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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:
External Email - Use CautionHi 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