Hi,
I first tried to output the registered annotation mask as structure IDs and was able to visualize the outline overlay on top of my slice using matlab. See the Figure 1. I also marked the two dots on the base corner of my Grin Lens track (huge rectangle hollow on the right hemisphere above medial dorsal thalamus, MD). I want to read out the coordinate of this two dots in Allen atlas space and thus visualize them using brainrender later. I went ahead to output the registered mask as micron coordinates instead, and try to locate the (x,y,z) position of those two dots. I am not sure what are the three values of the micron coordinates corresponding to, in the order of ap, ml, dv? The best match I can get is shown in the figure 2, it looks like it shifts in ML to the left hemisphere. Those two dots should be on the right hemisphere just above MD (highlight in pink area).
I really like the none-rigid registration function and don't want to switch to other package to make this work. I am wondering if you can provide me with some guidance of how to map those micron coordinate values in brainrender. Thank you so much!!
figure1:
figure2:
Hi,
I first tried to output the registered annotation mask as structure IDs and was able to visualize the outline overlay on top of my slice using matlab. See the Figure 1. I also marked the two dots on the base corner of my Grin Lens track (huge rectangle hollow on the right hemisphere above medial dorsal thalamus, MD). I want to read out the coordinate of this two dots in Allen atlas space and thus visualize them using brainrender later. I went ahead to output the registered mask as micron coordinates instead, and try to locate the (x,y,z) position of those two dots. I am not sure what are the three values of the micron coordinates corresponding to, in the order of ap, ml, dv? The best match I can get is shown in the figure 2, it looks like it shifts in ML to the left hemisphere. Those two dots should be on the right hemisphere just above MD (highlight in pink area).
I really like the none-rigid registration function and don't want to switch to other package to make this work. I am wondering if you can provide me with some guidance of how to map those micron coordinate values in brainrender. Thank you so much!!
figure1:
figure2: