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Hi Bruce,

Thank you for your input, the paper really helped me to understand the concept of the Euler number.

So that means anyone interested in using the Euler number as a quality measure will have to use the ?h.orig.nofix surfaces as input, right?

And smaller Euler numbers would mean more topological defects i.e. worse quality?

I am confused though as to which extend this number is of relevance as like you pointed out FreeSurfer will correct the topology of the surfaces until Euler number = 2 and thus have fixed the defects. Meaning in the end successfully processed data sets won’t have topological defects no matter how bad the Euler number originally was. Or does it still matter?

Would be happy to hear from you again!

Best, Lea

------------------------------ Lea Backhausen Research Assistant

Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://www.uniklinikum-dresden.dehttp://www.uniklinikum-dresden.de/

____________________________________________________________________

Date: Thu, 12 Jul 2018 11:01:36 -0400 (EDT)

From: Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu>

Subject: Re: [Freesurfer] Euler number as quantitative quality measure

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>

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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