It seems problematic to me to use a nightly dev build for publication.

cheers,
-MH

-- 
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mharms@wustl.edu

From: Matthieu Vanhoutte <matthieuvanhoutte@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, December 15, 2015 11:13 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Segmentation comparison between FS5.3 and FS6beta

Hi Bruce,

Is it better to overestimate than underestimate ? Please find joined this two saggital images (FS v5.3 and FS v6_beta) of brain segmentation. Cerebellum in v6_beta really seems to go outside of its borderlines even if cerebellum in v5.3 is indeed lightly underestimated.

Looking at the cerebral cortex I found the segmentation less "smoothed" in v6_beta (with more irregularities near pial surface) than in v5.3 according to coronal views of segmentations joined.

What do you think about it ?  Would you advise me to go on with the v6_beta anyway ?

Would it be better and coherent to use a more recent "nightly dev builds" of FreeSurfer for future publication ?

Thanks in advance for helping !

Best regards,

Matthieu

2015-12-15 17:38 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
Hi Matthieu

I think 6.0 looks better overall, even in the beta that you have. The 5.3
segmentation looks like it is underestimating cerebellum and hippocampus to
me.

cheers
Bruce


On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

> Dear FS's experts,
>
> I have tried the recon-all process on one subject with both FS v5.3 and v6_beta.
>
> Although subcortical structures seems to be better segmented in v6_beta, I find that v6_beta over-segmented some other
> structures as cerebellum, hippocampus, ...
>
> I will attached in the FileDrop my T1.mgz, and aparc.a2009s+aseg.mgz files for both freesurfer versions.
>
> Could you please look at it and tell me what do you think about and advise me ?
>
> Thank you !
>
> Best regards,
> Matthieu
>
>
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