Fixed: Corrected wrong labels of thalamic nuclei atlas. Thanks to Jon…

…as Krauß for poiting to this error and Manoj Saranathan for help with the atlas labels. Changed paths: M CHANGES.txt M Contents.m M doc/cat.html M templates_MNI152NLin2009cAsym/thalamic_nuclei.csv M templates_MNI152NLin2009cAsym/thalamic_nuclei.nii M templates_MNI152NLin2009cAsym/thalamic_nuclei.txt
ChristianGaser · May 25, 2024 · 54257ae · 54257ae
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diff --git a/CHANGES.txt b/CHANGES.txt
@@ -1,4 +1,18 @@
 ------------------------------------------------------------------------
+r2583 | gaser | 2024-05-25 15:33:40
+
+Changed paths:
+ M CHANGES.txt
+ M Contents.m
+ M doc/cat.html
+ M templates_MNI152NLin2009cAsym/thalamic_nuclei.csv
+ M templates_MNI152NLin2009cAsym/thalamic_nuclei.nii
+ M templates_MNI152NLin2009cAsym/thalamic_nuclei.txt
+
+Fixed: Corrected wrong labels of thalamic nuclei atlas. Thanks to Jonas Krauß
+       for poiting to this error and Manoj Saranathan for help with the atlas
+       labels.
+------------------------------------------------------------------------
 r2582 | gaser | 2024-05-21 01:23:31
 
 Changed paths:

diff --git a/Contents.m b/Contents.m
@@ -1,5 +1,5 @@
 % Computational Anatomy Toolbox
-% Version 2559 (CAT12.9) 2024-03-02
+% Version 2582 (CAT12.9) 2024-05-21
 % ______________________________________________________________________
 %
 % Christian Gaser, Robert Dahnke

diff --git a/doc/cat.html b/doc/cat.html
@@ -9,7 +9,7 @@
 
     <div id="content">
       <br />
-      <p align="center" style="text-align:center;">This is <b>CAT12.9 (r2559) from 2024-03-02</b><br />You can update your copy of CAT12 here: <a href="matlab:cat_update(1);">Check for update</a>.<br />If you find any bug, please report them at <a href="mailto:vbmweb@gmail.com">vbmweb@gmail.com</a>.</p>
+      <p align="center" style="text-align:center;">This is <b>CAT12.9 (r2582) from 2024-05-21</b><br />You can update your copy of CAT12 here: <a href="matlab:cat_update(1);">Check for update</a>.<br />If you find any bug, please report them at <a href="mailto:vbmweb@gmail.com">vbmweb@gmail.com</a>.</p>
       <h1 style="text-align:center;"><img src="images/CAT.png" width=40% height=auto alt="CAT" ></h1>
 
       <hr />

diff --git a/templates_MNI152NLin2009cAsym/thalamic_nuclei.csv b/templates_MNI152NLin2009cAsym/thalamic_nuclei.csv
@@ -1,23 +1,25 @@
-ROIid;ROIabbr;ROIname
-1;lAnteroventral;left anteroventral
-2;lVentral_Anterior;left ventral anterior
-3;lVentral_Lateral_Anterior;left ventral lateral anterior
-4;lVentral_Lateral_Posterior;left ventral lateral posterior
-5;lVentral_Posterolateral;left ventral posterolateral
-6;lPulvinar;left pulvinar
-7;lLateral_Geniculate;left lateral geniculate
-8;lMedial_Geniculate;left medial geniculate
-9;lCentromedian;left centromedian
-10;lMediodorsal;left mediodorsal
-11;lHabenula;left habenula
-12;rAnteroventral;right anteroventral
-13;rVentral_Anterior;right ventral anterior
-14;rVentral_Lateral_Anterior;right ventral lateral anterior
-15;rVentral_Lateral_Posterior;right ventral lateral posterior
-16;rVentral_Posterolateral;right ventral posterolateral
-17;rPulvinar;right pulvinar
-18;rLateral_Geniculate;right lateral geniculate
-19;rMedial_Geniculate;right medial geniculate
-20;rCentromedian;right centromedian
-21;rMediodorsal;right mediodorsal
-22;rHabenula;right habenula
+ROIid;ROIabbr;ROIname
+2;lAnteroventral;left anteroventral
+4;lVentral_Anterior;left ventral anterior
+5;lVentral_Lateral_Anterior;left ventral lateral anterior
+6;lVentral_Lateral_Posterior;left ventral lateral posterior
+7;lVentral_Posterolateral;left ventral posterolateral
+8;lPulvinar;left pulvinar
+9;lLateral_Geniculate;left lateral geniculate
+10;lMedial_Geniculate;left medial geniculate
+11;lCentromedian;left centromedian
+12;lMediodorsal;left mediodorsal
+13;lHabenula;left habenula
+14;lMTT;left mammillothalamic tract
+16;rAnteroventral;right anteroventral
+18;rVentral_Anterior;right ventral anterior
+19;rVentral_Lateral_Anterior;right ventral lateral anterior
+20;rVentral_Lateral_Posterior;right ventral lateral posterior
+21;rVentral_Posterolateral;right ventral posterolateral
+22;rPulvinar;right pulvinar
+23;rLateral_Geniculate;right lateral geniculate
+24;rMedial_Geniculate;right medial geniculate
+25;rCentromedian;right centromedian
+26;rMediodorsal;right mediodorsal
+27;rHabenula;right habenula
+28;rMTT;right mammillothalamic tract
diff --git a/templates_MNI152NLin2009cAsym/thalamic_nuclei.nii b/templates_MNI152NLin2009cAsym/thalamic_nuclei.nii
diff --git a/templates_MNI152NLin2009cAsym/thalamic_nuclei.txt b/templates_MNI152NLin2009cAsym/thalamic_nuclei.txt
@@ -10,9 +10,9 @@ If you use this atlas, please cite the references below.
 
 Websites:
 A) https://github.com/thalamicseg/thomas_new
+B) https://zenodo.org/records/5499504
 
 References:
-
 1) Su JH, Thomas FT, Kasoff WS, Tourdias T, Choi EY, Rutt BK, Saranathan M.
 Thalamus Optimized Multi Atlas Segmentation (THOMAS): fast, fully automated
 segmentation of thalamic nuclei from structural MRI. Neuroimage. 2019 Jul