You can look in the recon-all.log file to see how wmparc.mgz is created. Which version of FS are you using? If V6, then the command will be mri_aparc2aseg. If V7, then it will mri_surf2volseg. Either way, modify the command to use your annotation.

On 8/12/2020 5:18 AM, Ellen Ji wrote:

External Email - Use Caution

Dear Freesurfer experts,

I have a surface parcellation (annotation) with 318 labels; see attachments for each hemi. I wish to extract volume-based features (FA and MD) corresponding to these 318 labels. I believe I should perform something like surf2vol to extend the labels into FA space. However, my surface parcellation is not a surface overlay (which I need for --so). Any other ways to do this?

I wish for the output to be a single volume-based parcellation of 318 labels, corresponding to the two surface parcellation annotation files. I will then use this output to get FA measures for each of the 318 regions.

Thank you,
Ellen

---
Ellen Ji, PhD
Postdoctoral Research Fellow
Psychiatric University Hospital
University of Zürich
ellen.ji@bli.uzh.ch
homanlab.github.io/ellen/
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