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Dear Emma,

to see the labels for native space data or surfaces (e.g., <subject>/surf/lh.thickness), you should use the $SUBJECTS_DIR/<subject>/label/?h.aparc.annot files.

For data that has been mapped to fsaverage (e.g., lh.thickness.fwhm10.fsaverage.mgh), you should use the fsaverage versions in $FREESURFER_HOME/subjects/fsaverage/label/?h.aparc.annot.

Unless something went wrong with the registration, they both should look fine.

Best,

Tim

On May 11, 2019 at 4:53 PM "Bunting, Emma" e.bunting.18@ucl.ac.uk wrote:

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Hi Freesurfer experts,

Does reconall register each T1 to fsaverage space?

And if yes, are the Desikan-Killany and Destrieux atlas labels still applicable?

I am asking because I noticed that when I overlayed the Desikan-Killany atlas onto our reconall outputs they didn’t seem to align properly,

Thanks,

Emma

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-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany