Hi,
I would like to add the habenula structure to the Schaefer 2018 parcellations: Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity MRI | Cerebral Cortex | Oxford Academic
Does anyone know about an Atlas that contains the habenula and the steps necessary to merge 2 existing Atlases? Is there any software that you would recommend to me?
This paper here provides MNI coordinates of the Habenula (Defining the habenula in human neuroimaging studies - PMC):
Accordingly, normalisation from native to MNI space, on average, increased habenula volume in most participants. Mean normalised habenula volume was 44.6 mm3 (SD 5.8, range 31.7-60.2) on the right and 43.2 mm3 (SD 7.7, range 31.0–58.0) on the left. For the normalised right habenula, the mean x-coordinate was 4.8 (SD 0.39, range 4.3 to 6.0), the mean y-coordinate was − 24.1 (SD 0.55, range − 23.4 to − 25.3) and the mean z-coordinate was 2.2 (SD 0.47, range 1.4 to 3.5). For the normalised left habenula, the mean x-coordinate was − 2.8 (SD 0.4, range − 2.0 to − 3.7), mean y-coordinate was − 24.4 (SD 0.59, range − 23.4 to − 25.6) and mean z-coordinate was 2.3 (SD 0.53, range 1.3 to 3.7).
So, one way to do it, create a mask yourself and merge it into the atlas of choice. For example, this nilearn tutorial shows how to create a mask for ROIs at given coordinates: Computing a Region of Interest (ROI) mask manually - Nilearn. This blog also shows how to create ROI masks from coordinates in FSL: Andy's Brain Blog: FSL Tutorial: Creating ROIs from Coordinates and some more options here: Andy's Brain Blog: MakeSpheres.py