'transverse' Display Probe Track

[Flavia0310]

Hi,
I'm facing a problem to reconstruct the probe trajectory using the transverse plane.

As you can see in the picture while I use the "Display_Probe_Track. m" I get sparse points, I don't understand why and also I have this error:
"getting probe scaling from histology data...
Index in position 1 exceeds array bounds (must not exceed 800).
Error in Display_Probe_Track (line 162)
ann = av_plot(round(m(1)),round(m(2)),round(m(3))); %until hitting the top"

Do you have an idea about this error source?

[philshams]

I was able to replicate that error message and fix the bug that caused it (in theory). It was just a matter of changing the variable 'av_plot' to 'av', in lines 159 and 163. Does updating to the latest version of the repo (or making that change yourself) fix your problem?

[Flavia0310]

Thank you, I don't have the error anymore, but still scattered points. That could be a slice alignment problem, even though my probes should be both on the right hemisphere and as you can see here are very random. What do you think it’s due to?

[philshams]

Are you saying that the points you click during the probe-marking step are not scattered, but then the data get somehow messed up and appear scattered? Or just that the points you click are scattered? If the latter, I imagine it's a matter of making sure your slices are all properly aligned (especially in the area where you're marking the probe) and that whatever track you're clicking on is indeed thin and linear.