How to get regions defined in schaefer 2018 atlas from MNI coordinate (x, y, z)


I’m working on seed-based functional connectivity with Schaefer 2018 atlas. Now the seeds I have are defined in previous studies with their MNI coordinates, but I did not find a tool to convert the MNI coordinate to the ROI name in the altas. Can anyone recommend a tool for that? I have checked mni2altas but unluckily they do not support converting to Schaefer 2018 atlas.

Thanks in advance,

Hi Ray, welcome to Neurostars!

I guess it is not as automatized as with mni2atlas but you can use FSL to get the coordinates of your atlas’ ROIs:;f1573b90.0907

I hope it helps,


Thank you Julien! I’ll try that!

You can also use nilearn’s function to find center coordinates for any parcellation file: nilearn.plotting.find_parcellation_cut_coords - Nilearn

In case someone needs it, there was an update to the Schafer-Yeo atlases here:


Described here:

And to use in a script or command line, you could do something like this (depending on the version (number of parcels and number of networks)):

 whereami -atlas Schaefer_Yeo_17n_400 -lpi 10 20 30
++ Input coordinates orientation set by user to LPI
+++++++ nearby Atlas structures +++++++

Original input data coordinates in TLRC space

Focus point (LPI)=
    10.00 mm [R],  20.00 mm [A],  30.00 mm [S] {TLRC}

Atlas Schaefer_Yeo_17n_400: Schaefer-Yeo 2018 400parcels, 17networks (AFNI mod)
   Focus point:  RH_SalVentAttnB_PFCmp_2 
 * Within 7 mm: RH_DefaultA_PFCm_6

This also works in the AFNI GUI’s whereami function.