Freesurfer aseg ROIs' centroid coordinates

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i’m wondering if there is a spreadsheet available somewhere which contains the centroid coordinates of freesurfer’s aseg atlas ROIs? Of is there a way i can extract the centroid coordinates from some freesurfer files?

I need these coordinates for the purpose feeding them into a visualization script

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Hi @gerardyu, did you see this thread which seems related? MNI Coordinates for the center of masses of the destrieux atlas a2009s?

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yes that’s what i’m looking for, but the brainGraph data does not include the ventralDC, brainstem and cerebellum though

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found the python function to do this if anyone is interested

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Hey, could you provide some code? What input files did you use? :slight_smile:

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from nilearn import plotting
import numpy as np

coordinates = plotting.find_parcellation_cut_coords("atlas.nii.gz")
np.savetxt('coordinates.csv',coordinates,delimiter=',',fmt='%f')

altlas.nii.gz is basically any atlas that has regions labelled from 1 to N consecutively, where N is the number of regions in the atlas

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But which file exactly did you use? What’s the filename and is it stored in the Freesurfer installation directory?

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for the purpose of my study, i created an atlas by combining the schaefer-100 atlas with 19 subcortical GM segmentations from freesurfer.

i guess if need a volumetric version of the destrieux atlas, you can get it from here NeuroVault: Destrieux Atlas (2009)

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I downloaded the atlas from neurovault, but it has 192 instead of the expected 162 labels (148 cortical + 14 subcortical regions). Besides, the labels deviate from the official freesurfer labels, so without corresponding atlas info, it’s not possible to map each number to the name of a brain region of the Destrieux a2009s atlas.