Node coordinates in MNI space?


Hi mrtrix experts!

To go further with connectome analysis and visualization, most of the programs require node coordinates.

What is the easiest way to know them for 84 nodes used in standard “fs_default.txt” I use in mrtrix.

Thank you in advance!

Node Coordinates in MNI space

Hi David,

Definition of the location of the nodes within that parcellation is slightly ambiguous, since the cortical parcels are defined on FreeSurfer’s spherical template rather than within a volumetric template like MNI.

In mrview's connectome tool, this is handled by calculating from the parcellation image the centre of mass of each parcel; the positions are therefore subject-specific.

If it’s only for visualisation and not specifically anatomical reporting, I suppose what you could do is either:

  • Calculate the centre of mass of each parcel in subject space, register your subject’s T1 image to MNI space, then transform each centre of mass according to the estimated transformation;
  • Register your subject’s T1 image to MNI space, transform the subject’s parcellation image to MNI space, then calculate the centre of mass of each parcel.

The calculation of centre-of-mass can be done using this command. To run it for each parcel, you could do something like:

for i in {1..84}; do mrcalc parcellation.mif $i -eq - -quiet | mrcentre - scanner; done

That should give you a 84x3 table at the command-line, containing the XYZ scanner-space position of each parcel.



Hi Rob,

I too have the same question as David and I’m grateful for the steps you have provided. However I have run into a few issues:
When I run the last step suggested to get MNI coordinates for the parcellated brain I receive this error:
mrcalc: [SYSTEM FATAL CODE: SIGPIPE (13)] Nothing on receiving end of pipe
-bash: mrcentre: command not found

This is after incoporating the ‘mrcentre.cpp’ file in the mrtrix3 script bin. How can I incoporate the mrcentre command into the code for it to work?