Hi Ziad, thank you so much for the help!
I was able to visualize correctly the surface and the regions in SUMA and to extract the timeseries, adding the option -pad_to_node 0 and keeping everything in orig space.
If try to use the standard mesh and I use the option -pad_to_node ld141 my dataset looks ok but the region is distorted, parcelleted and in a wrong position in the surface. I plotted both of them in suma with the std.141 spec file.
My last step, it's trying to get the RAS coordinates from the nodes indexes of my regions. I first tried to use the -xyz option with the function 3dmaskdump but I got just a list of zeros. So now I'm trying to use Surf2VolCoord. I think I know how to get the coordinates of one node but I did not understand how to get the coordinates of a list of nodes.
Surf2VolCoord -i_fs /usr/local/freesurfer/subjects/DM/SUMA/lh.smoothwm.asc -sv /usr/local/freesurfer/subjects/DM/SUMA/DM_SurfVol+orig.BRIK -grid_parent DM_movie_run1_al+orig.BRIK -one_node 86 > node85coordinates.txt
Thanks!
Best
Francesca
