nii.gz b/atlas/PAM50_atlas_13.nii.gz
diff --git a/atlas/PAM50_atlas_14.nii.gz b/atlas/PAM50_atlas_14.nii.gz
diff --git a/atlas/PAM50_atlas_15.nii.gz b/atlas/PAM50_atlas_15.nii.gz
diff --git a/atlas/PAM50_atlas_16.nii.gz b/atlas/PAM50_atlas_16.nii.gz
diff --git a/atlas/PAM50_atlas_17.nii.gz b/atlas/PAM50_atlas_17.nii.gz
diff --git a/atlas/PAM50_atlas_18.nii.gz b/atlas/PAM50_atlas_18.nii.gz
diff --git a/atlas/PAM50_atlas_19.nii.gz b/atlas/PAM50_atlas_19.nii.gz
diff --git a/atlas/PAM50_atlas_20.nii.gz b/atlas/PAM50_atlas_20.nii.gz
diff --git a/atlas/PAM50_atlas_21.nii.gz b/atlas/PAM50_atlas_21.nii.gz
diff --git a/atlas/PAM50_atlas_22.nii.gz b/atlas/PAM50_atlas_22.nii.gz
diff --git a/atlas/PAM50_atlas_23.nii.gz b/atlas/PAM50_atlas_23.nii.gz
diff --git a/atlas/PAM50_atlas_24.nii.gz b/atlas/PAM50_atlas_24.nii.gz
diff --git a/atlas/PAM50_atlas_25.nii.gz b/atlas/PAM50_atlas_25.nii.gz
diff --git a/atlas/PAM50_atlas_26.nii.gz b/atlas/PAM50_atlas_26.nii.gz
diff --git a/atlas/PAM50_atlas_27.nii.gz b/atlas/PAM50_atlas_27.nii.gz
diff --git a/atlas/PAM50_atlas_28.nii.gz b/atlas/PAM50_atlas_28.nii.gz
diff --git a/atlas/PAM50_atlas_29.nii.gz b/atlas/PAM50_atlas_29.nii.gz
diff --git a/atlas/PAM50_atlas_30.nii.gz b/atlas/PAM50_atlas_30.nii.gz
diff --git a/atlas/PAM50_atlas_31.nii.gz b/atlas/PAM50_atlas_31.nii.gz
diff --git a/atlas/PAM50_atlas_32.nii.gz b/atlas/PAM50_atlas_32.nii.gz
diff --git a/atlas/PAM50_atlas_33.nii.gz b/atlas/PAM50_atlas_33.nii.gz
diff --git a/atlas/PAM50_atlas_34.nii.gz b/atlas/PAM50_atlas_34.nii.gz
diff --git a/atlas/PAM50_atlas_35.nii.gz b/atlas/PAM50_atlas_35.nii.gz
diff --git a/atlas/PAM50_atlas_36.nii.gz b/atlas/PAM50_atlas_36.nii.gz
diff --git a/atlas/info_label.txt b/atlas/info_label.txt
@@ -1,4 +1,6 @@
 # White matter atlas. Generated on: 01-Sep-2016
+#
+# Keyword=IndivLabels (Please DO NOT change this line)
 # ID, name, file
 0, WM left fasciculus gracilis, PAM50_atlas_00.nii.gz
 1, WM right fasciculus gracilis, PAM50_atlas_01.nii.gz
@@ -39,10 +41,18 @@
 36, CSF contour, PAM50_atlas_36.nii.gz
 
 # Combined labels
-# ID, name, file
+# Keyword=CombinedLabels (Please DO NOT change this line)
+# ID, name, IDgroup
 50, spinal cord, 0:35
 51, white matter, 0:29
 52, gray matter, 30:35
 52, dorsal columns, 0:3
 53, lateral funiculi, 4:13
 54, ventral funiculi, 14:29
+
+# Clusters used for the first step of the MAP estimation (for advanced users only)
+# Keyword=MAPLabels (Please DO NOT change this line)
+# Name, IDgroup
+white matter, 0:29
+gray matter, 30:35
+CSF, 36
diff --git a/template/PAM50_cord.nii.gz b/template/PAM50_cord.nii.gz
diff --git a/template/PAM50_cord_labeled.nii.gz b/template/PAM50_cord_labeled.nii.gz
diff --git a/template/PAM50_gm.nii.gz b/template/PAM50_gm.nii.gz
diff --git a/template/PAM50_label_disc.nii.gz b/template/PAM50_label_disc.nii.gz
diff --git a/template/PAM50_wm.nii.gz b/template/PAM50_wm.nii.gz
diff --git a/template/info_label.txt b/template/info_label.txt
@@ -1,5 +1,5 @@
 # Template labels
-# PLEASE DO NOT EDIT THE 2nd FIELD! (name)
+# Keyword=IndivLabels (Please DO NOT change this line)
 # ID, name, file
 0, T1-weighted template, PAM50_t1.nii.gz
 1, T2-weighted template, PAM50_t2.nii.gz
@@ -9,4 +9,3 @@
 5, gray matter, PAM50_gm.nii.gz
 6, cerebrospinal fluid, PAM50_csf.nii.gz
 7, vertebral labeling, PAM50_levels.nii.gz
-8, spine, PAM50_spine.nii.gz