How to project multiple coordinates on MNI template space for viewing

I want to visualize the peak TMS coordinates transformed into MNI coordinates of 20 participants in relationship to the stimulation site. In my case I have the ROIs normalised to the MNI standard space. Now I would like to create a saggital view of my Tms coordinates. My objective is to view the coordinates of all participants on one template brain.

So, if I understand, you already have locations — a set of (x, y, z) coordinates — for each subject, and these are already in the space you want (MNI)? If the coordinates are in subject-anatomical space still, that can be addressed with using volumetric alignment, but I’ll assume that isn’t the case yet.

So, starting with a 3-column file of (x, y, z) coordinates, you could use AFNI’s 3dUndump program to turn the coordinates into a map of ROIs. There is a parameter to set a radius around each to paint in, and you can then visualize each as spheres.

For example, this would take a file of xyz-coordinate triplets (in RAI-DICOM sign-notation) called vol_sphere_coords_labeled.1D and create a map of spheres with a 3.5 mm radius in the DSET_MNI_TEMPLATE space:

3dUndump                               \
    -master     DSET_MNI_TEMPLATE      \
    -srad       3.5                    \
    -prefix     DSET_MAP_SPHERES       \
    -overwrite                         \
    -xyz                               \
    -orient     RAI                    \

You could also provide explicit enumeration for each ROI, as well, through providing more information in the simple text file:

  • If a line has 3 numbers, those are interpreted as coordinates.
  • If a line has 4 numbers, that is interpreted as coordinates and a value for the ROI to be given.
  • If a line has 5 numbers, that is interpreted as coordinates, a value for the ROI to be given, and a radius particular to that ROI (hence, each sphere could have a different radius, as opposed to using a global -srad .. value).

There are more examples of creating visualizing spheres in AFNI and SUMA (surface-based viewing) here:


I have converted the coordinates into MNI already for each subjects. I just want to visualized all the subject hotspots onto one template space. Thanks

you may want to use nilearn’s plot_markers function.