Currently trying to extract the volumes of brainstem subnuclei (PAG, VTA, ... ) via custom template.
It seems that the whole brainstem is mapped to WM, as below.
cat_main_LAS.m
% mapping of the brainstem to the WM (well there were some small GM
% structures, but the should not effect the local segmentation to much.
and based on atlas .csv files, calculation of brainstem volume is also based on WM (0:1:0),
templates_MNI152NLin2009cAsym/lpba40.csv
182;bBst;Bothside Brainstem;0;1;0;
If I run roi segmentation for brainstem nuclei volume using custom atlas in cat segmentation process,
Should I make ROIs 0:1:0 and get the value from WM (mwp2)?
The interesting part is if I put 1:1:0 and check both mwp1 and mwp2, both file has non-zero values, (mwp2 is greater than mwp1).
(i.e. PAG 0.4302 for mwp1 (GM), 0.8107 for mwp2 (WM) )
Currently trying to extract the volumes of brainstem subnuclei (PAG, VTA, ... ) via custom template. It seems that the whole brainstem is mapped to WM, as below.
cat_main_LAS.m % mapping of the brainstem to the WM (well there were some small GM % structures, but the should not effect the local segmentation to much.
and based on atlas .csv files, calculation of brainstem volume is also based on WM (0:1:0), templates_MNI152NLin2009cAsym/lpba40.csv 182;bBst;Bothside Brainstem;0;1;0;
If I run roi segmentation for brainstem nuclei volume using custom atlas in cat segmentation process, Should I make ROIs 0:1:0 and get the value from WM (mwp2)? The interesting part is if I put 1:1:0 and check both mwp1 and mwp2, both file has non-zero values, (mwp2 is greater than mwp1).
(i.e. PAG 0.4302 for mwp1 (GM), 0.8107 for mwp2 (WM) )