Loading freesurfer apac+aseg overlay on top T1

[soichih]

(Related to https://github.com/rii-mango/Papaya/issues/55)

I have a t1w and aparc+aseg generated by freesurfer from the same T1w. I am wondering if I can recreate the freeview visualization that shows various parcellation on top of the T1.

Like this..

If I just load both t1 and aparc+aseg, papaya currently shows all parcellation with similar colors.

params["images"] = ["../fs/T1.nii.gz", "../fs/aparc+aseg.nii.gz"]     

Is there a way to load the freesurfer LUT color table?

[madeyoso66]

Hi, I'm having the same issue above. When applying freeSurferColorLUT, the order somehow makes the subcortical regions disappear. Below are examples of comparing the correct display on Freeview next to the papaya attempt

This first one has the aparc+asec listed first, while T1 is overlayed on top(with transparency). This almost has the correct result; however, the overall colors seem faded with the T1 on top.

This second attempt has the order flipped. T1 is listed first, while aparc+aseg is overlayed as second. Now the colors are proper, but the subcortical regions arent showing

Can this set of regions be displayed in the papaya viewer while aparc+aseg is the overlayed image?