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SCT commit: 3bd045d3e37776c48dd88ed0d98ce0bf838b3edd SCT commit message: OPT: download_data: updated PAM50 (issue #968) Former-commit-id: 8ce908cd02830c04532e0e35129e2e361270f662 [formerly be04acd52924344d89760111dbd7ca34dbbd11c8] Former-commit-id: 9b95547c902e0dadb7a8c2558691ee2888f02f3b Former-commit-id: 1284a9b09766916cd685c77bfdc3bb2f68c07a98
spinalcordtoolbox · Sep 6, 2016 · 43813bf · 43813bf
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,25 @@
 #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
+~~~
+
 ##2016-07-15 (JCA)
 - Modified cord segmentation because slightly too large.
 - Symmetrized cord segmentation

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 +1,4 @@
-# White matter atlas. Generated on: 16-Jul-2016
+# White matter atlas. Generated on: 01-Sep-2016
 # ID, name, file
 0, WM left fasciculus gracilis, PAM50_atlas_00.nii.gz
 1, WM right fasciculus gracilis, PAM50_atlas_01.nii.gz

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
@@ -9,3 +9,4 @@
 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