How to get region from (x,y,z) coords

slab15 · January 11, 2022, 9:03am

Hi,
I have (x,y,z) coords in MNI space.
What is the best way to get the region of the point?
e.g. if my coords are (-22,-34,18), what is the respective region? (vmPFC, broca, etc)
Also, the same question given activation maps (as attached - generated using plot_stat_map and plot_prob_atlas) - how can I associate activation to actual regions?

Steven · January 11, 2022, 1:21pm

You can use this tool: mni2atlas - File Exchange - MATLAB Central

slab15 · January 11, 2022, 1:33pm

@Steven Is there a Python equivalent?

Steven · January 11, 2022, 1:50pm

Not sure, but it looks like there are some alternative solutions found here (I have not used any of these): https://www.researchgate.net/post/Can-anyone-suggest-an-online-tool-for-entering-coordinates-to-view-brain-location-eg-MNI-vs-Talairach

KamalakerD · January 11, 2022, 2:29pm

I haven’t explored this package https://github.com/miykael/atlasreader.
Worth to check if it serves your purpose.

Also, I have written some code while ago that finds labels given coordinates based on Harvard Oxford atlas.

gist.github.com

https://gist.github.com/KamalakerDadi/39167adb02cb2dc387a96b8f02a36517

brain_areas_based_on_coordinates.py

"""Utilities developed based on Nilearn
"""

import collections
import warnings

import numpy as np
import pandas as pd

from sklearn.datasets.base import Bunch

This file has been truncated. show original

Feel free to use the code.

Best,
Kamalakar

slab15 · January 11, 2022, 3:29pm

@KamalakerD Thanks! When running your code, I get the error:
AttributeError: 'str' object has no attribute 'affine' in the line: affine = atlas_img.affine
I checked, and atlas_img is indeed a string:
'<path>/nilearn_data/fsl/data/atlases/HarvardOxford/HarvardOxford-cort-maxprob-thr0-1mm.nii.gz'

Any idea what should be changed?

ptaylor · January 11, 2022, 3:45pm

There is “whereami” functionality in AFNI: If your data is in the same space as a known atlas, you can click in the GUI to see where you are WRT that atlas; you can add that region to the overlay visualization; and you can use the commandline program “whereami”. You can get information from several atlases as once, and you also get distances to nearby regions (because alignment isn’t always perfect, and brain regions/definitions are probably not really “binarized” in reality).

See here in the AFNI Academy tutorials about that (and that playlist covers a lot of ROI/atlas/template considerations):

Here is the command line program help:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/whereami_sphx.html

–pt

ptaylor · January 11, 2022, 4:01pm

Also, please note that when referring to coordinates, you have to be careful about what the signs denote. For example, saying that a point of interest is at (-1, 2, -3) is not enough information: you need to also note what coordinate system you are using (e.g., RAI DICOM, or LPI, etc.), to denote both the ordering of coords and where positive is Right or Left, etc. BUUUUT even that isn’t good enough: you have to denote further what those letters mean, because they mean different things to different software/scanners/people. It is an underappreciated point of confusion (and difficulty for meta-analysis) within the field.

For example, to be complete you should say: “I want point (-1, 2, -3) in RAI coordinates, where right/anterior/inferior are negative.” Because some software might list “RAI” but mean that right/ant/inf are all relatively positive, relative to the coordinate origin. Sigh.

–pt