Why are you looking at it on the surface? How did you even get it there? These are volume labels. As for getting them into MNI152, you could just run recon-all on the MNI152.

On 3/8/2022 1:00 PM, Hua, Jessica wrote:

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Hi FreeSurfer,

I am trying to extract CC subregion labels from aparc+aseg.mgz (ids: 251-255) into a format that is compatible with MNI space in FSL. I was planning on extracting CC labels and then converting the labels from fsaverage space to MNI space. I first tried to extract the 5 separate CC labels using the command: mri_vol2label --c aparc+aseg.mgz --id 255 --l 255.label. When viewed in FreeView, the labels were spotty looking. Did I do this mgz to label extraction correctly?

And also do you have a recommended code to convert FreeSurfer CC subregions into MNI space ROIs for FSL?

Best,

Jessica
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