# Visualize the brain based on coordinate points

Hi,
I have selected 264 coordinate points to analyze the brain. I have been using a 2mm sphere to calculate the time series data around the coordinate points. I was wondering is there any way to visualize those 264 points each covering all the voxels in the 2mm sphare?

Hi-

I can’t quite picture what you want to visualize. Can you please clarify what exactly you want to view? For starters, are you wanting to view the average time series, or the locations in the brain?

If you have 264 points spread around the brain, with 2mm (radius?) spheres drawn around those, and want to view all the voxels covered by that, it seems like you would likely need a slice-by-slice view of the whole 3D volume? Do you want to view a slice through each of the 264 points, or do you want to view a slice through all parts of each sphere (which would probably be a loooot of slices, depending on how they are arranged)?

By the way, what resolution is your dset? Most FMRI dsets have lower resolution than 2mm…

–pt

Hi,
I don’t require a slice by slice view. An overall view of the whole brain would work. Something like this in the picture. Where I can just visualize the ROIs that I am defining using the coordinates and the sphere. https://upload.wikimedia.org/wikipedia/commons/thumb/3/35/Lateral_surface_of_cerebral_cortex_-_gyri.png/1200px-Lateral_surface_of_cerebral_cortex_-_gyri.png.

We have SUMA, the surface viewer, and so you could make surface ROIs of each sphere and view that in 3D, with some background volume-- is that what you would want?

–pt

Hi,
Yes, that’s what I am looking for. Can you direct me towards some tutorials related to this problem? Thank you so much though!

I’m still not sure how you want to use spheres, but there are at least a few possibilities.
simple location markers
“connections” with connecting spheres
spheres that change colors with user interaction or to show changes with time or some other series

The number of spheres you have mentioned is a fairly large number. It’s doable, but you will have to think about how you really want to visualize this. Take a look at these examples all made with AFNI and SUMA and see what is closest to what you want.

Pursuant to this point, Daniel has constructed a nice tutorial about different ways (no less than 5!) to make+view spheres in SUMA:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/rois_corr_vis/suma_spheres.html

These could be combined with some of the automatic snapshotting capability of SUMA, too; for example, see here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/rois_corr_vis/cat_netcorr.html#drive-suma-to-save-snapshots-of-the-surface-view-along-some-major-planes

–pt