Map Harvard-Oxford Cortical Atlas to Surface

Software Support
1

Hi all,

I’m interested in parcellating the cortex using Harvard-Oxford’s cortical atlas. I have analyzed my subject’s T1 images using FreeSurfer, and ideally, I can map those regions to the surface if I have corresponding “label” files. I have two questions:

  1. How can I find those files online? Unfortunately, I couldn’t find the Harvard-Oxford labels.
  2. Is it possible to map the 3D Harvard-Oxford atlas template to the cortical mesh?

My goal is to utilize this cortical parcellation as a basis for generating a structural connectome using MRtrix.

Best,
Amir

2

Hi @AmirHussein,

If you are trying to make a FreeSurfer annot, perhaps a combination of mri_vol2label (mri_vol2label - Free Surfer Wiki) and mri_label2annot (mris_label2annot - Free Surfer Wiki) will serve you well. You can find volumetric parcellations of the HO atlas and labels as part of Nilearn: nilearn.datasets.fetch_atlas_harvard_oxford - Nilearn.

Best,
Steven