These numbers are output automatically in the aseg.stats file in v6, eg,

# Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 17, unitless # Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces prior to fixing, 12, unitless # Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces prior to fixing, 29, unitless

They will be included as global measures when you run asegstats2table

On 07/12/2018 11:01 AM, Bruce Fischl wrote:

Hi Lea

the Euler number is an integer, so it will never be 2.5. In fact, in our reconstructed surfaces it will always be exactly 2, except for the *nofix* surfaces, as we explicitly correct the topology of the surfaces (see the Automated Manifold Surgery paper if you are interested in the details)

cheers Bruce

On Thu, 12 Jul 2018, Backhausen, Lea wrote:

...

External Email - Use Caution

Hey Freesurfer Experts,

I would like to use the Euler number as a quantitative quality measure of my reconstructed data as Rosen et al. (2017) recommend in their recently published paper. https://www.sciencedirect.com/science/article/pii/S1053811917310832

I figured I can use:

mris_euler_number [<options>] insurf     to get the euler number for each data set.

Which surface should I use though? The white or pial surface area or is there no preference?

Does anybody have experience with what range of Euler number would be acceptable? I read that 2 would be perfect but is 2.5 still ok? Or 1? Somehow I could not find any recommendation in the Rosen paper about thresholds or something similar. Did I miss something?

Any advice would be highly appreciated! Thanks!

Best, Lea

---

Lea Backhausen, B.Sc.

Student Research Assistant

Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und –psychotherapie Tel. +49 (0)351 458-7166 Fax +49 (0)351 458-5754

Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

External Email - Use Caution

Dear Freesurfer Developers,

My goal is to build a study-specific pediatric template brain to rerun the recon-all-all. I am encountering the same error while running make_average_subject Freesurfer version 6.0.0 on MacOS High Sierra 10.13.6 as described here and implemented the suggested changes replacing mri_glmfit-sim, make_average_subject, make_average_surface, and mri_aparc2aseg: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-November/054933....

Yet, another error persists.

Any help would be appreciated.

Thanks,

Laurel

Laurel Raffington

Postdoctoral Researcher

Center for Lifespan Psychology

Max Planck Institute for Human Development

Lentzeallee 94, 14195 Berlin, Germany

https://www.mpib-berlin.mpg.de/en/staff/laurel-raffington