You can do it in two ways.
- First, you can just apply mri_segstats with the --annot option to get
the mean NODDI values using the ?h.aparc.stats file, then compute the LI
on the ROIs
- Second, you can compute the map of the LI values (just added this here
https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi), then use mri_segstats
on the map to get the ROI means
The second option may be slightly preferred because the LI value will be
representative of the vertices in the ROI. Also in ?h.aparc.annot were
not generated in a symmetric way, so they may have asymmetries in them.
On 6/16/2021 8:29 AM, Gugger, James J wrote:
External Email - Use Caution
Good morning,
I am working with NODDI data and have created surface overlays in
FreeSurfer space with NODDI values. I am interested in calculating
vertex-wise asymmetry indexes utilizing fsaverage_sym similar to Greve
et al Journal of Cognitive Neuroscience 25:9, pp. 1477–1492. I would
ultimately like to extract average AIs for an ROI analysis. My
question is how do I extract the overlay stats from the surface
overlay mgh file to obtain average AI in each ROI?
Thanks!
Jim Gugger
James Gugger, MD, PharmD
Instructor of Neurology
University of Pennsylvania
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If
the e-mail was sent to you in error but does not contain patient information,
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
