diff --git a/CHANGES.md b/CHANGES.md index a2b3aa7..48f5100 100644 --- 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 index 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+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 index 8f054a8..4dc8bd9 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 new file mode 100644 index 0000000..ac504b3 Binary files /dev/null and b/template/PAM50_cord_labeled.nii.gz differ diff --git a/template/PAM50_gm.nii.gz b/template/PAM50_gm.nii.gz index 4ce1bc6..026c445 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 4a0d07d..162351b 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 721a351..e7b4967 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 96c3442..54c99d7 100644 --- 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