diff --git a/CHANGES.md b/CHANGES.md index 48f5100..a0ea1fa 100644 --- 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 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+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 \ No newline at end of file diff --git a/template/PAM50_cord.nii.gz b/template/PAM50_cord.nii.gz index 4dc8bd9..8f054a8 100644 Binary files a/template/PAM50_cord.nii.gz and b/template/PAM50_cord.nii.gz differ diff --git a/template/PAM50_cord_labeled.nii.gz b/template/PAM50_cord_labeled.nii.gz deleted file mode 100644 index ac504b3..0000000 Binary files a/template/PAM50_cord_labeled.nii.gz and /dev/null differ diff --git a/template/PAM50_gm.nii.gz b/template/PAM50_gm.nii.gz index 026c445..4ce1bc6 100644 Binary files a/template/PAM50_gm.nii.gz and b/template/PAM50_gm.nii.gz differ diff --git a/template/PAM50_label_disc.nii.gz b/template/PAM50_label_disc.nii.gz index 162351b..4a0d07d 100644 Binary files a/template/PAM50_label_disc.nii.gz and b/template/PAM50_label_disc.nii.gz differ diff --git a/template/PAM50_wm.nii.gz b/template/PAM50_wm.nii.gz index e7b4967..721a351 100644 Binary files a/template/PAM50_wm.nii.gz and b/template/PAM50_wm.nii.gz differ diff --git a/template/info_label.txt b/template/info_label.txt index 54c99d7..5239f31 100644 --- 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