How to overlay classification accuracies in gii file over a flat brain?

1

Hi everyone!

I am struggling with a plotting problem.
I performed a surface-based analysis using CosmoMVPA and as output I obtained accuracies in the length of 81924 vertices. I saved the accuracies in gii file and would like to plot on a Freesurfer flat map, but Freesurfer just doesn’t recognize the file. I tried to register, it didn’t work. I thought about combining the inflated brain with the accuracies gii file but I am not sure how I can do that.
Simple overlay of acc over inflated brain works well even with Matlab, but the overlays are very small (as you can see below), that’s why I thought about plotting over a flat brain.

plot|690x385

I am running out of ideas, so any ideas of how to plot that will be extremely welcome.!

Thanks a lot in advance
Camila

2

What is the format of your file ? Is it a gifti file ?

For plotting flat maps, I use pycortex (GitHub - gallantlab/pycortex: Pycortex is a python-based toolkit for surface visualization of fMRI).

As far as I can see, under Nilearn this is still under development (Plotting flat maps + plotting additional data as transparency · Issue #2658 · nilearn/nilearn · GitHub).
HTH,
Bertrand

3

Hi Bertrand,

Thanks for the reply and recommendations. Yes. I am using gifti file. Does Pycortex aslo work with gifti or just nifit?

Best,
Camila

4

I think that when I use it, I simply read the gitfti file as a numpy array and give it to pycortex.
See e.g. public_analysis_code/script_retino.py at master · hbp-brain-charting/public_analysis_code · GitHub
HTH,
B

5

Great!! Thank you so much =D