Now I try to apply Schafer or Yeo's atlases onto my lh.pial as you describe here and I got message saying number of vertices are not matching!
How are you proceeding?
we can define the number of vertices when we upload the freesurfer anatomy folder to brainstorm, would this make any effect on the number of vertices of already segmented surface files or does it only related to source reconstruction related definitions, I mean saying to Brainstorm how many of those vertices I want a dipole to be fitted?
Brainstorm imports the high-resolution surfaces generated by FreeSurfer, loads the atlases on top of them, and then downsamples the surfaces with Matlab's reducepatch function to get a reasonable number of dipoles for source reconstruction. The import procedure is detailed here, and these are the instructions you should refer to to load any additional atlas:
https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#Manual_import_of_the_anatomy
If not is there any other way of downsampling the number of vertices of our surface files to the one required for the atlas we would like to use? I would really appreciate if you could help me with that please.
You won't be able to do anything like this. You have to start with full resolution surfaces, import all the atlases, and then downsample.
The Schaefer 2018 atlases are available through the CAT12 segmentation:
https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12#Cortical_parcellations
Hopefully you'll manage to make this work, it would be a lot easier for you to get these atlases for you subjects.